From 65a6d540fd01c714d9ad7b68bd79655a4eabb51a Mon Sep 17 00:00:00 2001 From: stemangiola Date: Fri, 10 May 2024 05:18:32 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20stemangi?= =?UTF-8?q?ola/tidySingleCellExperiment@8c092dbe8cb1137b2e34e9fc51f8ad69ac?= =?UTF-8?q?c080cf=20=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- 404.html | 2 +- articles/index.html | 2 +- articles/introduction.html | 192 +++++++++--------- .../figure-html/plot2-1.png | Bin 46943 -> 46828 bytes .../figure-html/unnamed-chunk-12-1.png | Bin 120115 -> 120020 bytes authors.html | 6 +- index.html | 187 ++++++++--------- pkgdown.yml | 4 +- reference/add_class.html | 2 +- reference/aggregate_cells.html | 2 +- reference/arrange.html | 28 +-- reference/as_tibble.html | 28 +-- reference/bind_rows.html | 50 ++--- reference/cell_type_df.html | 2 +- reference/count.html | 4 +- reference/distinct.html | 4 +- reference/drop_class.html | 2 +- reference/extract.html | 28 +-- reference/filter.html | 28 +-- reference/formatting.html | 28 +-- reference/full_join.html | 28 +-- reference/ggplot.html | 6 +- reference/glimpse.html | 2 +- reference/group_by.html | 28 +-- reference/group_split.html | 54 ++--- reference/index.html | 2 +- reference/inner_join.html | 28 +-- reference/join_features.html | 28 +-- reference/join_transcripts.html | 2 +- reference/left_join.html | 54 ++--- reference/mutate.html | 28 +-- reference/nest.html | 28 +-- reference/pbmc_small.html | 2 +- reference/pbmc_small_nested_interactions.html | 2 +- reference/pipe.html | 2 +- reference/pivot_longer.html | 28 +-- reference/plot_ly.html | 4 +- reference/pull.html | 2 +- reference/quo_names.html | 2 +- reference/rename.html | 30 +-- reference/return_arguments_of.html | 2 +- reference/right_join.html | 28 +-- reference/rowwise.html | 2 +- reference/sample_n.html | 48 ++--- reference/select.html | 26 +-- reference/separate.html | 28 +-- reference/slice.html | 152 +++++++------- reference/summarise.html | 4 +- reference/tbl_format_header.html | 2 +- reference/tidy.html | 28 +-- reference/unite.html | 28 +-- reference/unnest.html | 28 +-- 52 files changed, 670 insertions(+), 665 deletions(-) diff --git a/404.html b/404.html index a05721c..b0f3951 100644 --- a/404.html +++ b/404.html @@ -32,7 +32,7 @@ tidySingleCellExperiment - 1.13.3 + 1.15.1 diff --git a/articles/index.html b/articles/index.html index 7ec0ec1..5e0444f 100644 --- a/articles/index.html +++ b/articles/index.html @@ -17,7 +17,7 @@ tidySingleCellExperiment - 1.13.3 + 1.15.1 diff --git a/articles/introduction.html b/articles/introduction.html index 145e307..fd0682f 100644 --- a/articles/introduction.html +++ b/articles/introduction.html @@ -33,7 +33,7 @@ tidySingleCellExperiment - 1.13.3 + 1.15.1 @@ -209,22 +209,22 @@

Data representation of

It looks like a tibble…

 pbmc_small_tidy
-
## # A SingleCellExperiment-tibble abstraction: 80 × 17
+
## # A SingleCellExperiment-tibble abstraction: 80 x 17
 ## # Features=230 | Cells=80 | Assays=counts, logcounts
 ##    .cell orig.ident nCount_RNA nFeature_RNA RNA_snn_res.0.8 letter.idents groups
 ##    <chr> <fct>           <dbl>        <int> <fct>           <fct>         <chr> 
-##  1 ATGC… SeuratPro…         70           47 0               A             g2    
-##  2 CATG… SeuratPro…         85           52 0               A             g1    
-##  3 GAAC… SeuratPro…         87           50 1               B             g2    
-##  4 TGAC… SeuratPro…        127           56 0               A             g2    
-##  5 AGTC… SeuratPro…        173           53 0               A             g2    
-##  6 TCTG… SeuratPro…         70           48 0               A             g1    
-##  7 TGGT… SeuratPro…         64           36 0               A             g1    
-##  8 GCAG… SeuratPro…         72           45 0               A             g1    
-##  9 GATA… SeuratPro…         52           36 0               A             g1    
-## 10 AATG… SeuratPro…        100           41 0               A             g1    
-## # ℹ 70 more rows
-## # ℹ 10 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>,
+##  1 ATGC~ SeuratPro~         70           47 0               A             g2    
+##  2 CATG~ SeuratPro~         85           52 0               A             g1    
+##  3 GAAC~ SeuratPro~         87           50 1               B             g2    
+##  4 TGAC~ SeuratPro~        127           56 0               A             g2    
+##  5 AGTC~ SeuratPro~        173           53 0               A             g2    
+##  6 TCTG~ SeuratPro~         70           48 0               A             g1    
+##  7 TGGT~ SeuratPro~         64           36 0               A             g1    
+##  8 GCAG~ SeuratPro~         72           45 0               A             g1    
+##  9 GATA~ SeuratPro~         52           36 0               A             g1    
+## 10 AATG~ SeuratPro~        100           41 0               A             g1    
+## # i 70 more rows
+## # i 10 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>,
 ## #   PC_1 <dbl>, PC_2 <dbl>, PC_3 <dbl>, PC_4 <dbl>, PC_5 <dbl>, tSNE_1 <dbl>,
 ## #   tSNE_2 <dbl>

 
…but it is a SingleCellExperiment after
@@ -283,22 +283,22 @@ 
Annotation polishing# Reorder to have sample column up front
 pbmc_small_polished %>%
     select(sample, everything())
-
## # A SingleCellExperiment-tibble abstraction: 80 × 18
+
## # A SingleCellExperiment-tibble abstraction: 80 x 18
 ## # Features=230 | Cells=80 | Assays=counts, logcounts
 ##    .cell sample orig.ident nCount_RNA nFeature_RNA RNA_snn_res.0.8 letter.idents
 ##    <chr> <chr>  <fct>           <dbl>        <int> <fct>           <fct>        
-##  1 ATGC… sampl… SeuratPro…         70           47 0               A            
-##  2 CATG… sampl… SeuratPro…         85           52 0               A            
-##  3 GAAC… sampl… SeuratPro…         87           50 1               B            
-##  4 TGAC… sampl… SeuratPro…        127           56 0               A            
-##  5 AGTC… sampl… SeuratPro…        173           53 0               A            
-##  6 TCTG… sampl… SeuratPro…         70           48 0               A            
-##  7 TGGT… sampl… SeuratPro…         64           36 0               A            
-##  8 GCAG… sampl… SeuratPro…         72           45 0               A            
-##  9 GATA… sampl… SeuratPro…         52           36 0               A            
-## 10 AATG… sampl… SeuratPro…        100           41 0               A            
-## # ℹ 70 more rows
-## # ℹ 11 more variables: groups <chr>, RNA_snn_res.1 <fct>, file <chr>,
+##  1 ATGC~ sampl~ SeuratPro~         70           47 0               A            
+##  2 CATG~ sampl~ SeuratPro~         85           52 0               A            
+##  3 GAAC~ sampl~ SeuratPro~         87           50 1               B            
+##  4 TGAC~ sampl~ SeuratPro~        127           56 0               A            
+##  5 AGTC~ sampl~ SeuratPro~        173           53 0               A            
+##  6 TCTG~ sampl~ SeuratPro~         70           48 0               A            
+##  7 TGGT~ sampl~ SeuratPro~         64           36 0               A            
+##  8 GCAG~ sampl~ SeuratPro~         72           45 0               A            
+##  9 GATA~ sampl~ SeuratPro~         52           36 0               A            
+## 10 AATG~ sampl~ SeuratPro~        100           41 0               A            
+## # i 70 more rows
+## # i 11 more variables: groups <chr>, RNA_snn_res.1 <fct>, file <chr>,
 ## #   ident <fct>, PC_1 <dbl>, PC_2 <dbl>, PC_3 <dbl>, PC_4 <dbl>, PC_5 <dbl>,
 ## #   tSNE_1 <dbl>, tSNE_2 <dbl>

 
@@ -373,22 +373,22 @@ 
PreprocessingrunPCA(subset_row=variable_genes)
 
 pbmc_small_pca
-
## # A SingleCellExperiment-tibble abstraction: 80 × 18
+
## # A SingleCellExperiment-tibble abstraction: 80 x 18
 ## # Features=230 | Cells=80 | Assays=counts, logcounts
 ##    .cell orig.ident nCount_RNA nFeature_RNA RNA_snn_res.0.8 letter.idents groups
 ##    <chr> <fct>           <dbl>        <int> <fct>           <fct>         <chr> 
-##  1 ATGC… SeuratPro…         70           47 0               A             g2    
-##  2 CATG… SeuratPro…         85           52 0               A             g1    
-##  3 GAAC… SeuratPro…         87           50 1               B             g2    
-##  4 TGAC… SeuratPro…        127           56 0               A             g2    
-##  5 AGTC… SeuratPro…        173           53 0               A             g2    
-##  6 TCTG… SeuratPro…         70           48 0               A             g1    
-##  7 TGGT… SeuratPro…         64           36 0               A             g1    
-##  8 GCAG… SeuratPro…         72           45 0               A             g1    
-##  9 GATA… SeuratPro…         52           36 0               A             g1    
-## 10 AATG… SeuratPro…        100           41 0               A             g1    
-## # ℹ 70 more rows
-## # ℹ 11 more variables: RNA_snn_res.1 <fct>, file <chr>, sample <chr>,
+##  1 ATGC~ SeuratPro~         70           47 0               A             g2    
+##  2 CATG~ SeuratPro~         85           52 0               A             g1    
+##  3 GAAC~ SeuratPro~         87           50 1               B             g2    
+##  4 TGAC~ SeuratPro~        127           56 0               A             g2    
+##  5 AGTC~ SeuratPro~        173           53 0               A             g2    
+##  6 TCTG~ SeuratPro~         70           48 0               A             g1    
+##  7 TGGT~ SeuratPro~         64           36 0               A             g1    
+##  8 GCAG~ SeuratPro~         72           45 0               A             g1    
+##  9 GATA~ SeuratPro~         52           36 0               A             g1    
+## 10 AATG~ SeuratPro~        100           41 0               A             g1    
+## # i 70 more rows
+## # i 11 more variables: RNA_snn_res.1 <fct>, file <chr>, sample <chr>,
 ## #   ident <fct>, PC1 <dbl>, PC2 <dbl>, PC3 <dbl>, PC4 <dbl>, PC5 <dbl>,
 ## #   tSNE_1 <dbl>, tSNE_2 <dbl>

 
If a tidyverse-compatible package is not included in the
@@ -423,22 +423,22 @@ 
Clustering# Reorder columns
 pbmc_small_cluster %>%
     select(label, everything())
-
## # A SingleCellExperiment-tibble abstraction: 80 × 19
+
## # A SingleCellExperiment-tibble abstraction: 80 x 19
 ## # Features=230 | Cells=80 | Assays=counts, logcounts
 ##    .cell  label orig.ident nCount_RNA nFeature_RNA RNA_snn_res.0.8 letter.idents
 ##    <chr>  <fct> <fct>           <dbl>        <int> <fct>           <fct>        
-##  1 ATGCC… 2     SeuratPro…         70           47 0               A            
-##  2 CATGG… 2     SeuratPro…         85           52 0               A            
-##  3 GAACC… 2     SeuratPro…         87           50 1               B            
-##  4 TGACT… 1     SeuratPro…        127           56 0               A            
-##  5 AGTCA… 2     SeuratPro…        173           53 0               A            
-##  6 TCTGA… 2     SeuratPro…         70           48 0               A            
-##  7 TGGTA… 1     SeuratPro…         64           36 0               A            
-##  8 GCAGC… 2     SeuratPro…         72           45 0               A            
-##  9 GATAT… 2     SeuratPro…         52           36 0               A            
-## 10 AATGT… 2     SeuratPro…        100           41 0               A            
-## # ℹ 70 more rows
-## # ℹ 12 more variables: groups <chr>, RNA_snn_res.1 <fct>, file <chr>,
+##  1 ATGCC~ 2     SeuratPro~         70           47 0               A            
+##  2 CATGG~ 2     SeuratPro~         85           52 0               A            
+##  3 GAACC~ 2     SeuratPro~         87           50 1               B            
+##  4 TGACT~ 1     SeuratPro~        127           56 0               A            
+##  5 AGTCA~ 2     SeuratPro~        173           53 0               A            
+##  6 TCTGA~ 2     SeuratPro~         70           48 0               A            
+##  7 TGGTA~ 1     SeuratPro~         64           36 0               A            
+##  8 GCAGC~ 2     SeuratPro~         72           45 0               A            
+##  9 GATAT~ 2     SeuratPro~         52           36 0               A            
+## 10 AATGT~ 2     SeuratPro~        100           41 0               A            
+## # i 70 more rows
+## # i 12 more variables: groups <chr>, RNA_snn_res.1 <fct>, file <chr>,
 ## #   sample <chr>, ident <fct>, PC1 <dbl>, PC2 <dbl>, PC3 <dbl>, PC4 <dbl>,
 ## #   PC5 <dbl>, tSNE_1 <dbl>, tSNE_2 <dbl>

 
And interrogate the output as if it was a regular
@@ -447,7 +447,7 @@ 
Clustering# Count number of cells for each cluster per group
 pbmc_small_cluster %>%
     count(groups, label)
-
## # A tibble: 8 × 3
+
## # A tibble: 8 x 3
 ##   groups label     n
 ##   <chr>  <fct> <int>
 ## 1 g1     1        12
@@ -534,22 +534,22 @@ 
Cell type prediction# Reorder columns
 pbmc_small_cell_type %>%
     select(cell, first.labels, everything())

-
## # A SingleCellExperiment-tibble abstraction: 80 × 23
+
## # A SingleCellExperiment-tibble abstraction: 80 x 23
 ## # Features=230 | Cells=80 | Assays=counts, logcounts
 ##    cell          first.labels orig.ident nCount_RNA nFeature_RNA RNA_snn_res.0.8
 ##    <chr>         <chr>        <fct>           <dbl>        <int> <fct>          
-##  1 ATGCCAGAACGA… CD4+ T-cells SeuratPro…         70           47 0              
-##  2 CATGGCCTGTGC… CD8+ T-cells SeuratPro…         85           52 0              
-##  3 GAACCTGATGAA… CD8+ T-cells SeuratPro…         87           50 1              
-##  4 TGACTGGATTCT… CD4+ T-cells SeuratPro…        127           56 0              
-##  5 AGTCAGACTGCA… CD4+ T-cells SeuratPro…        173           53 0              
-##  6 TCTGATACACGT… CD4+ T-cells SeuratPro…         70           48 0              
-##  7 TGGTATCTAAAC… CD4+ T-cells SeuratPro…         64           36 0              
-##  8 GCAGCTCTGTTT… CD4+ T-cells SeuratPro…         72           45 0              
-##  9 GATATAACACGC… CD4+ T-cells SeuratPro…         52           36 0              
-## 10 AATGTTGACAGT… CD4+ T-cells SeuratPro…        100           41 0              
-## # ℹ 70 more rows
-## # ℹ 17 more variables: letter.idents <fct>, groups <chr>, RNA_snn_res.1 <fct>,
+##  1 ATGCCAGAACGA~ CD4+ T-cells SeuratPro~         70           47 0              
+##  2 CATGGCCTGTGC~ CD8+ T-cells SeuratPro~         85           52 0              
+##  3 GAACCTGATGAA~ CD8+ T-cells SeuratPro~         87           50 1              
+##  4 TGACTGGATTCT~ CD4+ T-cells SeuratPro~        127           56 0              
+##  5 AGTCAGACTGCA~ CD4+ T-cells SeuratPro~        173           53 0              
+##  6 TCTGATACACGT~ CD4+ T-cells SeuratPro~         70           48 0              
+##  7 TGGTATCTAAAC~ CD4+ T-cells SeuratPro~         64           36 0              
+##  8 GCAGCTCTGTTT~ CD4+ T-cells SeuratPro~         72           45 0              
+##  9 GATATAACACGC~ CD4+ T-cells SeuratPro~         52           36 0              
+## 10 AATGTTGACAGT~ CD4+ T-cells SeuratPro~        100           41 0              
+## # i 70 more rows
+## # i 17 more variables: letter.idents <fct>, groups <chr>, RNA_snn_res.1 <fct>,
 ## #   file <chr>, sample <chr>, ident <fct>, label <fct>, PC1 <dbl>, PC2 <dbl>,
 ## #   PC3 <dbl>, PC4 <dbl>, PC5 <dbl>, tSNE_1 <dbl>, tSNE_2 <dbl>, UMAP1 <dbl>,
 ## #   UMAP2 <dbl>, UMAP3 <dbl>

@@ -559,7 +559,7 @@ 
Cell type prediction# Count number of cells for each cell type per cluster
 pbmc_small_cell_type %>%
     count(label, first.labels)

-
## # A tibble: 11 × 3
+
## # A tibble: 11 x 3
 ##    label first.labels     n
 ##    <fct> <chr>        <int>
 ##  1 1     CD4+ T-cells     2
@@ -621,7 +621,7 @@ 
Nested analyses    nest(data=-cell_class)
 
 pbmc_small_nested

-
## # A tibble: 2 × 2
+
## # A tibble: 2 x 2
 ##   cell_class data           
 ##   <chr>      <list>         
 ## 1 lymphoid   <SnglCllE[,40]>
@@ -650,7 +650,7 @@ 
Nested analyses        return(.x)
     }))
 pbmc_small_nested_reanalysed

-
## # A tibble: 2 × 2
+
## # A tibble: 2 x 2
 ##   cell_class data           
 ##   <chr>      <list>         
 ## 1 lymphoid   <SnglCllE[,40]>
@@ -709,21 +709,21 @@ 
Nested analyses
 data(pbmc_small_nested_interactions)
 pbmc_small_nested_interactions

-
## # A tibble: 100 × 9
+
## # A tibble: 100 x 9
 ##    sample  ligand          receptor ligand.name receptor.name origin destination
 ##    <chr>   <chr>           <chr>    <chr>       <chr>         <chr>  <chr>      
-##  1 sample1 cluster 1.PTMA  cluster… PTMA        VIPR1         clust… cluster 2  
-##  2 sample1 cluster 1.B2M   cluster… B2M         KLRD1         clust… cluster 2  
-##  3 sample1 cluster 1.IL16  cluster… IL16        CD4           clust… cluster 2  
-##  4 sample1 cluster 1.HLA-B cluster… HLA-B       KLRD1         clust… cluster 2  
-##  5 sample1 cluster 1.CALM1 cluster… CALM1       VIPR1         clust… cluster 2  
-##  6 sample1 cluster 1.HLA-E cluster… HLA-E       KLRD1         clust… cluster 2  
-##  7 sample1 cluster 1.GNAS  cluster… GNAS        VIPR1         clust… cluster 2  
-##  8 sample1 cluster 1.B2M   cluster… B2M         HFE           clust… cluster 2  
-##  9 sample1 cluster 1.PTMA  cluster… PTMA        VIPR1         clust… cluster 3  
-## 10 sample1 cluster 1.CALM1 cluster… CALM1       VIPR1         clust… cluster 3  
-## # ℹ 90 more rows
-## # ℹ 2 more variables: interaction.type <chr>, LRscore <dbl>

+##  1 sample1 cluster 1.PTMA  cluster~ PTMA        VIPR1         clust~ cluster 2  
+##  2 sample1 cluster 1.B2M   cluster~ B2M         KLRD1         clust~ cluster 2  
+##  3 sample1 cluster 1.IL16  cluster~ IL16        CD4           clust~ cluster 2  
+##  4 sample1 cluster 1.HLA-B cluster~ HLA-B       KLRD1         clust~ cluster 2  
+##  5 sample1 cluster 1.CALM1 cluster~ CALM1       VIPR1         clust~ cluster 2  
+##  6 sample1 cluster 1.HLA-E cluster~ HLA-E       KLRD1         clust~ cluster 2  
+##  7 sample1 cluster 1.GNAS  cluster~ GNAS        VIPR1         clust~ cluster 2  
+##  8 sample1 cluster 1.B2M   cluster~ B2M         HFE           clust~ cluster 2  
+##  9 sample1 cluster 1.PTMA  cluster~ PTMA        VIPR1         clust~ cluster 3  
+## 10 sample1 cluster 1.CALM1 cluster~ CALM1       VIPR1         clust~ cluster 3  
+## # i 90 more rows
+## # i 2 more variables: interaction.type <chr>, LRscore <dbl>

 
 

 
Aggregating cells
@@ -742,7 +742,8 @@ 
Aggregating cells## metadata(0):
 ## assays(1): counts
 ## rownames(230): ACAP1 ACRBP ... ZNF330 ZNF76
-## rowData names(0):
+## rowData names(5): vst.mean vst.variance vst.variance.expected
+##   vst.variance.standardized vst.variable
 ## colnames(2): g1 g2
 ## colData names(4): .aggregated_cells groups orig.ident file

 
@@ -751,7 +752,7 @@ 
Session Info
 sessionInfo()

-
## R version 4.4.0 Patched (2024-04-24 r86483)
+
## R version 4.4.0 (2024-04-24)
 ## Platform: x86_64-pc-linux-gnu
 ## Running under: Ubuntu 22.04.4 LTS
 ## 
@@ -760,12 +761,7 @@ 
Session Info## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0
 ## 
 ## locale:
-##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
-##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
-##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
-##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
-##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
-## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
+## [1] C
 ## 
 ## time zone: UTC
 ## tzcode source: system (glibc)
@@ -777,7 +773,7 @@ 
Session Info## other attached packages:
 ##  [1] dittoSeq_1.17.0                 Matrix_1.7-0                   
 ##  [3] ttservice_0.4.0                 tidyr_1.3.1                    
-##  [5] dplyr_1.1.4                     tidySingleCellExperiment_1.13.3
+##  [5] dplyr_1.1.4                     tidySingleCellExperiment_1.15.1
 ##  [7] tidyHeatmap_1.8.1               GGally_2.2.1                   
 ##  [9] purrr_1.0.2                     SingleCellSignalR_1.17.0       
 ## [11] SingleR_2.7.0                   celldex_1.15.0                 
@@ -797,7 +793,7 @@ 
Session Info##   [5] lifecycle_1.0.4           httr2_1.0.1              
 ##   [7] doParallel_1.0.17         edgeR_4.3.0              
 ##   [9] MASS_7.3-60.2             lattice_0.22-6           
-##  [11] alabaster.base_1.5.0      dendextend_1.17.1        
+##  [11] alabaster.base_1.5.1      dendextend_1.17.1        
 ##  [13] magrittr_2.0.3            plotly_4.10.4            
 ##  [15] limma_3.61.0              sass_0.4.9               
 ##  [17] rmarkdown_2.26            jquerylib_0.1.4          
@@ -819,10 +815,10 @@ 
Session Info##  [49] ellipsis_0.3.2            ggridges_0.5.6           
 ##  [51] survival_3.6-4            iterators_1.0.14         
 ##  [53] systemfonts_1.0.6         foreach_1.5.2            
-##  [55] tools_4.4.0               ragg_1.3.0               
+##  [55] tools_4.4.0               ragg_1.3.1               
 ##  [57] Rcpp_1.0.12               glue_1.7.0               
-##  [59] gridExtra_2.3             SparseArray_1.5.0        
-##  [61] xfun_0.43                 HDF5Array_1.31.6         
+##  [59] gridExtra_2.3             SparseArray_1.5.1        
+##  [61] xfun_0.43                 HDF5Array_1.33.0         
 ##  [63] gypsum_1.1.0              withr_3.0.0              
 ##  [65] BiocManager_1.30.23       fastmap_1.1.1            
 ##  [67] rhdf5filters_1.17.0       bluster_1.15.0           
@@ -858,7 +854,7 @@ 
Session Info## [127] crayon_1.5.2              paws.common_0.7.2        
 ## [129] labeling_0.4.3            plyr_1.8.9               
 ## [131] fs_1.6.4                  ggbeeswarm_0.7.2         
-## [133] stringi_1.8.3             viridisLite_0.4.2        
+## [133] stringi_1.8.4             viridisLite_0.4.2        
 ## [135] alabaster.se_1.5.0        BiocParallel_1.39.0      
 ## [137] munsell_0.5.1             Biostrings_2.73.0        
 ## [139] lazyeval_0.2.2            ExperimentHub_2.13.0     
@@ -872,7 +868,7 @@ 
Session Info
 
References
 

-

+

 

 Amezquita, Robert A, Aaron TL Lun, Etienne Becht, Vince J Carey, Lindsay
 N Carpp, Ludwig Geistlinger, Federico Martini, et al. 2019.
diff --git a/articles/introduction_files/figure-html/plot2-1.png b/articles/introduction_files/figure-html/plot2-1.png
index 44f9cbabe85d830f2b2aa29cdea9b7642e3bc098..d319270b3ee0f1c1306517c158d49cb64bdcfed4 100644
GIT binary patch
delta 16379
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zBZ?Vn;{lQ&Fhl_X2B++M^ob#eA7^^yC*9+B)rPDQVMmPa9W&2^M$=eTXCd7MnX%N~
zuK=r?E(3!gn-ZQR_U*#jT9@wyTre-#N_z;YU{9t0cfGx<0CFPK$sDM${0xOII2g1y
zeez_p!>Xoya5!SIxV5*paeqD^CxN>^1`~pzi3v@i(cr*MJi57Tpj3zdyxlpK(r5HF
zBpFwI`diq=t$()z$J)`+@lmGVjo8z$=478AVOv;49qg2Dy87?o&d2bE1Rymx6S|YhZAx!z8wY#68sH3oo!ChTw=&1SSE7`HJy6o(GzWR`kk)?X6v*>nw}A
z(i1JRI}yV3KD>S{AwA_jgV`ScLlM+9R
       
         tidySingleCellExperiment
-        1.13.3
+        1.15.1
       
     

 
@@ -70,13 +70,13 @@ 
Citation

 
     
Mangiola S (2024).
 tidySingleCellExperiment: Brings SingleCellExperiment to the Tidyverse.
-R package version 1.13.3, https://github.com/stemangiola/tidySingleCellExperiment. 
+R package version 1.15.1, https://github.com/stemangiola/tidySingleCellExperiment. 
 

     
@Manual{,
   title = {tidySingleCellExperiment: Brings SingleCellExperiment to the Tidyverse},
   author = {Stefano Mangiola},
   year = {2024},
-  note = {R package version 1.13.3},
+  note = {R package version 1.15.1},
   url = {https://github.com/stemangiola/tidySingleCellExperiment},
 }

 
diff --git a/index.html b/index.html
index adcb83c..30954ff 100644
--- a/index.html
+++ b/index.html
@@ -33,7 +33,7 @@
       
       
         tidySingleCellExperiment
-        1.13.3
+        1.15.1
       
     

 
@@ -209,22 +209,22 @@ 
Data representation of
 
It looks like a tibble

 
 pbmc_small

-
## [90m# A SingleCellExperiment-tibble abstraction: 80 × 17[39m
+
## [90m# A SingleCellExperiment-tibble abstraction: 80 x 17[39m
 ## [90m# [90mFeatures=230 | Cells=80 | Assays=counts, logcounts[0m[39m
 ##    .cell orig.ident nCount_RNA nFeature_RNA RNA_snn_res.0.8 letter.idents groups
 ##    [3m[90m<chr>[39m[23m [3m[90m<fct>[39m[23m           [3m[90m<dbl>[39m[23m        [3m[90m<int>[39m[23m [3m[90m<fct>[39m[23m           [3m[90m<fct>[39m[23m         [3m[90m<chr>[39m[23m 
-## [90m 1[39m ATGC… SeuratPro…         70           47 0               A             g2    
-## [90m 2[39m CATG… SeuratPro…         85           52 0               A             g1    
-## [90m 3[39m GAAC… SeuratPro…         87           50 1               B             g2    
-## [90m 4[39m TGAC… SeuratPro…        127           56 0               A             g2    
-## [90m 5[39m AGTC… SeuratPro…        173           53 0               A             g2    
-## [90m 6[39m TCTG… SeuratPro…         70           48 0               A             g1    
-## [90m 7[39m TGGT… SeuratPro…         64           36 0               A             g1    
-## [90m 8[39m GCAG… SeuratPro…         72           45 0               A             g1    
-## [90m 9[39m GATA… SeuratPro…         52           36 0               A             g1    
-## [90m10[39m AATG… SeuratPro…        100           41 0               A             g1    
-## [90m# ℹ 70 more rows[39m
-## [90m# ℹ 10 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>,[39m
+## [90m 1[39m ATGC~ SeuratPro~         70           47 0               A             g2    
+## [90m 2[39m CATG~ SeuratPro~         85           52 0               A             g1    
+## [90m 3[39m GAAC~ SeuratPro~         87           50 1               B             g2    
+## [90m 4[39m TGAC~ SeuratPro~        127           56 0               A             g2    
+## [90m 5[39m AGTC~ SeuratPro~        173           53 0               A             g2    
+## [90m 6[39m TCTG~ SeuratPro~         70           48 0               A             g1    
+## [90m 7[39m TGGT~ SeuratPro~         64           36 0               A             g1    
+## [90m 8[39m GCAG~ SeuratPro~         72           45 0               A             g1    
+## [90m 9[39m GATA~ SeuratPro~         52           36 0               A             g1    
+## [90m10[39m AATG~ SeuratPro~        100           41 0               A             g1    
+## [90m# i 70 more rows[39m
+## [90m# i 10 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>,[39m
 ## [90m#   PC_1 <dbl>, PC_2 <dbl>, PC_3 <dbl>, PC_4 <dbl>, PC_5 <dbl>, tSNE_1 <dbl>,[39m
 ## [90m#   tSNE_2 <dbl>[39m

 
But it is a SingleCellExperiment object after all

@@ -283,22 +283,22 @@ 
Annotation polishing# Reorder to have sample column up front
 pbmc_small_polished |>
     select(sample, everything())

-
## [90m# A SingleCellExperiment-tibble abstraction: 80 × 18[39m
+
## [90m# A SingleCellExperiment-tibble abstraction: 80 x 18[39m
 ## [90m# [90mFeatures=230 | Cells=80 | Assays=counts, logcounts[0m[39m
 ##    .cell sample orig.ident nCount_RNA nFeature_RNA RNA_snn_res.0.8 letter.idents
 ##    [3m[90m<chr>[39m[23m [3m[90m<chr>[39m[23m  [3m[90m<fct>[39m[23m           [3m[90m<dbl>[39m[23m        [3m[90m<int>[39m[23m [3m[90m<fct>[39m[23m           [3m[90m<fct>[39m[23m        
-## [90m 1[39m ATGC… sampl… SeuratPro…         70           47 0               A            
-## [90m 2[39m CATG… sampl… SeuratPro…         85           52 0               A            
-## [90m 3[39m GAAC… sampl… SeuratPro…         87           50 1               B            
-## [90m 4[39m TGAC… sampl… SeuratPro…        127           56 0               A            
-## [90m 5[39m AGTC… sampl… SeuratPro…        173           53 0               A            
-## [90m 6[39m TCTG… sampl… SeuratPro…         70           48 0               A            
-## [90m 7[39m TGGT… sampl… SeuratPro…         64           36 0               A            
-## [90m 8[39m GCAG… sampl… SeuratPro…         72           45 0               A            
-## [90m 9[39m GATA… sampl… SeuratPro…         52           36 0               A            
-## [90m10[39m AATG… sampl… SeuratPro…        100           41 0               A            
-## [90m# ℹ 70 more rows[39m
-## [90m# ℹ 11 more variables: groups <chr>, RNA_snn_res.1 <fct>, file <chr>,[39m
+## [90m 1[39m ATGC~ sampl~ SeuratPro~         70           47 0               A            
+## [90m 2[39m CATG~ sampl~ SeuratPro~         85           52 0               A            
+## [90m 3[39m GAAC~ sampl~ SeuratPro~         87           50 1               B            
+## [90m 4[39m TGAC~ sampl~ SeuratPro~        127           56 0               A            
+## [90m 5[39m AGTC~ sampl~ SeuratPro~        173           53 0               A            
+## [90m 6[39m TCTG~ sampl~ SeuratPro~         70           48 0               A            
+## [90m 7[39m TGGT~ sampl~ SeuratPro~         64           36 0               A            
+## [90m 8[39m GCAG~ sampl~ SeuratPro~         72           45 0               A            
+## [90m 9[39m GATA~ sampl~ SeuratPro~         52           36 0               A            
+## [90m10[39m AATG~ sampl~ SeuratPro~        100           41 0               A            
+## [90m# i 70 more rows[39m
+## [90m# i 11 more variables: groups <chr>, RNA_snn_res.1 <fct>, file <chr>,[39m
 ## [90m#   ident <fct>, PC_1 <dbl>, PC_2 <dbl>, PC_3 <dbl>, PC_4 <dbl>, PC_5 <dbl>,[39m
 ## [90m#   tSNE_1 <dbl>, tSNE_2 <dbl>[39m

 

@@ -330,7 +330,7 @@ 
Preliminary plots)
     )

 
## Warning: [1m[22mThe `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
-## [36mℹ[39m Please use the `linewidth` argument instead.
+## [36mi[39m Please use the `linewidth` argument instead.
 ## [90mThis warning is displayed once every 8 hours.[39m
 ## [90mCall `lifecycle::last_lifecycle_warnings()` to see where this warning was[39m
 ## [90mgenerated.[39m

@@ -383,25 +383,29 @@ 
Preprocess the dataset
 ## Warning in (function (A, nv = 5, nu = nv, maxit = 1000, work = nv + 7, reorth =
 ## TRUE, : You're computing too large a percentage of total singular values, use a
-## standard svd instead.

+## standard svd instead.
+
+## Warning in (function (A, nv = 5, nu = nv, maxit = 1000, work = nv + 7, reorth =
+## TRUE, : did not converge--results might be invalid!; try increasing work or
+## maxit

 
 pbmc_small_pca

-
## [90m# A SingleCellExperiment-tibble abstraction: 80 × 18[39m
+
## [90m# A SingleCellExperiment-tibble abstraction: 80 x 18[39m
 ## [90m# [90mFeatures=230 | Cells=80 | Assays=counts, logcounts[0m[39m
 ##    .cell orig.ident nCount_RNA nFeature_RNA RNA_snn_res.0.8 letter.idents groups
 ##    [3m[90m<chr>[39m[23m [3m[90m<fct>[39m[23m           [3m[90m<dbl>[39m[23m        [3m[90m<int>[39m[23m [3m[90m<fct>[39m[23m           [3m[90m<fct>[39m[23m         [3m[90m<chr>[39m[23m 
-## [90m 1[39m ATGC… SeuratPro…         70           47 0               A             g2    
-## [90m 2[39m CATG… SeuratPro…         85           52 0               A             g1    
-## [90m 3[39m GAAC… SeuratPro…         87           50 1               B             g2    
-## [90m 4[39m TGAC… SeuratPro…        127           56 0               A             g2    
-## [90m 5[39m AGTC… SeuratPro…        173           53 0               A             g2    
-## [90m 6[39m TCTG… SeuratPro…         70           48 0               A             g1    
-## [90m 7[39m TGGT… SeuratPro…         64           36 0               A             g1    
-## [90m 8[39m GCAG… SeuratPro…         72           45 0               A             g1    
-## [90m 9[39m GATA… SeuratPro…         52           36 0               A             g1    
-## [90m10[39m AATG… SeuratPro…        100           41 0               A             g1    
-## [90m# ℹ 70 more rows[39m
-## [90m# ℹ 11 more variables: RNA_snn_res.1 <fct>, file <chr>, sample <chr>,[39m
+## [90m 1[39m ATGC~ SeuratPro~         70           47 0               A             g2    
+## [90m 2[39m CATG~ SeuratPro~         85           52 0               A             g1    
+## [90m 3[39m GAAC~ SeuratPro~         87           50 1               B             g2    
+## [90m 4[39m TGAC~ SeuratPro~        127           56 0               A             g2    
+## [90m 5[39m AGTC~ SeuratPro~        173           53 0               A             g2    
+## [90m 6[39m TCTG~ SeuratPro~         70           48 0               A             g1    
+## [90m 7[39m TGGT~ SeuratPro~         64           36 0               A             g1    
+## [90m 8[39m GCAG~ SeuratPro~         72           45 0               A             g1    
+## [90m 9[39m GATA~ SeuratPro~         52           36 0               A             g1    
+## [90m10[39m AATG~ SeuratPro~        100           41 0               A             g1    
+## [90m# i 70 more rows[39m
+## [90m# i 11 more variables: RNA_snn_res.1 <fct>, file <chr>, sample <chr>,[39m
 ## [90m#   ident <fct>, PC1 <dbl>, PC2 <dbl>, PC3 <dbl>, PC4 <dbl>, PC5 <dbl>,[39m
 ## [90m#   tSNE_1 <dbl>, tSNE_2 <dbl>[39m

 
If a tidyverse-compatible package is not included in the tidySingleCellExperiment collection, we can use as_tibble to permanently convert tidySingleCellExperiment into a tibble.

@@ -436,22 +440,22 @@ 
Identify clusters
 # Reorder columns
 pbmc_small_cluster |> select(label, everything())

-
## [90m# A SingleCellExperiment-tibble abstraction: 80 × 19[39m
+
## [90m# A SingleCellExperiment-tibble abstraction: 80 x 19[39m
 ## [90m# [90mFeatures=230 | Cells=80 | Assays=counts, logcounts[0m[39m
 ##    .cell  label orig.ident nCount_RNA nFeature_RNA RNA_snn_res.0.8 letter.idents
 ##    [3m[90m<chr>[39m[23m  [3m[90m<fct>[39m[23m [3m[90m<fct>[39m[23m           [3m[90m<dbl>[39m[23m        [3m[90m<int>[39m[23m [3m[90m<fct>[39m[23m           [3m[90m<fct>[39m[23m        
-## [90m 1[39m ATGCC… 2     SeuratPro…         70           47 0               A            
-## [90m 2[39m CATGG… 2     SeuratPro…         85           52 0               A            
-## [90m 3[39m GAACC… 2     SeuratPro…         87           50 1               B            
-## [90m 4[39m TGACT… 1     SeuratPro…        127           56 0               A            
-## [90m 5[39m AGTCA… 2     SeuratPro…        173           53 0               A            
-## [90m 6[39m TCTGA… 2     SeuratPro…         70           48 0               A            
-## [90m 7[39m TGGTA… 1     SeuratPro…         64           36 0               A            
-## [90m 8[39m GCAGC… 2     SeuratPro…         72           45 0               A            
-## [90m 9[39m GATAT… 2     SeuratPro…         52           36 0               A            
-## [90m10[39m AATGT… 2     SeuratPro…        100           41 0               A            
-## [90m# ℹ 70 more rows[39m
-## [90m# ℹ 12 more variables: groups <chr>, RNA_snn_res.1 <fct>, file <chr>,[39m
+## [90m 1[39m ATGCC~ 2     SeuratPro~         70           47 0               A            
+## [90m 2[39m CATGG~ 2     SeuratPro~         85           52 0               A            
+## [90m 3[39m GAACC~ 2     SeuratPro~         87           50 1               B            
+## [90m 4[39m TGACT~ 1     SeuratPro~        127           56 0               A            
+## [90m 5[39m AGTCA~ 2     SeuratPro~        173           53 0               A            
+## [90m 6[39m TCTGA~ 2     SeuratPro~         70           48 0               A            
+## [90m 7[39m TGGTA~ 1     SeuratPro~         64           36 0               A            
+## [90m 8[39m GCAGC~ 2     SeuratPro~         72           45 0               A            
+## [90m 9[39m GATAT~ 2     SeuratPro~         52           36 0               A            
+## [90m10[39m AATGT~ 2     SeuratPro~        100           41 0               A            
+## [90m# i 70 more rows[39m
+## [90m# i 12 more variables: groups <chr>, RNA_snn_res.1 <fct>, file <chr>,[39m
 ## [90m#   sample <chr>, ident <fct>, PC1 <dbl>, PC2 <dbl>, PC3 <dbl>, PC4 <dbl>,[39m
 ## [90m#   PC5 <dbl>, tSNE_1 <dbl>, tSNE_2 <dbl>[39m

 
And interrogate the output as if it was a regular tibble.

@@ -461,7 +465,7 @@ 
Identify clusterscount(groups, label)

 
## tidySingleCellExperiment says: A data frame is returned for independent data analysis.
 
-## [90m# A tibble: 8 × 3[39m
+## [90m# A tibble: 8 x 3[39m
 ##   groups label     n
 ##   [3m[90m<chr>[39m[23m  [3m[90m<fct>[39m[23m [3m[90m<int>[39m[23m
 ## [90m1[39m g1     1        12
@@ -494,7 +498,7 @@ 
Identify clusters## tidyHeatmap says: (once per session) from release 1.7.0 the scaling is set to "none" by default. Please use scale = "row", "column" or "both" to apply scaling
 
 ## Warning: [1m[22mThe `.scale` argument of `heatmap()` is deprecated as of tidyHeatmap 1.7.0.
-## [36mℹ[39m Please use scale (without dot prefix) instead: heatmap(scale = ...)
+## [36mi[39m Please use scale (without dot prefix) instead: heatmap(scale = ...)
 ## [90mThis warning is displayed once every 8 hours.[39m
 ## [90mCall `lifecycle::last_lifecycle_warnings()` to see where this warning was[39m
 ## [90mgenerated.[39m

@@ -564,22 +568,22 @@ 
Cell type prediction## returned with the old-style vocabulary (cell), however, we suggest to update
 ## your workflow to reflect the new vocabulary (.cell).
 
-## [90m# A SingleCellExperiment-tibble abstraction: 80 × 23[39m
+## [90m# A SingleCellExperiment-tibble abstraction: 80 x 23[39m
 ## [90m# [90mFeatures=230 | Cells=80 | Assays=counts, logcounts[0m[39m
 ##    cell          first.labels orig.ident nCount_RNA nFeature_RNA RNA_snn_res.0.8
 ##    [3m[90m<chr>[39m[23m         [3m[90m<chr>[39m[23m        [3m[90m<fct>[39m[23m           [3m[90m<dbl>[39m[23m        [3m[90m<int>[39m[23m [3m[90m<fct>[39m[23m          
-## [90m 1[39m ATGCCAGAACGA… CD4+ T-cells SeuratPro…         70           47 0              
-## [90m 2[39m CATGGCCTGTGC… CD8+ T-cells SeuratPro…         85           52 0              
-## [90m 3[39m GAACCTGATGAA… CD8+ T-cells SeuratPro…         87           50 1              
-## [90m 4[39m TGACTGGATTCT… CD4+ T-cells SeuratPro…        127           56 0              
-## [90m 5[39m AGTCAGACTGCA… CD4+ T-cells SeuratPro…        173           53 0              
-## [90m 6[39m TCTGATACACGT… CD4+ T-cells SeuratPro…         70           48 0              
-## [90m 7[39m TGGTATCTAAAC… CD4+ T-cells SeuratPro…         64           36 0              
-## [90m 8[39m GCAGCTCTGTTT… CD4+ T-cells SeuratPro…         72           45 0              
-## [90m 9[39m GATATAACACGC… CD4+ T-cells SeuratPro…         52           36 0              
-## [90m10[39m AATGTTGACAGT… CD4+ T-cells SeuratPro…        100           41 0              
-## [90m# ℹ 70 more rows[39m
-## [90m# ℹ 17 more variables: letter.idents <fct>, groups <chr>, RNA_snn_res.1 <fct>,[39m
+## [90m 1[39m ATGCCAGAACGA~ CD4+ T-cells SeuratPro~         70           47 0              
+## [90m 2[39m CATGGCCTGTGC~ CD8+ T-cells SeuratPro~         85           52 0              
+## [90m 3[39m GAACCTGATGAA~ CD8+ T-cells SeuratPro~         87           50 1              
+## [90m 4[39m TGACTGGATTCT~ CD4+ T-cells SeuratPro~        127           56 0              
+## [90m 5[39m AGTCAGACTGCA~ CD4+ T-cells SeuratPro~        173           53 0              
+## [90m 6[39m TCTGATACACGT~ CD4+ T-cells SeuratPro~         70           48 0              
+## [90m 7[39m TGGTATCTAAAC~ CD4+ T-cells SeuratPro~         64           36 0              
+## [90m 8[39m GCAGCTCTGTTT~ CD4+ T-cells SeuratPro~         72           45 0              
+## [90m 9[39m GATATAACACGC~ CD4+ T-cells SeuratPro~         52           36 0              
+## [90m10[39m AATGTTGACAGT~ CD4+ T-cells SeuratPro~        100           41 0              
+## [90m# i 70 more rows[39m
+## [90m# i 17 more variables: letter.idents <fct>, groups <chr>, RNA_snn_res.1 <fct>,[39m
 ## [90m#   file <chr>, sample <chr>, ident <fct>, label <fct>, PC1 <dbl>, PC2 <dbl>,[39m
 ## [90m#   PC3 <dbl>, PC4 <dbl>, PC5 <dbl>, tSNE_1 <dbl>, tSNE_2 <dbl>, UMAP1 <dbl>,[39m
 ## [90m#   UMAP2 <dbl>, UMAP3 <dbl>[39m

@@ -590,7 +594,7 @@ 
Cell type predictioncount(label, first.labels)

 
## tidySingleCellExperiment says: A data frame is returned for independent data analysis.
 
-## [90m# A tibble: 11 × 3[39m
+## [90m# A tibble: 11 x 3[39m
 ##    label first.labels     n
 ##    [3m[90m<fct>[39m[23m [3m[90m<chr>[39m[23m        [3m[90m<int>[39m[23m
 ## [90m 1[39m 1     CD4+ T-cells     2
@@ -655,13 +659,13 @@ 
Nested analyses    nest(data=-cell_class)

 
## Warning: [1m[22mThere were 2 warnings in `mutate()`.
 ## The first warning was:
-## [1m[22m[36mℹ[39m In argument: `data = map(...)`.
+## [1m[22m[36mi[39m In argument: `data = map(...)`.
 ## Caused by warning in `is_sample_feature_deprecated_used()`:
 ## [33m![39m tidySingleCellExperiment says: from version 1.3.1, the special columns including cell id (colnames(se)) has changed to ".cell". This dataset is returned with the old-style vocabulary (cell), however, we suggest to update your workflow to reflect the new vocabulary (.cell).
-## [1m[22m[36mℹ[39m Run `dplyr::last_dplyr_warnings()` to see the 1 remaining warning.

+## [1m[22m[36mi[39m Run `dplyr::last_dplyr_warnings()` to see the 1 remaining warning.
 pbmc_small_nested
-
## [90m# A tibble: 2 × 2[39m
+
## [90m# A tibble: 2 x 2[39m
 ##   cell_class data           
 ##   [3m[90m<chr>[39m[23m      [3m[90m<list>[39m[23m         
 ## [90m1[39m lymphoid   [90m<SnglCllE[,40]>[39m
@@ -691,7 +695,7 @@ 
Nested analyses    ))
 
 pbmc_small_nested_reanalysed

-
## [90m# A tibble: 2 × 2[39m
+
## [90m# A tibble: 2 x 2[39m
 ##   cell_class data           
 ##   [3m[90m<chr>[39m[23m      [3m[90m<list>[39m[23m         
 ## [90m1[39m lymphoid   [90m<SnglCllE[,40]>[39m
@@ -747,21 +751,21 @@ 
Nested analyses
 data(pbmc_small_nested_interactions)
 pbmc_small_nested_interactions

-
## [90m# A tibble: 100 × 9[39m
+
## [90m# A tibble: 100 x 9[39m
 ##    sample  ligand          receptor ligand.name receptor.name origin destination
 ##    [3m[90m<chr>[39m[23m   [3m[90m<chr>[39m[23m           [3m[90m<chr>[39m[23m    [3m[90m<chr>[39m[23m       [3m[90m<chr>[39m[23m         [3m[90m<chr>[39m[23m  [3m[90m<chr>[39m[23m      
-## [90m 1[39m sample1 cluster 1.PTMA  cluster… PTMA        VIPR1         clust… cluster 2  
-## [90m 2[39m sample1 cluster 1.B2M   cluster… B2M         KLRD1         clust… cluster 2  
-## [90m 3[39m sample1 cluster 1.IL16  cluster… IL16        CD4           clust… cluster 2  
-## [90m 4[39m sample1 cluster 1.HLA-B cluster… HLA-B       KLRD1         clust… cluster 2  
-## [90m 5[39m sample1 cluster 1.CALM1 cluster… CALM1       VIPR1         clust… cluster 2  
-## [90m 6[39m sample1 cluster 1.HLA-E cluster… HLA-E       KLRD1         clust… cluster 2  
-## [90m 7[39m sample1 cluster 1.GNAS  cluster… GNAS        VIPR1         clust… cluster 2  
-## [90m 8[39m sample1 cluster 1.B2M   cluster… B2M         HFE           clust… cluster 2  
-## [90m 9[39m sample1 cluster 1.PTMA  cluster… PTMA        VIPR1         clust… cluster 3  
-## [90m10[39m sample1 cluster 1.CALM1 cluster… CALM1       VIPR1         clust… cluster 3  
-## [90m# ℹ 90 more rows[39m
-## [90m# ℹ 2 more variables: interaction.type <chr>, LRscore <dbl>[39m

+## [90m 1[39m sample1 cluster 1.PTMA  cluster~ PTMA        VIPR1         clust~ cluster 2  
+## [90m 2[39m sample1 cluster 1.B2M   cluster~ B2M         KLRD1         clust~ cluster 2  
+## [90m 3[39m sample1 cluster 1.IL16  cluster~ IL16        CD4           clust~ cluster 2  
+## [90m 4[39m sample1 cluster 1.HLA-B cluster~ HLA-B       KLRD1         clust~ cluster 2  
+## [90m 5[39m sample1 cluster 1.CALM1 cluster~ CALM1       VIPR1         clust~ cluster 2  
+## [90m 6[39m sample1 cluster 1.HLA-E cluster~ HLA-E       KLRD1         clust~ cluster 2  
+## [90m 7[39m sample1 cluster 1.GNAS  cluster~ GNAS        VIPR1         clust~ cluster 2  
+## [90m 8[39m sample1 cluster 1.B2M   cluster~ B2M         HFE           clust~ cluster 2  
+## [90m 9[39m sample1 cluster 1.PTMA  cluster~ PTMA        VIPR1         clust~ cluster 3  
+## [90m10[39m sample1 cluster 1.CALM1 cluster~ CALM1       VIPR1         clust~ cluster 3  
+## [90m# i 90 more rows[39m
+## [90m# i 2 more variables: interaction.type <chr>, LRscore <dbl>[39m

 

 

 
Aggregating cells
@@ -776,9 +780,10 @@ 
Aggregating cells## metadata(0):
 ## assays(1): counts
 ## rownames(230): ACAP1 ACRBP ... ZNF330 ZNF76
-## rowData names(0):
-## colnames(2): g1 g2
-## colData names(4): .aggregated_cells groups orig.ident file
+## rowData names(5): vst.mean vst.variance vst.variance.expected +## vst.variance.standardized vst.variable +## colnames(2): g1 g2 +## colData names(4): .aggregated_cells groups orig.ident file diff --git a/pkgdown.yml b/pkgdown.yml index 7b75823..355a456 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -1,7 +1,7 @@ -pandoc: 3.1.1 +pandoc: 3.1.13 pkgdown: 2.0.9 pkgdown_sha: ~ articles: introduction: introduction.html -last_built: 2024-05-04T10:34Z +last_built: 2024-05-10T05:17Z diff --git a/reference/add_class.html b/reference/add_class.html index 55779aa..3706cfd 100644 --- a/reference/add_class.html +++ b/reference/add_class.html @@ -17,7 +17,7 @@ tidySingleCellExperiment - 1.13.3 + 1.15.1 diff --git a/reference/aggregate_cells.html b/reference/aggregate_cells.html index 9b12a4b..5e1b13e 100644 --- a/reference/aggregate_cells.html +++ b/reference/aggregate_cells.html @@ -17,7 +17,7 @@ tidySingleCellExperiment - 1.13.3 + 1.15.1 diff --git a/reference/arrange.html b/reference/arrange.html index 4e6a793..3bcaaa8 100644 --- a/reference/arrange.html +++ b/reference/arrange.html @@ -22,7 +22,7 @@ tidySingleCellExperiment - 1.13.3 + 1.15.1 @@ -141,22 +141,22 @@

Examples

data(pbmc_small)
 pbmc_small |> 
     arrange(nFeature_RNA)
-#> # A SingleCellExperiment-tibble abstraction: 80 × 17
+#> # A SingleCellExperiment-tibble abstraction: 80 x 17
 #> # Features=230 | Cells=80 | Assays=counts, logcounts
 #>    .cell orig.ident nCount_RNA nFeature_RNA RNA_snn_res.0.8 letter.idents groups
 #>    <chr> <fct>           <dbl>        <int> <fct>           <fct>         <chr> 
-#>  1 CATG… SeuratPro…         51           26 0               A             g2    
-#>  2 GGCA… SeuratPro…        172           29 0               A             g1    
-#>  3 AGTC… SeuratPro…        157           29 0               A             g1    
-#>  4 GACG… SeuratPro…        202           30 0               A             g2    
-#>  5 GGAA… SeuratPro…        150           30 0               A             g2    
-#>  6 AGGT… SeuratPro…         62           31 0               A             g2    
-#>  7 CTTC… SeuratPro…         41           32 0               A             g2    
-#>  8 GTAA… SeuratPro…         67           33 0               A             g2    
-#>  9 GTCA… SeuratPro…        210           33 0               A             g2    
-#> 10 TGGT… SeuratPro…         64           36 0               A             g1    
-#> # ℹ 70 more rows
-#> # ℹ 10 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>,
+#>  1 CATG~ SeuratPro~         51           26 0               A             g2    
+#>  2 GGCA~ SeuratPro~        172           29 0               A             g1    
+#>  3 AGTC~ SeuratPro~        157           29 0               A             g1    
+#>  4 GACG~ SeuratPro~        202           30 0               A             g2    
+#>  5 GGAA~ SeuratPro~        150           30 0               A             g2    
+#>  6 AGGT~ SeuratPro~         62           31 0               A             g2    
+#>  7 CTTC~ SeuratPro~         41           32 0               A             g2    
+#>  8 GTAA~ SeuratPro~         67           33 0               A             g2    
+#>  9 GTCA~ SeuratPro~        210           33 0               A             g2    
+#> 10 TGGT~ SeuratPro~         64           36 0               A             g1    
+#> # i 70 more rows
+#> # i 10 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>,
 #> #   PC_1 <dbl>, PC_2 <dbl>, PC_3 <dbl>, PC_4 <dbl>, PC_5 <dbl>, tSNE_1 <dbl>,
 #> #   tSNE_2 <dbl>
     
diff --git a/reference/as_tibble.html b/reference/as_tibble.html
index b31f88f..1cdd76c 100644
--- a/reference/as_tibble.html
+++ b/reference/as_tibble.html
@@ -32,7 +32,7 @@
       
       
         tidySingleCellExperiment
-        1.13.3
+        1.15.1
@@ -170,21 +170,21 @@

See also

Examples

data(pbmc_small)
 pbmc_small |> as_tibble()
-#> # A tibble: 80 × 31
+#> # A tibble: 80 x 31
 #>    .cell orig.ident nCount_RNA nFeature_RNA RNA_snn_res.0.8 letter.idents groups
 #>    <chr> <fct>           <dbl>        <int> <fct>           <fct>         <chr> 
-#>  1 ATGC… SeuratPro…         70           47 0               A             g2    
-#>  2 CATG… SeuratPro…         85           52 0               A             g1    
-#>  3 GAAC… SeuratPro…         87           50 1               B             g2    
-#>  4 TGAC… SeuratPro…        127           56 0               A             g2    
-#>  5 AGTC… SeuratPro…        173           53 0               A             g2    
-#>  6 TCTG… SeuratPro…         70           48 0               A             g1    
-#>  7 TGGT… SeuratPro…         64           36 0               A             g1    
-#>  8 GCAG… SeuratPro…         72           45 0               A             g1    
-#>  9 GATA… SeuratPro…         52           36 0               A             g1    
-#> 10 AATG… SeuratPro…        100           41 0               A             g1    
-#> # ℹ 70 more rows
-#> # ℹ 24 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>,
+#>  1 ATGC~ SeuratPro~         70           47 0               A             g2    
+#>  2 CATG~ SeuratPro~         85           52 0               A             g1    
+#>  3 GAAC~ SeuratPro~         87           50 1               B             g2    
+#>  4 TGAC~ SeuratPro~        127           56 0               A             g2    
+#>  5 AGTC~ SeuratPro~        173           53 0               A             g2    
+#>  6 TCTG~ SeuratPro~         70           48 0               A             g1    
+#>  7 TGGT~ SeuratPro~         64           36 0               A             g1    
+#>  8 GCAG~ SeuratPro~         72           45 0               A             g1    
+#>  9 GATA~ SeuratPro~         52           36 0               A             g1    
+#> 10 AATG~ SeuratPro~        100           41 0               A             g1    
+#> # i 70 more rows
+#> # i 24 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>,
 #> #   PC_1 <dbl>, PC_2 <dbl>, PC_3 <dbl>, PC_4 <dbl>, PC_5 <dbl>, PC_6 <dbl>,
 #> #   PC_7 <dbl>, PC_8 <dbl>, PC_9 <dbl>, PC_10 <dbl>, PC_11 <dbl>, PC_12 <dbl>,
 #> #   PC_13 <dbl>, PC_14 <dbl>, PC_15 <dbl>, PC_16 <dbl>, PC_17 <dbl>,
diff --git a/reference/bind_rows.html b/reference/bind_rows.html
index f013333..fb5e4f1 100644
--- a/reference/bind_rows.html
+++ b/reference/bind_rows.html
@@ -22,7 +22,7 @@
       
       
         tidySingleCellExperiment
-        1.13.3
+        1.15.1
@@ -129,22 +129,22 @@

Examples

tt <- pbmc_small bind_rows(tt, tt) #> Warning: tidySingleCellExperiment says: you have duplicated cell names; they will be made unique. -#> # A SingleCellExperiment-tibble abstraction: 160 × 17 +#> # A SingleCellExperiment-tibble abstraction: 160 x 17 #> # Features=230 | Cells=160 | Assays=counts, logcounts #> .cell orig.ident nCount_RNA nFeature_RNA RNA_snn_res.0.8 letter.idents groups #> <chr> <fct> <dbl> <int> <fct> <fct> <chr> -#> 1 ATGC… SeuratPro… 70 47 0 A g2 -#> 2 CATG… SeuratPro… 85 52 0 A g1 -#> 3 GAAC… SeuratPro… 87 50 1 B g2 -#> 4 TGAC… SeuratPro… 127 56 0 A g2 -#> 5 AGTC… SeuratPro… 173 53 0 A g2 -#> 6 TCTG… SeuratPro… 70 48 0 A g1 -#> 7 TGGT… SeuratPro… 64 36 0 A g1 -#> 8 GCAG… SeuratPro… 72 45 0 A g1 -#> 9 GATA… SeuratPro… 52 36 0 A g1 -#> 10 AATG… SeuratPro… 100 41 0 A g1 -#> # ℹ 150 more rows -#> # ℹ 10 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>, +#> 1 ATGC~ SeuratPro~ 70 47 0 A g2 +#> 2 CATG~ SeuratPro~ 85 52 0 A g1 +#> 3 GAAC~ SeuratPro~ 87 50 1 B g2 +#> 4 TGAC~ SeuratPro~ 127 56 0 A g2 +#> 5 AGTC~ SeuratPro~ 173 53 0 A g2 +#> 6 TCTG~ SeuratPro~ 70 48 0 A g1 +#> 7 TGGT~ SeuratPro~ 64 36 0 A g1 +#> 8 GCAG~ SeuratPro~ 72 45 0 A g1 +#> 9 GATA~ SeuratPro~ 52 36 0 A g1 +#> 10 AATG~ SeuratPro~ 100 41 0 A g1 +#> # i 150 more rows +#> # i 10 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>, #> # PC_1 <dbl>, PC_2 <dbl>, PC_3 <dbl>, PC_4 <dbl>, PC_5 <dbl>, tSNE_1 <dbl>, #> # tSNE_2 <dbl> @@ -152,16 +152,16 @@

Examples

#> tidySingleCellExperiment says: Key columns are missing. A data frame is returned for independent data analysis. tt |> bind_cols(tt_bind) #> New names: -#> • `nCount_RNA` -> `nCount_RNA...2` -#> • `nFeature_RNA` -> `nFeature_RNA...3` -#> • `nCount_RNA` -> `nCount_RNA...10` -#> • `nFeature_RNA` -> `nFeature_RNA...11` +#> * `nCount_RNA` -> `nCount_RNA...2` +#> * `nFeature_RNA` -> `nFeature_RNA...3` +#> * `nCount_RNA` -> `nCount_RNA...10` +#> * `nFeature_RNA` -> `nFeature_RNA...11` #> New names: -#> • `nCount_RNA...2` -> `nCount_RNA...3` -#> • `nFeature_RNA...3` -> `nFeature_RNA...4` -#> • `nCount_RNA...10` -> `nCount_RNA...11` -#> • `nFeature_RNA...11` -> `nFeature_RNA...12` -#> # A SingleCellExperiment-tibble abstraction: 80 × 19 +#> * `nCount_RNA...2` -> `nCount_RNA...3` +#> * `nFeature_RNA...3` -> `nFeature_RNA...4` +#> * `nCount_RNA...10` -> `nCount_RNA...11` +#> * `nFeature_RNA...11` -> `nFeature_RNA...12` +#> # A SingleCellExperiment-tibble abstraction: 80 x 19 #> # Features=230 | Cells=80 | Assays=counts, logcounts #> .cell orig.ident nCount_RNA...3 nFeature_RNA...4 RNA_snn_res.0.8 #> <chr> <fct> <dbl> <int> <fct> @@ -175,8 +175,8 @@

Examples

#> 8 GCAGCTCTGTTTCT SeuratProject 72 45 0 #> 9 GATATAACACGCAT SeuratProject 52 36 0 #> 10 AATGTTGACAGTCA SeuratProject 100 41 0 -#> # ℹ 70 more rows -#> # ℹ 14 more variables: letter.idents <fct>, groups <chr>, RNA_snn_res.1 <fct>, +#> # i 70 more rows +#> # i 14 more variables: letter.idents <fct>, groups <chr>, RNA_snn_res.1 <fct>, #> # file <chr>, ident <fct>, nCount_RNA...11 <dbl>, nFeature_RNA...12 <int>, #> # PC_1 <dbl>, PC_2 <dbl>, PC_3 <dbl>, PC_4 <dbl>, PC_5 <dbl>, tSNE_1 <dbl>, #> # tSNE_2 <dbl> diff --git a/reference/cell_type_df.html b/reference/cell_type_df.html index a75ba77..230b4a4 100644 --- a/reference/cell_type_df.html +++ b/reference/cell_type_df.html @@ -17,7 +17,7 @@ tidySingleCellExperiment - 1.13.3 + 1.15.1 diff --git a/reference/count.html b/reference/count.html index 0657b4e..95c7a76 100644 --- a/reference/count.html +++ b/reference/count.html @@ -25,7 +25,7 @@ tidySingleCellExperiment - 1.13.3 + 1.15.1 @@ -144,7 +144,7 @@

Examples

data(pbmc_small)
 pbmc_small |> count(groups)
 #> tidySingleCellExperiment says: A data frame is returned for independent data analysis.
-#> # A tibble: 2 × 2
+#> # A tibble: 2 x 2
 #>   groups     n
 #>   <chr>  <int>
 #> 1 g1        44
diff --git a/reference/distinct.html b/reference/distinct.html
index 1ea083f..3ed81ad 100644
--- a/reference/distinct.html
+++ b/reference/distinct.html
@@ -18,7 +18,7 @@
       
       
         tidySingleCellExperiment
-        1.13.3
+        1.15.1
@@ -116,7 +116,7 @@

Examples

data(pbmc_small)
 pbmc_small |> distinct(groups)
 #> tidySingleCellExperiment says: A data frame is returned for independent data analysis.
-#> # A tibble: 2 × 1
+#> # A tibble: 2 x 1
 #>   groups
 #>   <chr> 
 #> 1 g2    
diff --git a/reference/drop_class.html b/reference/drop_class.html
index 9c300a9..722aff8 100644
--- a/reference/drop_class.html
+++ b/reference/drop_class.html
@@ -17,7 +17,7 @@
       
       
         tidySingleCellExperiment
-        1.13.3
+        1.15.1
diff --git a/reference/extract.html b/reference/extract.html index 7b23722..845a423 100644 --- a/reference/extract.html +++ b/reference/extract.html @@ -24,7 +24,7 @@ tidySingleCellExperiment - 1.13.3 + 1.15.1 @@ -141,22 +141,22 @@

Examples

into="g", regex="g([0-9])", convert=TRUE) -#> # A SingleCellExperiment-tibble abstraction: 80 × 17 +#> # A SingleCellExperiment-tibble abstraction: 80 x 17 #> # Features=230 | Cells=80 | Assays=counts, logcounts #> .cell orig.ident nCount_RNA nFeature_RNA RNA_snn_res.0.8 letter.idents g #> <chr> <fct> <dbl> <int> <fct> <fct> <int> -#> 1 ATGCC… SeuratPro… 70 47 0 A 2 -#> 2 CATGG… SeuratPro… 85 52 0 A 1 -#> 3 GAACC… SeuratPro… 87 50 1 B 2 -#> 4 TGACT… SeuratPro… 127 56 0 A 2 -#> 5 AGTCA… SeuratPro… 173 53 0 A 2 -#> 6 TCTGA… SeuratPro… 70 48 0 A 1 -#> 7 TGGTA… SeuratPro… 64 36 0 A 1 -#> 8 GCAGC… SeuratPro… 72 45 0 A 1 -#> 9 GATAT… SeuratPro… 52 36 0 A 1 -#> 10 AATGT… SeuratPro… 100 41 0 A 1 -#> # ℹ 70 more rows -#> # ℹ 10 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>, +#> 1 ATGCC~ SeuratPro~ 70 47 0 A 2 +#> 2 CATGG~ SeuratPro~ 85 52 0 A 1 +#> 3 GAACC~ SeuratPro~ 87 50 1 B 2 +#> 4 TGACT~ SeuratPro~ 127 56 0 A 2 +#> 5 AGTCA~ SeuratPro~ 173 53 0 A 2 +#> 6 TCTGA~ SeuratPro~ 70 48 0 A 1 +#> 7 TGGTA~ SeuratPro~ 64 36 0 A 1 +#> 8 GCAGC~ SeuratPro~ 72 45 0 A 1 +#> 9 GATAT~ SeuratPro~ 52 36 0 A 1 +#> 10 AATGT~ SeuratPro~ 100 41 0 A 1 +#> # i 70 more rows +#> # i 10 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>, #> # PC_1 <dbl>, PC_2 <dbl>, PC_3 <dbl>, PC_4 <dbl>, PC_5 <dbl>, tSNE_1 <dbl>, #> # tSNE_2 <dbl> diff --git a/reference/filter.html b/reference/filter.html index c6ac9bb..1b5c750 100644 --- a/reference/filter.html +++ b/reference/filter.html @@ -21,7 +21,7 @@ tidySingleCellExperiment - 1.13.3 + 1.15.1 @@ -171,22 +171,22 @@

See also

Examples

data(pbmc_small)
 pbmc_small |> filter(groups == "g1")
-#> # A SingleCellExperiment-tibble abstraction: 44 × 17
+#> # A SingleCellExperiment-tibble abstraction: 44 x 17
 #> # Features=230 | Cells=44 | Assays=counts, logcounts
 #>    .cell orig.ident nCount_RNA nFeature_RNA RNA_snn_res.0.8 letter.idents groups
 #>    <chr> <fct>           <dbl>        <int> <fct>           <fct>         <chr> 
-#>  1 CATG… SeuratPro…         85           52 0               A             g1    
-#>  2 TCTG… SeuratPro…         70           48 0               A             g1    
-#>  3 TGGT… SeuratPro…         64           36 0               A             g1    
-#>  4 GCAG… SeuratPro…         72           45 0               A             g1    
-#>  5 GATA… SeuratPro…         52           36 0               A             g1    
-#>  6 AATG… SeuratPro…        100           41 0               A             g1    
-#>  7 AGAG… SeuratPro…        191           61 0               A             g1    
-#>  8 CTAA… SeuratPro…        168           44 0               A             g1    
-#>  9 TTGG… SeuratPro…        135           45 0               A             g1    
-#> 10 CATC… SeuratPro…         79           43 0               A             g1    
-#> # ℹ 34 more rows
-#> # ℹ 10 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>,
+#>  1 CATG~ SeuratPro~         85           52 0               A             g1    
+#>  2 TCTG~ SeuratPro~         70           48 0               A             g1    
+#>  3 TGGT~ SeuratPro~         64           36 0               A             g1    
+#>  4 GCAG~ SeuratPro~         72           45 0               A             g1    
+#>  5 GATA~ SeuratPro~         52           36 0               A             g1    
+#>  6 AATG~ SeuratPro~        100           41 0               A             g1    
+#>  7 AGAG~ SeuratPro~        191           61 0               A             g1    
+#>  8 CTAA~ SeuratPro~        168           44 0               A             g1    
+#>  9 TTGG~ SeuratPro~        135           45 0               A             g1    
+#> 10 CATC~ SeuratPro~         79           43 0               A             g1    
+#> # i 34 more rows
+#> # i 10 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>,
 #> #   PC_1 <dbl>, PC_2 <dbl>, PC_3 <dbl>, PC_4 <dbl>, PC_5 <dbl>, tSNE_1 <dbl>,
 #> #   tSNE_2 <dbl>
 
diff --git a/reference/formatting.html b/reference/formatting.html
index 4c5bf77..4c8658e 100644
--- a/reference/formatting.html
+++ b/reference/formatting.html
@@ -36,7 +36,7 @@
       
       
         tidySingleCellExperiment
-        1.13.3
+        1.15.1
@@ -133,22 +133,22 @@

Value

Examples

data(pbmc_small)
 print(pbmc_small)
-#> # A SingleCellExperiment-tibble abstraction: 80 × 17
+#> # A SingleCellExperiment-tibble abstraction: 80 x 17
 #> # Features=230 | Cells=80 | Assays=counts, logcounts
 #>    .cell orig.ident nCount_RNA nFeature_RNA RNA_snn_res.0.8 letter.idents groups
 #>    <chr> <fct>           <dbl>        <int> <fct>           <fct>         <chr> 
-#>  1 ATGC… SeuratPro…         70           47 0               A             g2    
-#>  2 CATG… SeuratPro…         85           52 0               A             g1    
-#>  3 GAAC… SeuratPro…         87           50 1               B             g2    
-#>  4 TGAC… SeuratPro…        127           56 0               A             g2    
-#>  5 AGTC… SeuratPro…        173           53 0               A             g2    
-#>  6 TCTG… SeuratPro…         70           48 0               A             g1    
-#>  7 TGGT… SeuratPro…         64           36 0               A             g1    
-#>  8 GCAG… SeuratPro…         72           45 0               A             g1    
-#>  9 GATA… SeuratPro…         52           36 0               A             g1    
-#> 10 AATG… SeuratPro…        100           41 0               A             g1    
-#> # ℹ 70 more rows
-#> # ℹ 10 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>,
+#>  1 ATGC~ SeuratPro~         70           47 0               A             g2    
+#>  2 CATG~ SeuratPro~         85           52 0               A             g1    
+#>  3 GAAC~ SeuratPro~         87           50 1               B             g2    
+#>  4 TGAC~ SeuratPro~        127           56 0               A             g2    
+#>  5 AGTC~ SeuratPro~        173           53 0               A             g2    
+#>  6 TCTG~ SeuratPro~         70           48 0               A             g1    
+#>  7 TGGT~ SeuratPro~         64           36 0               A             g1    
+#>  8 GCAG~ SeuratPro~         72           45 0               A             g1    
+#>  9 GATA~ SeuratPro~         52           36 0               A             g1    
+#> 10 AATG~ SeuratPro~        100           41 0               A             g1    
+#> # i 70 more rows
+#> # i 10 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>,
 #> #   PC_1 <dbl>, PC_2 <dbl>, PC_3 <dbl>, PC_4 <dbl>, PC_5 <dbl>, tSNE_1 <dbl>,
 #> #   tSNE_2 <dbl>
 
diff --git a/reference/full_join.html b/reference/full_join.html
index e8854d4..a4398fa 100644
--- a/reference/full_join.html
+++ b/reference/full_join.html
@@ -43,7 +43,7 @@
       
       
         tidySingleCellExperiment
-        1.13.3
+        1.15.1
@@ -246,21 +246,21 @@

Examples

tt |> full_join(tibble::tibble(groups="g1", other=1:4)) #> Joining with `by = join_by(groups)` #> tidySingleCellExperiment says: This operation lead to duplicated cell names. A data frame is returned for independent data analysis. -#> # A tibble: 212 × 32 +#> # A tibble: 212 x 32 #> .cell orig.ident nCount_RNA nFeature_RNA RNA_snn_res.0.8 letter.idents groups #> <chr> <fct> <dbl> <int> <fct> <fct> <chr> -#> 1 ATGC… SeuratPro… 70 47 0 A g2 -#> 2 CATG… SeuratPro… 85 52 0 A g1 -#> 3 CATG… SeuratPro… 85 52 0 A g1 -#> 4 CATG… SeuratPro… 85 52 0 A g1 -#> 5 CATG… SeuratPro… 85 52 0 A g1 -#> 6 GAAC… SeuratPro… 87 50 1 B g2 -#> 7 TGAC… SeuratPro… 127 56 0 A g2 -#> 8 AGTC… SeuratPro… 173 53 0 A g2 -#> 9 TCTG… SeuratPro… 70 48 0 A g1 -#> 10 TCTG… SeuratPro… 70 48 0 A g1 -#> # ℹ 202 more rows -#> # ℹ 25 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>, +#> 1 ATGC~ SeuratPro~ 70 47 0 A g2 +#> 2 CATG~ SeuratPro~ 85 52 0 A g1 +#> 3 CATG~ SeuratPro~ 85 52 0 A g1 +#> 4 CATG~ SeuratPro~ 85 52 0 A g1 +#> 5 CATG~ SeuratPro~ 85 52 0 A g1 +#> 6 GAAC~ SeuratPro~ 87 50 1 B g2 +#> 7 TGAC~ SeuratPro~ 127 56 0 A g2 +#> 8 AGTC~ SeuratPro~ 173 53 0 A g2 +#> 9 TCTG~ SeuratPro~ 70 48 0 A g1 +#> 10 TCTG~ SeuratPro~ 70 48 0 A g1 +#> # i 202 more rows +#> # i 25 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>, #> # PC_1 <dbl>, PC_2 <dbl>, PC_3 <dbl>, PC_4 <dbl>, PC_5 <dbl>, PC_6 <dbl>, #> # PC_7 <dbl>, PC_8 <dbl>, PC_9 <dbl>, PC_10 <dbl>, PC_11 <dbl>, PC_12 <dbl>, #> # PC_13 <dbl>, PC_14 <dbl>, PC_15 <dbl>, PC_16 <dbl>, PC_17 <dbl>, diff --git a/reference/ggplot.html b/reference/ggplot.html index 11b7890..1a42558 100644 --- a/reference/ggplot.html +++ b/reference/ggplot.html @@ -20,7 +20,7 @@ tidySingleCellExperiment - 1.13.3 + 1.15.1 @@ -123,6 +123,10 @@

Details

values are passed into the function in the right order. In the examples below, however, they are left in place for clarity.

+
+

See also

+

The first steps chapter of the online ggplot2 book.

+

Examples

diff --git a/reference/glimpse.html b/reference/glimpse.html index 55e4074..fe6cda9 100644 --- a/reference/glimpse.html +++ b/reference/glimpse.html @@ -24,7 +24,7 @@ tidySingleCellExperiment - 1.13.3 + 1.15.1
diff --git a/reference/group_by.html b/reference/group_by.html index 496ad6a..220d1e9 100644 --- a/reference/group_by.html +++ b/reference/group_by.html @@ -19,7 +19,7 @@ tidySingleCellExperiment - 1.13.3 + 1.15.1 @@ -164,22 +164,22 @@

Examples

data(pbmc_small)
 pbmc_small |> group_by(groups)
 #> tidySingleCellExperiment says: A data frame is returned for independent data analysis.
-#> # A tibble: 80 × 31
+#> # A tibble: 80 x 31
 #> # Groups:   groups [2]
 #>    .cell orig.ident nCount_RNA nFeature_RNA RNA_snn_res.0.8 letter.idents groups
 #>    <chr> <fct>           <dbl>        <int> <fct>           <fct>         <chr> 
-#>  1 ATGC… SeuratPro…         70           47 0               A             g2    
-#>  2 CATG… SeuratPro…         85           52 0               A             g1    
-#>  3 GAAC… SeuratPro…         87           50 1               B             g2    
-#>  4 TGAC… SeuratPro…        127           56 0               A             g2    
-#>  5 AGTC… SeuratPro…        173           53 0               A             g2    
-#>  6 TCTG… SeuratPro…         70           48 0               A             g1    
-#>  7 TGGT… SeuratPro…         64           36 0               A             g1    
-#>  8 GCAG… SeuratPro…         72           45 0               A             g1    
-#>  9 GATA… SeuratPro…         52           36 0               A             g1    
-#> 10 AATG… SeuratPro…        100           41 0               A             g1    
-#> # ℹ 70 more rows
-#> # ℹ 24 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>,
+#>  1 ATGC~ SeuratPro~         70           47 0               A             g2    
+#>  2 CATG~ SeuratPro~         85           52 0               A             g1    
+#>  3 GAAC~ SeuratPro~         87           50 1               B             g2    
+#>  4 TGAC~ SeuratPro~        127           56 0               A             g2    
+#>  5 AGTC~ SeuratPro~        173           53 0               A             g2    
+#>  6 TCTG~ SeuratPro~         70           48 0               A             g1    
+#>  7 TGGT~ SeuratPro~         64           36 0               A             g1    
+#>  8 GCAG~ SeuratPro~         72           45 0               A             g1    
+#>  9 GATA~ SeuratPro~         52           36 0               A             g1    
+#> 10 AATG~ SeuratPro~        100           41 0               A             g1    
+#> # i 70 more rows
+#> # i 24 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>,
 #> #   PC_1 <dbl>, PC_2 <dbl>, PC_3 <dbl>, PC_4 <dbl>, PC_5 <dbl>, PC_6 <dbl>,
 #> #   PC_7 <dbl>, PC_8 <dbl>, PC_9 <dbl>, PC_10 <dbl>, PC_11 <dbl>, PC_12 <dbl>,
 #> #   PC_13 <dbl>, PC_14 <dbl>, PC_15 <dbl>, PC_16 <dbl>, PC_17 <dbl>,
diff --git a/reference/group_split.html b/reference/group_split.html
index c53ec35..415b76e 100644
--- a/reference/group_split.html
+++ b/reference/group_split.html
@@ -29,7 +29,7 @@
       
       
         tidySingleCellExperiment
-        1.13.3
+        1.15.1
@@ -135,42 +135,42 @@

Examples

data(pbmc_small)
 pbmc_small |> group_split(groups)
 #> [[1]]
-#> # A SingleCellExperiment-tibble abstraction: 44 × 17
+#> # A SingleCellExperiment-tibble abstraction: 44 x 17
 #> # Features=230 | Cells=44 | Assays=counts, logcounts
 #>    .cell orig.ident nCount_RNA nFeature_RNA RNA_snn_res.0.8 letter.idents groups
 #>    <chr> <fct>           <dbl>        <int> <fct>           <fct>         <chr> 
-#>  1 CATG… SeuratPro…         85           52 0               A             g1    
-#>  2 TCTG… SeuratPro…         70           48 0               A             g1    
-#>  3 TGGT… SeuratPro…         64           36 0               A             g1    
-#>  4 GCAG… SeuratPro…         72           45 0               A             g1    
-#>  5 GATA… SeuratPro…         52           36 0               A             g1    
-#>  6 AATG… SeuratPro…        100           41 0               A             g1    
-#>  7 AGAG… SeuratPro…        191           61 0               A             g1    
-#>  8 CTAA… SeuratPro…        168           44 0               A             g1    
-#>  9 TTGG… SeuratPro…        135           45 0               A             g1    
-#> 10 CATC… SeuratPro…         79           43 0               A             g1    
-#> # ℹ 34 more rows
-#> # ℹ 10 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>,
+#>  1 CATG~ SeuratPro~         85           52 0               A             g1    
+#>  2 TCTG~ SeuratPro~         70           48 0               A             g1    
+#>  3 TGGT~ SeuratPro~         64           36 0               A             g1    
+#>  4 GCAG~ SeuratPro~         72           45 0               A             g1    
+#>  5 GATA~ SeuratPro~         52           36 0               A             g1    
+#>  6 AATG~ SeuratPro~        100           41 0               A             g1    
+#>  7 AGAG~ SeuratPro~        191           61 0               A             g1    
+#>  8 CTAA~ SeuratPro~        168           44 0               A             g1    
+#>  9 TTGG~ SeuratPro~        135           45 0               A             g1    
+#> 10 CATC~ SeuratPro~         79           43 0               A             g1    
+#> # i 34 more rows
+#> # i 10 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>,
 #> #   PC_1 <dbl>, PC_2 <dbl>, PC_3 <dbl>, PC_4 <dbl>, PC_5 <dbl>, tSNE_1 <dbl>,
 #> #   tSNE_2 <dbl>
 #> 
 #> [[2]]
-#> # A SingleCellExperiment-tibble abstraction: 36 × 17
+#> # A SingleCellExperiment-tibble abstraction: 36 x 17
 #> # Features=230 | Cells=36 | Assays=counts, logcounts
 #>    .cell orig.ident nCount_RNA nFeature_RNA RNA_snn_res.0.8 letter.idents groups
 #>    <chr> <fct>           <dbl>        <int> <fct>           <fct>         <chr> 
-#>  1 ATGC… SeuratPro…         70           47 0               A             g2    
-#>  2 GAAC… SeuratPro…         87           50 1               B             g2    
-#>  3 TGAC… SeuratPro…        127           56 0               A             g2    
-#>  4 AGTC… SeuratPro…        173           53 0               A             g2    
-#>  5 AGGT… SeuratPro…         62           31 0               A             g2    
-#>  6 GGGT… SeuratPro…        101           41 0               A             g2    
-#>  7 CATG… SeuratPro…         51           26 0               A             g2    
-#>  8 TACG… SeuratPro…         99           45 0               A             g2    
-#>  9 GTAA… SeuratPro…         67           33 0               A             g2    
-#> 10 TACA… SeuratPro…        109           41 0               A             g2    
-#> # ℹ 26 more rows
-#> # ℹ 10 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>,
+#>  1 ATGC~ SeuratPro~         70           47 0               A             g2    
+#>  2 GAAC~ SeuratPro~         87           50 1               B             g2    
+#>  3 TGAC~ SeuratPro~        127           56 0               A             g2    
+#>  4 AGTC~ SeuratPro~        173           53 0               A             g2    
+#>  5 AGGT~ SeuratPro~         62           31 0               A             g2    
+#>  6 GGGT~ SeuratPro~        101           41 0               A             g2    
+#>  7 CATG~ SeuratPro~         51           26 0               A             g2    
+#>  8 TACG~ SeuratPro~         99           45 0               A             g2    
+#>  9 GTAA~ SeuratPro~         67           33 0               A             g2    
+#> 10 TACA~ SeuratPro~        109           41 0               A             g2    
+#> # i 26 more rows
+#> # i 10 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>,
 #> #   PC_1 <dbl>, PC_2 <dbl>, PC_3 <dbl>, PC_4 <dbl>, PC_5 <dbl>, tSNE_1 <dbl>,
 #> #   tSNE_2 <dbl>
 #> 
diff --git a/reference/index.html b/reference/index.html
index 6c7822e..2667f1d 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -17,7 +17,7 @@
       
       
         tidySingleCellExperiment
-        1.13.3
+        1.15.1
diff --git a/reference/inner_join.html b/reference/inner_join.html index fa5bbc6..67bb3a8 100644 --- a/reference/inner_join.html +++ b/reference/inner_join.html @@ -43,7 +43,7 @@ tidySingleCellExperiment - 1.13.3 + 1.15.1 @@ -249,22 +249,22 @@

Examples

slice(1)) #> tidySingleCellExperiment says: A data frame is returned for independent data analysis. #> Joining with `by = join_by(groups)` -#> # A SingleCellExperiment-tibble abstraction: 36 × 18 +#> # A SingleCellExperiment-tibble abstraction: 36 x 18 #> # Features=230 | Cells=36 | Assays=counts, logcounts #> .cell orig.ident nCount_RNA nFeature_RNA RNA_snn_res.0.8 letter.idents groups #> <chr> <fct> <dbl> <int> <fct> <fct> <chr> -#> 1 ATGC… SeuratPro… 70 47 0 A g2 -#> 2 GAAC… SeuratPro… 87 50 1 B g2 -#> 3 TGAC… SeuratPro… 127 56 0 A g2 -#> 4 AGTC… SeuratPro… 173 53 0 A g2 -#> 5 AGGT… SeuratPro… 62 31 0 A g2 -#> 6 GGGT… SeuratPro… 101 41 0 A g2 -#> 7 CATG… SeuratPro… 51 26 0 A g2 -#> 8 TACG… SeuratPro… 99 45 0 A g2 -#> 9 GTAA… SeuratPro… 67 33 0 A g2 -#> 10 TACA… SeuratPro… 109 41 0 A g2 -#> # ℹ 26 more rows -#> # ℹ 11 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>, +#> 1 ATGC~ SeuratPro~ 70 47 0 A g2 +#> 2 GAAC~ SeuratPro~ 87 50 1 B g2 +#> 3 TGAC~ SeuratPro~ 127 56 0 A g2 +#> 4 AGTC~ SeuratPro~ 173 53 0 A g2 +#> 5 AGGT~ SeuratPro~ 62 31 0 A g2 +#> 6 GGGT~ SeuratPro~ 101 41 0 A g2 +#> 7 CATG~ SeuratPro~ 51 26 0 A g2 +#> 8 TACG~ SeuratPro~ 99 45 0 A g2 +#> 9 GTAA~ SeuratPro~ 67 33 0 A g2 +#> 10 TACA~ SeuratPro~ 109 41 0 A g2 +#> # i 26 more rows +#> # i 11 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>, #> # new_column <int>, PC_1 <dbl>, PC_2 <dbl>, PC_3 <dbl>, PC_4 <dbl>, #> # PC_5 <dbl>, tSNE_1 <dbl>, tSNE_2 <dbl> diff --git a/reference/join_features.html b/reference/join_features.html index 4ed309a..db21653 100644 --- a/reference/join_features.html +++ b/reference/join_features.html @@ -18,7 +18,7 @@ tidySingleCellExperiment - 1.13.3 + 1.15.1 @@ -118,21 +118,21 @@

Examples

pbmc_small %>% join_features( features=c("HLA-DRA", "LYZ")) #> tidySingleCellExperiment says: join_features produces duplicate cell names to accomadate the long data format. For this reason, a data frame is returned for independent data analysis. Assay feature abundance is appended as .abundance_counts and .abundance_logcounts. -#> # A tibble: 160 × 34 +#> # A tibble: 160 x 34 #> .cell .feature .abundance_counts .abundance_logcounts orig.ident nCount_RNA #> <chr> <chr> <dbl> <dbl> <fct> <dbl> -#> 1 ATGCCA… HLA-DRA 0 0 SeuratPro… 70 -#> 2 ATGCCA… LYZ 1 4.97 SeuratPro… 70 -#> 3 CATGGC… HLA-DRA 1 4.78 SeuratPro… 85 -#> 4 CATGGC… LYZ 1 4.78 SeuratPro… 85 -#> 5 GAACCT… HLA-DRA 0 0 SeuratPro… 87 -#> 6 GAACCT… LYZ 1 4.75 SeuratPro… 87 -#> 7 TGACTG… HLA-DRA 0 0 SeuratPro… 127 -#> 8 TGACTG… LYZ 0 0 SeuratPro… 127 -#> 9 AGTCAG… HLA-DRA 1 4.07 SeuratPro… 173 -#> 10 AGTCAG… LYZ 0 0 SeuratPro… 173 -#> # ℹ 150 more rows -#> # ℹ 28 more variables: nFeature_RNA <int>, RNA_snn_res.0.8 <fct>, +#> 1 ATGCCA~ HLA-DRA 0 0 SeuratPro~ 70 +#> 2 ATGCCA~ LYZ 1 4.97 SeuratPro~ 70 +#> 3 CATGGC~ HLA-DRA 1 4.78 SeuratPro~ 85 +#> 4 CATGGC~ LYZ 1 4.78 SeuratPro~ 85 +#> 5 GAACCT~ HLA-DRA 0 0 SeuratPro~ 87 +#> 6 GAACCT~ LYZ 1 4.75 SeuratPro~ 87 +#> 7 TGACTG~ HLA-DRA 0 0 SeuratPro~ 127 +#> 8 TGACTG~ LYZ 0 0 SeuratPro~ 127 +#> 9 AGTCAG~ HLA-DRA 1 4.07 SeuratPro~ 173 +#> 10 AGTCAG~ LYZ 0 0 SeuratPro~ 173 +#> # i 150 more rows +#> # i 28 more variables: nFeature_RNA <int>, RNA_snn_res.0.8 <fct>, #> # letter.idents <fct>, groups <chr>, RNA_snn_res.1 <fct>, file <chr>, #> # ident <fct>, PC_1 <dbl>, PC_2 <dbl>, PC_3 <dbl>, PC_4 <dbl>, PC_5 <dbl>, #> # PC_6 <dbl>, PC_7 <dbl>, PC_8 <dbl>, PC_9 <dbl>, PC_10 <dbl>, PC_11 <dbl>, diff --git a/reference/join_transcripts.html b/reference/join_transcripts.html index e554e4e..1811014 100644 --- a/reference/join_transcripts.html +++ b/reference/join_transcripts.html @@ -17,7 +17,7 @@ tidySingleCellExperiment - 1.13.3 + 1.15.1 diff --git a/reference/left_join.html b/reference/left_join.html index ae620e3..06099c9 100644 --- a/reference/left_join.html +++ b/reference/left_join.html @@ -43,7 +43,7 @@ tidySingleCellExperiment - 1.13.3 + 1.15.1 @@ -248,22 +248,22 @@

Examples

mutate(new_column=1:2)) #> tidySingleCellExperiment says: A data frame is returned for independent data analysis. #> Joining with `by = join_by(groups)` -#> # A SingleCellExperiment-tibble abstraction: 80 × 18 +#> # A SingleCellExperiment-tibble abstraction: 80 x 18 #> # Features=230 | Cells=80 | Assays=counts, logcounts #> .cell orig.ident nCount_RNA nFeature_RNA RNA_snn_res.0.8 letter.idents groups #> <chr> <fct> <dbl> <int> <fct> <fct> <chr> -#> 1 ATGC… SeuratPro… 70 47 0 A g2 -#> 2 CATG… SeuratPro… 85 52 0 A g1 -#> 3 GAAC… SeuratPro… 87 50 1 B g2 -#> 4 TGAC… SeuratPro… 127 56 0 A g2 -#> 5 AGTC… SeuratPro… 173 53 0 A g2 -#> 6 TCTG… SeuratPro… 70 48 0 A g1 -#> 7 TGGT… SeuratPro… 64 36 0 A g1 -#> 8 GCAG… SeuratPro… 72 45 0 A g1 -#> 9 GATA… SeuratPro… 52 36 0 A g1 -#> 10 AATG… SeuratPro… 100 41 0 A g1 -#> # ℹ 70 more rows -#> # ℹ 11 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>, +#> 1 ATGC~ SeuratPro~ 70 47 0 A g2 +#> 2 CATG~ SeuratPro~ 85 52 0 A g1 +#> 3 GAAC~ SeuratPro~ 87 50 1 B g2 +#> 4 TGAC~ SeuratPro~ 127 56 0 A g2 +#> 5 AGTC~ SeuratPro~ 173 53 0 A g2 +#> 6 TCTG~ SeuratPro~ 70 48 0 A g1 +#> 7 TGGT~ SeuratPro~ 64 36 0 A g1 +#> 8 GCAG~ SeuratPro~ 72 45 0 A g1 +#> 9 GATA~ SeuratPro~ 52 36 0 A g1 +#> 10 AATG~ SeuratPro~ 100 41 0 A g1 +#> # i 70 more rows +#> # i 11 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>, #> # new_column <int>, PC_1 <dbl>, PC_2 <dbl>, PC_3 <dbl>, PC_4 <dbl>, #> # PC_5 <dbl>, tSNE_1 <dbl>, tSNE_2 <dbl> @@ -275,22 +275,22 @@

Examples

#> tidySingleCellExperiment says: A data frame is returned for independent data analysis. tt |> left_join(DF) #> Joining with `by = join_by(groups)` -#> # A SingleCellExperiment-tibble abstraction: 80 × 18 +#> # A SingleCellExperiment-tibble abstraction: 80 x 18 #> # Features=230 | Cells=80 | Assays=counts, logcounts #> .cell orig.ident nCount_RNA nFeature_RNA RNA_snn_res.0.8 letter.idents groups #> <chr> <fct> <dbl> <int> <fct> <fct> <chr> -#> 1 ATGC… SeuratPro… 70 47 0 A g2 -#> 2 CATG… SeuratPro… 85 52 0 A g1 -#> 3 GAAC… SeuratPro… 87 50 1 B g2 -#> 4 TGAC… SeuratPro… 127 56 0 A g2 -#> 5 AGTC… SeuratPro… 173 53 0 A g2 -#> 6 TCTG… SeuratPro… 70 48 0 A g1 -#> 7 TGGT… SeuratPro… 64 36 0 A g1 -#> 8 GCAG… SeuratPro… 72 45 0 A g1 -#> 9 GATA… SeuratPro… 52 36 0 A g1 -#> 10 AATG… SeuratPro… 100 41 0 A g1 -#> # ℹ 70 more rows -#> # ℹ 11 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>, +#> 1 ATGC~ SeuratPro~ 70 47 0 A g2 +#> 2 CATG~ SeuratPro~ 85 52 0 A g1 +#> 3 GAAC~ SeuratPro~ 87 50 1 B g2 +#> 4 TGAC~ SeuratPro~ 127 56 0 A g2 +#> 5 AGTC~ SeuratPro~ 173 53 0 A g2 +#> 6 TCTG~ SeuratPro~ 70 48 0 A g1 +#> 7 TGGT~ SeuratPro~ 64 36 0 A g1 +#> 8 GCAG~ SeuratPro~ 72 45 0 A g1 +#> 9 GATA~ SeuratPro~ 52 36 0 A g1 +#> 10 AATG~ SeuratPro~ 100 41 0 A g1 +#> # i 70 more rows +#> # i 11 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>, #> # new_column <int>, PC_1 <dbl>, PC_2 <dbl>, PC_3 <dbl>, PC_4 <dbl>, #> # PC_5 <dbl>, tSNE_1 <dbl>, tSNE_2 <dbl> diff --git a/reference/mutate.html b/reference/mutate.html index c824fc3..99de8a9 100644 --- a/reference/mutate.html +++ b/reference/mutate.html @@ -19,7 +19,7 @@ tidySingleCellExperiment - 1.13.3 + 1.15.1 @@ -161,22 +161,22 @@

See also

Examples

data(pbmc_small)
 pbmc_small |> mutate(nFeature_RNA=1)
-#> # A SingleCellExperiment-tibble abstraction: 80 × 17
+#> # A SingleCellExperiment-tibble abstraction: 80 x 17
 #> # Features=230 | Cells=80 | Assays=counts, logcounts
 #>    .cell orig.ident nCount_RNA nFeature_RNA RNA_snn_res.0.8 letter.idents groups
 #>    <chr> <fct>           <dbl>        <dbl> <fct>           <fct>         <chr> 
-#>  1 ATGC… SeuratPro…         70            1 0               A             g2    
-#>  2 CATG… SeuratPro…         85            1 0               A             g1    
-#>  3 GAAC… SeuratPro…         87            1 1               B             g2    
-#>  4 TGAC… SeuratPro…        127            1 0               A             g2    
-#>  5 AGTC… SeuratPro…        173            1 0               A             g2    
-#>  6 TCTG… SeuratPro…         70            1 0               A             g1    
-#>  7 TGGT… SeuratPro…         64            1 0               A             g1    
-#>  8 GCAG… SeuratPro…         72            1 0               A             g1    
-#>  9 GATA… SeuratPro…         52            1 0               A             g1    
-#> 10 AATG… SeuratPro…        100            1 0               A             g1    
-#> # ℹ 70 more rows
-#> # ℹ 10 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>,
+#>  1 ATGC~ SeuratPro~         70            1 0               A             g2    
+#>  2 CATG~ SeuratPro~         85            1 0               A             g1    
+#>  3 GAAC~ SeuratPro~         87            1 1               B             g2    
+#>  4 TGAC~ SeuratPro~        127            1 0               A             g2    
+#>  5 AGTC~ SeuratPro~        173            1 0               A             g2    
+#>  6 TCTG~ SeuratPro~         70            1 0               A             g1    
+#>  7 TGGT~ SeuratPro~         64            1 0               A             g1    
+#>  8 GCAG~ SeuratPro~         72            1 0               A             g1    
+#>  9 GATA~ SeuratPro~         52            1 0               A             g1    
+#> 10 AATG~ SeuratPro~        100            1 0               A             g1    
+#> # i 70 more rows
+#> # i 10 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>,
 #> #   PC_1 <dbl>, PC_2 <dbl>, PC_3 <dbl>, PC_4 <dbl>, PC_5 <dbl>, tSNE_1 <dbl>,
 #> #   tSNE_2 <dbl>
 
diff --git a/reference/nest.html b/reference/nest.html
index b6d6570..a134d40 100644
--- a/reference/nest.html
+++ b/reference/nest.html
@@ -22,7 +22,7 @@
       
       
         tidySingleCellExperiment
-        1.13.3
+        1.15.1
@@ -149,22 +149,22 @@

Examples

pbmc_small |> nest(data=-groups) |> unnest(data) -#> # A SingleCellExperiment-tibble abstraction: 80 × 17 +#> # A SingleCellExperiment-tibble abstraction: 80 x 17 #> # Features=230 | Cells=80 | Assays=counts, logcounts #> .cell orig.ident nCount_RNA nFeature_RNA RNA_snn_res.0.8 letter.idents #> <chr> <fct> <dbl> <int> <fct> <fct> -#> 1 ATGCCAGAACG… SeuratPro… 70 47 0 A -#> 2 GAACCTGATGA… SeuratPro… 87 50 1 B -#> 3 TGACTGGATTC… SeuratPro… 127 56 0 A -#> 4 AGTCAGACTGC… SeuratPro… 173 53 0 A -#> 5 AGGTCATGAGT… SeuratPro… 62 31 0 A -#> 6 GGGTAACTCTA… SeuratPro… 101 41 0 A -#> 7 CATGAGACACG… SeuratPro… 51 26 0 A -#> 8 TACGCCACTCC… SeuratPro… 99 45 0 A -#> 9 GTAAGCACTCA… SeuratPro… 67 33 0 A -#> 10 TACATCACGCT… SeuratPro… 109 41 0 A -#> # ℹ 70 more rows -#> # ℹ 11 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>, +#> 1 ATGCCAGAACG~ SeuratPro~ 70 47 0 A +#> 2 GAACCTGATGA~ SeuratPro~ 87 50 1 B +#> 3 TGACTGGATTC~ SeuratPro~ 127 56 0 A +#> 4 AGTCAGACTGC~ SeuratPro~ 173 53 0 A +#> 5 AGGTCATGAGT~ SeuratPro~ 62 31 0 A +#> 6 GGGTAACTCTA~ SeuratPro~ 101 41 0 A +#> 7 CATGAGACACG~ SeuratPro~ 51 26 0 A +#> 8 TACGCCACTCC~ SeuratPro~ 99 45 0 A +#> 9 GTAAGCACTCA~ SeuratPro~ 67 33 0 A +#> 10 TACATCACGCT~ SeuratPro~ 109 41 0 A +#> # i 70 more rows +#> # i 11 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>, #> # groups <chr>, PC_1 <dbl>, PC_2 <dbl>, PC_3 <dbl>, PC_4 <dbl>, PC_5 <dbl>, #> # tSNE_1 <dbl>, tSNE_2 <dbl> diff --git a/reference/pbmc_small.html b/reference/pbmc_small.html index 240d3e7..2eb10d7 100644 --- a/reference/pbmc_small.html +++ b/reference/pbmc_small.html @@ -17,7 +17,7 @@ tidySingleCellExperiment - 1.13.3 + 1.15.1 diff --git a/reference/pbmc_small_nested_interactions.html b/reference/pbmc_small_nested_interactions.html index 376e4b1..eeec29b 100644 --- a/reference/pbmc_small_nested_interactions.html +++ b/reference/pbmc_small_nested_interactions.html @@ -19,7 +19,7 @@ tidySingleCellExperiment - 1.13.3 + 1.15.1 diff --git a/reference/pipe.html b/reference/pipe.html index 27db3f2..6efdacd 100644 --- a/reference/pipe.html +++ b/reference/pipe.html @@ -17,7 +17,7 @@ tidySingleCellExperiment - 1.13.3 + 1.15.1 diff --git a/reference/pivot_longer.html b/reference/pivot_longer.html index b6fb9b9..38cb70b 100644 --- a/reference/pivot_longer.html +++ b/reference/pivot_longer.html @@ -20,7 +20,7 @@ tidySingleCellExperiment - 1.13.3 + 1.15.1 @@ -214,21 +214,21 @@

Examples

cols=c(orig.ident, groups), names_to="name", values_to="value") #> tidySingleCellExperiment says: A data frame is returned for independent data analysis. -#> # A tibble: 160 × 31 +#> # A tibble: 160 x 31 #> .cell nCount_RNA nFeature_RNA RNA_snn_res.0.8 letter.idents RNA_snn_res.1 #> <chr> <dbl> <int> <fct> <fct> <fct> -#> 1 ATGCCAGA… 70 47 0 A 0 -#> 2 ATGCCAGA… 70 47 0 A 0 -#> 3 CATGGCCT… 85 52 0 A 0 -#> 4 CATGGCCT… 85 52 0 A 0 -#> 5 GAACCTGA… 87 50 1 B 0 -#> 6 GAACCTGA… 87 50 1 B 0 -#> 7 TGACTGGA… 127 56 0 A 0 -#> 8 TGACTGGA… 127 56 0 A 0 -#> 9 AGTCAGAC… 173 53 0 A 0 -#> 10 AGTCAGAC… 173 53 0 A 0 -#> # ℹ 150 more rows -#> # ℹ 25 more variables: file <chr>, ident <fct>, PC_1 <dbl>, PC_2 <dbl>, +#> 1 ATGCCAGA~ 70 47 0 A 0 +#> 2 ATGCCAGA~ 70 47 0 A 0 +#> 3 CATGGCCT~ 85 52 0 A 0 +#> 4 CATGGCCT~ 85 52 0 A 0 +#> 5 GAACCTGA~ 87 50 1 B 0 +#> 6 GAACCTGA~ 87 50 1 B 0 +#> 7 TGACTGGA~ 127 56 0 A 0 +#> 8 TGACTGGA~ 127 56 0 A 0 +#> 9 AGTCAGAC~ 173 53 0 A 0 +#> 10 AGTCAGAC~ 173 53 0 A 0 +#> # i 150 more rows +#> # i 25 more variables: file <chr>, ident <fct>, PC_1 <dbl>, PC_2 <dbl>, #> # PC_3 <dbl>, PC_4 <dbl>, PC_5 <dbl>, PC_6 <dbl>, PC_7 <dbl>, PC_8 <dbl>, #> # PC_9 <dbl>, PC_10 <dbl>, PC_11 <dbl>, PC_12 <dbl>, PC_13 <dbl>, #> # PC_14 <dbl>, PC_15 <dbl>, PC_16 <dbl>, PC_17 <dbl>, PC_18 <dbl>, diff --git a/reference/plot_ly.html b/reference/plot_ly.html index 284314d..d09c102 100644 --- a/reference/plot_ly.html +++ b/reference/plot_ly.html @@ -22,7 +22,7 @@ tidySingleCellExperiment - 1.13.3 + 1.15.1 @@ -274,7 +274,7 @@

Examples

pbmc_small |> plot_ly(x = ~ nCount_RNA, y = ~ nFeature_RNA)
- + diff --git a/reference/pull.html b/reference/pull.html index 2b86226..59725d5 100644 --- a/reference/pull.html +++ b/reference/pull.html @@ -19,7 +19,7 @@ tidySingleCellExperiment - 1.13.3 + 1.15.1 diff --git a/reference/quo_names.html b/reference/quo_names.html index 3e2cb91..1e981de 100644 --- a/reference/quo_names.html +++ b/reference/quo_names.html @@ -17,7 +17,7 @@ tidySingleCellExperiment - 1.13.3 + 1.15.1 diff --git a/reference/rename.html b/reference/rename.html index 944cec4..808e070 100644 --- a/reference/rename.html +++ b/reference/rename.html @@ -19,7 +19,7 @@ tidySingleCellExperiment - 1.13.3 + 1.15.1 @@ -101,7 +101,7 @@

Methods

implementations (methods) for other classes. See the documentation of individual methods for extra arguments and differences in behaviour.

The following methods are currently available in loaded packages: - (vector, Vector), dbplyr (tbl_lazy), dplyr (data.frame), plotly (plotly), tidySingleCellExperiment (SingleCellExperiment) + (Vector, vector), dbplyr (tbl_lazy), dplyr (data.frame), plotly (plotly), tidySingleCellExperiment (SingleCellExperiment) .

@@ -117,22 +117,22 @@

See also

Examples

data(pbmc_small)
 pbmc_small |> rename(s_score=nFeature_RNA)
-#> # A SingleCellExperiment-tibble abstraction: 80 × 17
+#> # A SingleCellExperiment-tibble abstraction: 80 x 17
 #> # Features=230 | Cells=80 | Assays=counts, logcounts
 #>    .cell      orig.ident nCount_RNA s_score RNA_snn_res.0.8 letter.idents groups
 #>    <chr>      <fct>           <dbl>   <int> <fct>           <fct>         <chr> 
-#>  1 ATGCCAGAA… SeuratPro…         70      47 0               A             g2    
-#>  2 CATGGCCTG… SeuratPro…         85      52 0               A             g1    
-#>  3 GAACCTGAT… SeuratPro…         87      50 1               B             g2    
-#>  4 TGACTGGAT… SeuratPro…        127      56 0               A             g2    
-#>  5 AGTCAGACT… SeuratPro…        173      53 0               A             g2    
-#>  6 TCTGATACA… SeuratPro…         70      48 0               A             g1    
-#>  7 TGGTATCTA… SeuratPro…         64      36 0               A             g1    
-#>  8 GCAGCTCTG… SeuratPro…         72      45 0               A             g1    
-#>  9 GATATAACA… SeuratPro…         52      36 0               A             g1    
-#> 10 AATGTTGAC… SeuratPro…        100      41 0               A             g1    
-#> # ℹ 70 more rows
-#> # ℹ 10 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>,
+#>  1 ATGCCAGAA~ SeuratPro~         70      47 0               A             g2    
+#>  2 CATGGCCTG~ SeuratPro~         85      52 0               A             g1    
+#>  3 GAACCTGAT~ SeuratPro~         87      50 1               B             g2    
+#>  4 TGACTGGAT~ SeuratPro~        127      56 0               A             g2    
+#>  5 AGTCAGACT~ SeuratPro~        173      53 0               A             g2    
+#>  6 TCTGATACA~ SeuratPro~         70      48 0               A             g1    
+#>  7 TGGTATCTA~ SeuratPro~         64      36 0               A             g1    
+#>  8 GCAGCTCTG~ SeuratPro~         72      45 0               A             g1    
+#>  9 GATATAACA~ SeuratPro~         52      36 0               A             g1    
+#> 10 AATGTTGAC~ SeuratPro~        100      41 0               A             g1    
+#> # i 70 more rows
+#> # i 10 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>,
 #> #   PC_1 <dbl>, PC_2 <dbl>, PC_3 <dbl>, PC_4 <dbl>, PC_5 <dbl>, tSNE_1 <dbl>,
 #> #   tSNE_2 <dbl>
 
diff --git a/reference/return_arguments_of.html b/reference/return_arguments_of.html
index 60126d7..40ccba0 100644
--- a/reference/return_arguments_of.html
+++ b/reference/return_arguments_of.html
@@ -17,7 +17,7 @@
       
       
         tidySingleCellExperiment
-        1.13.3
+        1.15.1
diff --git a/reference/right_join.html b/reference/right_join.html index da9f7c0..6d48e89 100644 --- a/reference/right_join.html +++ b/reference/right_join.html @@ -43,7 +43,7 @@ tidySingleCellExperiment - 1.13.3 + 1.15.1
@@ -249,22 +249,22 @@

Examples

slice(1)) #> tidySingleCellExperiment says: A data frame is returned for independent data analysis. #> Joining with `by = join_by(groups)` -#> # A SingleCellExperiment-tibble abstraction: 36 × 18 +#> # A SingleCellExperiment-tibble abstraction: 36 x 18 #> # Features=230 | Cells=36 | Assays=counts, logcounts #> .cell orig.ident nCount_RNA nFeature_RNA RNA_snn_res.0.8 letter.idents groups #> <chr> <fct> <dbl> <int> <fct> <fct> <chr> -#> 1 ATGC… SeuratPro… 70 47 0 A g2 -#> 2 GAAC… SeuratPro… 87 50 1 B g2 -#> 3 TGAC… SeuratPro… 127 56 0 A g2 -#> 4 AGTC… SeuratPro… 173 53 0 A g2 -#> 5 AGGT… SeuratPro… 62 31 0 A g2 -#> 6 GGGT… SeuratPro… 101 41 0 A g2 -#> 7 CATG… SeuratPro… 51 26 0 A g2 -#> 8 TACG… SeuratPro… 99 45 0 A g2 -#> 9 GTAA… SeuratPro… 67 33 0 A g2 -#> 10 TACA… SeuratPro… 109 41 0 A g2 -#> # ℹ 26 more rows -#> # ℹ 11 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>, +#> 1 ATGC~ SeuratPro~ 70 47 0 A g2 +#> 2 GAAC~ SeuratPro~ 87 50 1 B g2 +#> 3 TGAC~ SeuratPro~ 127 56 0 A g2 +#> 4 AGTC~ SeuratPro~ 173 53 0 A g2 +#> 5 AGGT~ SeuratPro~ 62 31 0 A g2 +#> 6 GGGT~ SeuratPro~ 101 41 0 A g2 +#> 7 CATG~ SeuratPro~ 51 26 0 A g2 +#> 8 TACG~ SeuratPro~ 99 45 0 A g2 +#> 9 GTAA~ SeuratPro~ 67 33 0 A g2 +#> 10 TACA~ SeuratPro~ 109 41 0 A g2 +#> # i 26 more rows +#> # i 11 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>, #> # new_column <int>, PC_1 <dbl>, PC_2 <dbl>, PC_3 <dbl>, PC_4 <dbl>, #> # PC_5 <dbl>, tSNE_1 <dbl>, tSNE_2 <dbl> diff --git a/reference/rowwise.html b/reference/rowwise.html index 9e5467a..b864e0e 100644 --- a/reference/rowwise.html +++ b/reference/rowwise.html @@ -21,7 +21,7 @@ tidySingleCellExperiment - 1.13.3 + 1.15.1 diff --git a/reference/sample_n.html b/reference/sample_n.html index dfa3963..9bf3274 100644 --- a/reference/sample_n.html +++ b/reference/sample_n.html @@ -34,7 +34,7 @@ tidySingleCellExperiment - 1.13.3 + 1.15.1 @@ -140,38 +140,38 @@

Value

Examples

data(pbmc_small)
 pbmc_small |> sample_n(50)
-#> # A SingleCellExperiment-tibble abstraction: 50 × 17
+#> # A SingleCellExperiment-tibble abstraction: 50 x 17
 #> # Features=230 | Cells=50 | Assays=counts, logcounts
 #>    .cell orig.ident nCount_RNA nFeature_RNA RNA_snn_res.0.8 letter.idents groups
 #>    <chr> <fct>           <dbl>        <int> <fct>           <fct>         <chr> 
-#>  1 CTGC… SeuratPro…        146           47 0               A             g1    
-#>  2 GCGC… SeuratPro…        213           48 1               B             g2    
-#>  3 GAGT… SeuratPro…        527           47 0               A             g1    
-#>  4 CATA… SeuratPro…        286           68 0               A             g1    
-#>  5 AAGC… SeuratPro…        126           48 0               A             g1    
-#>  6 CTAA… SeuratPro…        246           59 0               A             g1    
-#>  7 GATA… SeuratPro…        328           72 1               B             g1    
-#>  8 ATCA… SeuratPro…        168           37 0               A             g2    
-#>  9 AATG… SeuratPro…        389           73 1               B             g1    
-#> 10 AGTC… SeuratPro…        173           53 0               A             g2    
-#> # ℹ 40 more rows
-#> # ℹ 10 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>,
+#>  1 CTGC~ SeuratPro~        146           47 0               A             g1    
+#>  2 GCGC~ SeuratPro~        213           48 1               B             g2    
+#>  3 GAGT~ SeuratPro~        527           47 0               A             g1    
+#>  4 CATA~ SeuratPro~        286           68 0               A             g1    
+#>  5 AAGC~ SeuratPro~        126           48 0               A             g1    
+#>  6 CTAA~ SeuratPro~        246           59 0               A             g1    
+#>  7 GATA~ SeuratPro~        328           72 1               B             g1    
+#>  8 ATCA~ SeuratPro~        168           37 0               A             g2    
+#>  9 AATG~ SeuratPro~        389           73 1               B             g1    
+#> 10 AGTC~ SeuratPro~        173           53 0               A             g2    
+#> # i 40 more rows
+#> # i 10 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>,
 #> #   PC_1 <dbl>, PC_2 <dbl>, PC_3 <dbl>, PC_4 <dbl>, PC_5 <dbl>, tSNE_1 <dbl>,
 #> #   tSNE_2 <dbl>
 pbmc_small |> sample_frac(0.1)
-#> # A SingleCellExperiment-tibble abstraction: 8 × 17
+#> # A SingleCellExperiment-tibble abstraction: 8 x 17
 #> # Features=230 | Cells=8 | Assays=counts, logcounts
 #>   .cell  orig.ident nCount_RNA nFeature_RNA RNA_snn_res.0.8 letter.idents groups
 #>   <chr>  <fct>           <dbl>        <int> <fct>           <fct>         <chr> 
-#> 1 CCATC… SeuratPro…        224           50 1               B             g2    
-#> 2 CGGCA… SeuratPro…         94           55 0               A             g2    
-#> 3 TTACG… SeuratPro…        228           39 0               A             g1    
-#> 4 TACTC… SeuratPro…        156           48 0               A             g1    
-#> 5 CATGG… SeuratPro…         85           52 0               A             g1    
-#> 6 GAACC… SeuratPro…         87           50 1               B             g2    
-#> 7 ACAGG… SeuratPro…        151           59 0               A             g1    
-#> 8 GATAG… SeuratPro…        328           72 1               B             g1    
-#> # ℹ 10 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>,
+#> 1 CCATC~ SeuratPro~        224           50 1               B             g2    
+#> 2 CGGCA~ SeuratPro~         94           55 0               A             g2    
+#> 3 TTACG~ SeuratPro~        228           39 0               A             g1    
+#> 4 TACTC~ SeuratPro~        156           48 0               A             g1    
+#> 5 CATGG~ SeuratPro~         85           52 0               A             g1    
+#> 6 GAACC~ SeuratPro~         87           50 1               B             g2    
+#> 7 ACAGG~ SeuratPro~        151           59 0               A             g1    
+#> 8 GATAG~ SeuratPro~        328           72 1               B             g1    
+#> # i 10 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>,
 #> #   PC_1 <dbl>, PC_2 <dbl>, PC_3 <dbl>, PC_4 <dbl>, PC_5 <dbl>, tSNE_1 <dbl>,
 #> #   tSNE_2 <dbl>
 
diff --git a/reference/select.html b/reference/select.html
index 126745f..d3f8909 100644
--- a/reference/select.html
+++ b/reference/select.html
@@ -62,7 +62,7 @@
       
       
         tidySingleCellExperiment
-        1.13.3
+        1.15.1
@@ -330,21 +330,21 @@

Examples

data(pbmc_small)
 pbmc_small |> select(cell, orig.ident)
 #> Warning: tidySingleCellExperiment says: from version 1.3.1, the special columns including cell id (colnames(se)) has changed to ".cell". This dataset is returned with the old-style vocabulary (cell), however, we suggest to update your workflow to reflect the new vocabulary (.cell).
-#> # A SingleCellExperiment-tibble abstraction: 80 × 9
+#> # A SingleCellExperiment-tibble abstraction: 80 x 9
 #> # Features=230 | Cells=80 | Assays=counts, logcounts
 #>    cell           orig.ident     PC_1   PC_2   PC_3  PC_4   PC_5  tSNE_1  tSNE_2
 #>    <chr>          <fct>         <dbl>  <dbl>  <dbl> <dbl>  <dbl>   <dbl>   <dbl>
-#>  1 ATGCCAGAACGACT SeuratProj… -0.774  -0.900 -0.249 0.559  0.465   0.868  -8.10 
-#>  2 CATGGCCTGTGCAT SeuratProj… -0.0260 -0.347  0.665 0.418  0.585  -7.39   -8.77 
-#>  3 GAACCTGATGAACC SeuratProj… -0.457   0.180  1.32  2.01  -0.482 -28.2     0.241
-#>  4 TGACTGGATTCTCA SeuratProj… -0.812  -1.38  -1.00  0.139 -1.60   16.3   -11.2  
-#>  5 AGTCAGACTGCACA SeuratProj… -0.774  -0.900 -0.249 0.559  0.465   1.91  -11.2  
-#>  6 TCTGATACACGTGT SeuratProj… -0.774  -0.900 -0.249 0.559  0.465   3.15   -9.94 
-#>  7 TGGTATCTAAACAG SeuratProj… -0.460  -1.19  -0.312 0.716 -1.65   17.9    -9.90 
-#>  8 GCAGCTCTGTTTCT SeuratProj… -0.900  -0.388  0.693 0.404  0.536  -6.49   -8.39 
-#>  9 GATATAACACGCAT SeuratProj… -0.774  -0.900 -0.249 0.559  0.465   1.33   -9.68 
-#> 10 AATGTTGACAGTCA SeuratProj… -0.488  -1.16  -0.306 0.702 -1.47   17.0    -9.43 
-#> # ℹ 70 more rows
+#>  1 ATGCCAGAACGACT SeuratProj~ -0.774  -0.900 -0.249 0.559  0.465   0.868  -8.10 
+#>  2 CATGGCCTGTGCAT SeuratProj~ -0.0260 -0.347  0.665 0.418  0.585  -7.39   -8.77 
+#>  3 GAACCTGATGAACC SeuratProj~ -0.457   0.180  1.32  2.01  -0.482 -28.2     0.241
+#>  4 TGACTGGATTCTCA SeuratProj~ -0.812  -1.38  -1.00  0.139 -1.60   16.3   -11.2  
+#>  5 AGTCAGACTGCACA SeuratProj~ -0.774  -0.900 -0.249 0.559  0.465   1.91  -11.2  
+#>  6 TCTGATACACGTGT SeuratProj~ -0.774  -0.900 -0.249 0.559  0.465   3.15   -9.94 
+#>  7 TGGTATCTAAACAG SeuratProj~ -0.460  -1.19  -0.312 0.716 -1.65   17.9    -9.90 
+#>  8 GCAGCTCTGTTTCT SeuratProj~ -0.900  -0.388  0.693 0.404  0.536  -6.49   -8.39 
+#>  9 GATATAACACGCAT SeuratProj~ -0.774  -0.900 -0.249 0.559  0.465   1.33   -9.68 
+#> 10 AATGTTGACAGTCA SeuratProj~ -0.488  -1.16  -0.306 0.702 -1.47   17.0    -9.43 
+#> # i 70 more rows
diff --git a/reference/separate.html b/reference/separate.html index 86dde4f..ce76a55 100644 --- a/reference/separate.html +++ b/reference/separate.html @@ -24,7 +24,7 @@ tidySingleCellExperiment - 1.13.3 + 1.15.1 @@ -162,22 +162,22 @@

Examples

data(pbmc_small)
 un <- pbmc_small |> unite("new_col", c(orig.ident, groups))
 un |> separate(new_col, c("orig.ident", "groups"))
-#> # A SingleCellExperiment-tibble abstraction: 80 × 17
+#> # A SingleCellExperiment-tibble abstraction: 80 x 17
 #> # Features=230 | Cells=80 | Assays=counts, logcounts
 #>    .cell orig.ident groups nCount_RNA nFeature_RNA RNA_snn_res.0.8 letter.idents
 #>    <chr> <chr>      <chr>       <dbl>        <int> <fct>           <fct>        
-#>  1 ATGC… SeuratPro… g2             70           47 0               A            
-#>  2 CATG… SeuratPro… g1             85           52 0               A            
-#>  3 GAAC… SeuratPro… g2             87           50 1               B            
-#>  4 TGAC… SeuratPro… g2            127           56 0               A            
-#>  5 AGTC… SeuratPro… g2            173           53 0               A            
-#>  6 TCTG… SeuratPro… g1             70           48 0               A            
-#>  7 TGGT… SeuratPro… g1             64           36 0               A            
-#>  8 GCAG… SeuratPro… g1             72           45 0               A            
-#>  9 GATA… SeuratPro… g1             52           36 0               A            
-#> 10 AATG… SeuratPro… g1            100           41 0               A            
-#> # ℹ 70 more rows
-#> # ℹ 10 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>,
+#>  1 ATGC~ SeuratPro~ g2             70           47 0               A            
+#>  2 CATG~ SeuratPro~ g1             85           52 0               A            
+#>  3 GAAC~ SeuratPro~ g2             87           50 1               B            
+#>  4 TGAC~ SeuratPro~ g2            127           56 0               A            
+#>  5 AGTC~ SeuratPro~ g2            173           53 0               A            
+#>  6 TCTG~ SeuratPro~ g1             70           48 0               A            
+#>  7 TGGT~ SeuratPro~ g1             64           36 0               A            
+#>  8 GCAG~ SeuratPro~ g1             72           45 0               A            
+#>  9 GATA~ SeuratPro~ g1             52           36 0               A            
+#> 10 AATG~ SeuratPro~ g1            100           41 0               A            
+#> # i 70 more rows
+#> # i 10 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>,
 #> #   PC_1 <dbl>, PC_2 <dbl>, PC_3 <dbl>, PC_4 <dbl>, PC_5 <dbl>, tSNE_1 <dbl>,
 #> #   tSNE_2 <dbl>
 
diff --git a/reference/slice.html b/reference/slice.html
index 0e0c18b..de968bb 100644
--- a/reference/slice.html
+++ b/reference/slice.html
@@ -28,7 +28,7 @@
       
       
         tidySingleCellExperiment
-        1.13.3
+        1.15.1
@@ -220,7 +220,7 @@

Methods

These function are generics, which means that packages can provide implementations (methods) for other classes. See the documentation of individual methods for extra arguments and differences in behaviour.

-

Methods available in currently loaded packages:

  • slice(): (ANY, integer, numeric, Rle, RleList, XDouble, XInteger), dbplyr (tbl_lazy), dplyr (data.frame), plotly (plotly), tidySingleCellExperiment (SingleCellExperiment) +

    Methods available in currently loaded packages:

    • slice(): (ANY, Rle, RleList, XDouble, XInteger, integer, numeric), dbplyr (tbl_lazy), dplyr (data.frame), plotly (plotly), tidySingleCellExperiment (SingleCellExperiment) .

    • slice_head(): dbplyr (tbl_lazy), dplyr (data.frame), tidySingleCellExperiment (SingleCellExperiment) .

      • @@ -235,7 +235,7 @@

      Methods

    These function are generics, which means that packages can provide implementations (methods) for other classes. See the documentation of individual methods for extra arguments and differences in behaviour.

    -

    Methods available in currently loaded packages:

    • slice(): (ANY, integer, numeric, Rle, RleList, XDouble, XInteger), dbplyr (tbl_lazy), dplyr (data.frame), plotly (plotly), tidySingleCellExperiment (SingleCellExperiment) +

      Methods available in currently loaded packages:

      • slice(): (ANY, Rle, RleList, XDouble, XInteger, integer, numeric), dbplyr (tbl_lazy), dplyr (data.frame), plotly (plotly), tidySingleCellExperiment (SingleCellExperiment) .

      • slice_head(): dbplyr (tbl_lazy), dplyr (data.frame), tidySingleCellExperiment (SingleCellExperiment) .

        • @@ -250,7 +250,7 @@

        Methods

      These function are generics, which means that packages can provide implementations (methods) for other classes. See the documentation of individual methods for extra arguments and differences in behaviour.

      -

      Methods available in currently loaded packages:

      • slice(): (ANY, integer, numeric, Rle, RleList, XDouble, XInteger), dbplyr (tbl_lazy), dplyr (data.frame), plotly (plotly), tidySingleCellExperiment (SingleCellExperiment) +

        Methods available in currently loaded packages:

        • slice(): (ANY, Rle, RleList, XDouble, XInteger, integer, numeric), dbplyr (tbl_lazy), dplyr (data.frame), plotly (plotly), tidySingleCellExperiment (SingleCellExperiment) .

        • slice_head(): dbplyr (tbl_lazy), dplyr (data.frame), tidySingleCellExperiment (SingleCellExperiment) .

          • @@ -265,7 +265,7 @@

          Methods

        These function are generics, which means that packages can provide implementations (methods) for other classes. See the documentation of individual methods for extra arguments and differences in behaviour.

        -

        Methods available in currently loaded packages:

        • slice(): (ANY, integer, numeric, Rle, RleList, XDouble, XInteger), dbplyr (tbl_lazy), dplyr (data.frame), plotly (plotly), tidySingleCellExperiment (SingleCellExperiment) +

          Methods available in currently loaded packages:

          • slice(): (ANY, Rle, RleList, XDouble, XInteger, integer, numeric), dbplyr (tbl_lazy), dplyr (data.frame), plotly (plotly), tidySingleCellExperiment (SingleCellExperiment) .

          • slice_head(): dbplyr (tbl_lazy), dplyr (data.frame), tidySingleCellExperiment (SingleCellExperiment) .

            • @@ -280,7 +280,7 @@

            Methods

          These function are generics, which means that packages can provide implementations (methods) for other classes. See the documentation of individual methods for extra arguments and differences in behaviour.

          -

          Methods available in currently loaded packages:

          • slice(): (ANY, integer, numeric, Rle, RleList, XDouble, XInteger), dbplyr (tbl_lazy), dplyr (data.frame), plotly (plotly), tidySingleCellExperiment (SingleCellExperiment) +

            Methods available in currently loaded packages:

            • slice(): (ANY, Rle, RleList, XDouble, XInteger, integer, numeric), dbplyr (tbl_lazy), dplyr (data.frame), plotly (plotly), tidySingleCellExperiment (SingleCellExperiment) .

            • slice_head(): dbplyr (tbl_lazy), dplyr (data.frame), tidySingleCellExperiment (SingleCellExperiment) .

              • @@ -295,7 +295,7 @@

              Methods

            These function are generics, which means that packages can provide implementations (methods) for other classes. See the documentation of individual methods for extra arguments and differences in behaviour.

            -

            Methods available in currently loaded packages:

            • slice(): (ANY, integer, numeric, Rle, RleList, XDouble, XInteger), dbplyr (tbl_lazy), dplyr (data.frame), plotly (plotly), tidySingleCellExperiment (SingleCellExperiment) +

              Methods available in currently loaded packages:

              • slice(): (ANY, Rle, RleList, XDouble, XInteger, integer, numeric), dbplyr (tbl_lazy), dplyr (data.frame), plotly (plotly), tidySingleCellExperiment (SingleCellExperiment) .

              • slice_head(): dbplyr (tbl_lazy), dplyr (data.frame), tidySingleCellExperiment (SingleCellExperiment) .

                • @@ -321,71 +321,71 @@

                See also

                Examples

                data(pbmc_small)
 pbmc_small |> slice(1)
-#> # A SingleCellExperiment-tibble abstraction: 1 × 17
+#> # A SingleCellExperiment-tibble abstraction: 1 x 17
 #> # Features=230 | Cells=1 | Assays=counts, logcounts
 #>   .cell  orig.ident nCount_RNA nFeature_RNA RNA_snn_res.0.8 letter.idents groups
 #>   <chr>  <fct>           <dbl>        <int> <fct>           <fct>         <chr> 
-#> 1 ATGCC… SeuratPro…         70           47 0               A             g2    
-#> # ℹ 10 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>,
+#> 1 ATGCC~ SeuratPro~         70           47 0               A             g2    
+#> # i 10 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>,
 #> #   PC_1 <dbl>, PC_2 <dbl>, PC_3 <dbl>, PC_4 <dbl>, PC_5 <dbl>, tSNE_1 <dbl>,
 #> #   tSNE_2 <dbl>
 
 data(pbmc_small)
 pbmc_small |> slice_sample(n=1)
-#> # A SingleCellExperiment-tibble abstraction: 1 × 17
+#> # A SingleCellExperiment-tibble abstraction: 1 x 17
 #> # Features=230 | Cells=1 | Assays=counts, logcounts
 #>   .cell  orig.ident nCount_RNA nFeature_RNA RNA_snn_res.0.8 letter.idents groups
 #>   <chr>  <fct>           <dbl>        <int> <fct>           <fct>         <chr> 
-#> 1 GACAT… SeuratPro…        872           96 1               B             g1    
-#> # ℹ 10 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>,
+#> 1 GACAT~ SeuratPro~        872           96 1               B             g1    
+#> # i 10 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>,
 #> #   PC_1 <dbl>, PC_2 <dbl>, PC_3 <dbl>, PC_4 <dbl>, PC_5 <dbl>, tSNE_1 <dbl>,
 #> #   tSNE_2 <dbl>
 pbmc_small |> slice_sample(prop=0.1)
-#> # A SingleCellExperiment-tibble abstraction: 8 × 17
+#> # A SingleCellExperiment-tibble abstraction: 8 x 17
 #> # Features=230 | Cells=8 | Assays=counts, logcounts
 #>   .cell  orig.ident nCount_RNA nFeature_RNA RNA_snn_res.0.8 letter.idents groups
 #>   <chr>  <fct>           <dbl>        <int> <fct>           <fct>         <chr> 
-#> 1 TCTGA… SeuratPro…         70           48 0               A             g1    
-#> 2 ATAGG… SeuratPro…        406           74 1               B             g1    
-#> 3 CATCA… SeuratPro…         79           43 0               A             g1    
-#> 4 CATGG… SeuratPro…         85           52 0               A             g1    
-#> 5 TTTAG… SeuratPro…        462           86 1               B             g1    
-#> 6 CATTA… SeuratPro…        316           65 0               A             g2    
-#> 7 GACAT… SeuratPro…        872           96 1               B             g1    
-#> 8 CCATC… SeuratPro…        224           50 1               B             g2    
-#> # ℹ 10 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>,
+#> 1 TCTGA~ SeuratPro~         70           48 0               A             g1    
+#> 2 ATAGG~ SeuratPro~        406           74 1               B             g1    
+#> 3 CATCA~ SeuratPro~         79           43 0               A             g1    
+#> 4 CATGG~ SeuratPro~         85           52 0               A             g1    
+#> 5 TTTAG~ SeuratPro~        462           86 1               B             g1    
+#> 6 CATTA~ SeuratPro~        316           65 0               A             g2    
+#> 7 GACAT~ SeuratPro~        872           96 1               B             g1    
+#> 8 CCATC~ SeuratPro~        224           50 1               B             g2    
+#> # i 10 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>,
 #> #   PC_1 <dbl>, PC_2 <dbl>, PC_3 <dbl>, PC_4 <dbl>, PC_5 <dbl>, tSNE_1 <dbl>,
 #> #   tSNE_2 <dbl>
 
 data(pbmc_small)
 # First rows based on existing order
 pbmc_small |> slice_head(n=5)
-#> # A SingleCellExperiment-tibble abstraction: 5 × 17
+#> # A SingleCellExperiment-tibble abstraction: 5 x 17
 #> # Features=230 | Cells=5 | Assays=counts, logcounts
 #>   .cell  orig.ident nCount_RNA nFeature_RNA RNA_snn_res.0.8 letter.idents groups
 #>   <chr>  <fct>           <dbl>        <int> <fct>           <fct>         <chr> 
-#> 1 ATGCC… SeuratPro…         70           47 0               A             g2    
-#> 2 CATGG… SeuratPro…         85           52 0               A             g1    
-#> 3 GAACC… SeuratPro…         87           50 1               B             g2    
-#> 4 TGACT… SeuratPro…        127           56 0               A             g2    
-#> 5 AGTCA… SeuratPro…        173           53 0               A             g2    
-#> # ℹ 10 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>,
+#> 1 ATGCC~ SeuratPro~         70           47 0               A             g2    
+#> 2 CATGG~ SeuratPro~         85           52 0               A             g1    
+#> 3 GAACC~ SeuratPro~         87           50 1               B             g2    
+#> 4 TGACT~ SeuratPro~        127           56 0               A             g2    
+#> 5 AGTCA~ SeuratPro~        173           53 0               A             g2    
+#> # i 10 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>,
 #> #   PC_1 <dbl>, PC_2 <dbl>, PC_3 <dbl>, PC_4 <dbl>, PC_5 <dbl>, tSNE_1 <dbl>,
 #> #   tSNE_2 <dbl>
 
 data(pbmc_small)
 # First rows based on existing order
 pbmc_small |> slice_tail(n=5)
-#> # A SingleCellExperiment-tibble abstraction: 5 × 17
+#> # A SingleCellExperiment-tibble abstraction: 5 x 17
 #> # Features=230 | Cells=5 | Assays=counts, logcounts
 #>   .cell  orig.ident nCount_RNA nFeature_RNA RNA_snn_res.0.8 letter.idents groups
 #>   <chr>  <fct>           <dbl>        <int> <fct>           <fct>         <chr> 
-#> 1 GAGTT… SeuratPro…        527           47 0               A             g1    
-#> 2 GACGC… SeuratPro…        202           30 0               A             g2    
-#> 3 AGTCT… SeuratPro…        157           29 0               A             g1    
-#> 4 GGAAC… SeuratPro…        150           30 0               A             g2    
-#> 5 CTTGA… SeuratPro…        233           76 1               B             g1    
-#> # ℹ 10 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>,
+#> 1 GAGTT~ SeuratPro~        527           47 0               A             g1    
+#> 2 GACGC~ SeuratPro~        202           30 0               A             g2    
+#> 3 AGTCT~ SeuratPro~        157           29 0               A             g1    
+#> 4 GGAAC~ SeuratPro~        150           30 0               A             g2    
+#> 5 CTTGA~ SeuratPro~        233           76 1               B             g1    
+#> # i 10 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>,
 #> #   PC_1 <dbl>, PC_2 <dbl>, PC_3 <dbl>, PC_4 <dbl>, PC_5 <dbl>, tSNE_1 <dbl>,
 #> #   tSNE_2 <dbl>
 
@@ -393,90 +393,90 @@ 
                Examples
                
 
 # Rows with minimum and maximum values of a metadata variable
 pbmc_small |> slice_min(nFeature_RNA, n=5)
-#> # A SingleCellExperiment-tibble abstraction: 5 × 17
+#> # A SingleCellExperiment-tibble abstraction: 5 x 17
 #> # Features=230 | Cells=5 | Assays=counts, logcounts
 #>   .cell  orig.ident nCount_RNA nFeature_RNA RNA_snn_res.0.8 letter.idents groups
 #>   <chr>  <fct>           <dbl>        <int> <fct>           <fct>         <chr> 
-#> 1 CATGA… SeuratPro…         51           26 0               A             g2    
-#> 2 GGCAT… SeuratPro…        172           29 0               A             g1    
-#> 3 AGTCT… SeuratPro…        157           29 0               A             g1    
-#> 4 GACGC… SeuratPro…        202           30 0               A             g2    
-#> 5 GGAAC… SeuratPro…        150           30 0               A             g2    
-#> # ℹ 10 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>,
+#> 1 CATGA~ SeuratPro~         51           26 0               A             g2    
+#> 2 GGCAT~ SeuratPro~        172           29 0               A             g1    
+#> 3 AGTCT~ SeuratPro~        157           29 0               A             g1    
+#> 4 GACGC~ SeuratPro~        202           30 0               A             g2    
+#> 5 GGAAC~ SeuratPro~        150           30 0               A             g2    
+#> # i 10 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>,
 #> #   PC_1 <dbl>, PC_2 <dbl>, PC_3 <dbl>, PC_4 <dbl>, PC_5 <dbl>, tSNE_1 <dbl>,
 #> #   tSNE_2 <dbl>
 
 # slice_min() and slice_max() may return more rows than requested
 # in the presence of ties.
 pbmc_small |>  slice_min(nFeature_RNA, n=2)
-#> # A SingleCellExperiment-tibble abstraction: 3 × 17
+#> # A SingleCellExperiment-tibble abstraction: 3 x 17
 #> # Features=230 | Cells=3 | Assays=counts, logcounts
 #>   .cell  orig.ident nCount_RNA nFeature_RNA RNA_snn_res.0.8 letter.idents groups
 #>   <chr>  <fct>           <dbl>        <int> <fct>           <fct>         <chr> 
-#> 1 CATGA… SeuratPro…         51           26 0               A             g2    
-#> 2 GGCAT… SeuratPro…        172           29 0               A             g1    
-#> 3 AGTCT… SeuratPro…        157           29 0               A             g1    
-#> # ℹ 10 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>,
+#> 1 CATGA~ SeuratPro~         51           26 0               A             g2    
+#> 2 GGCAT~ SeuratPro~        172           29 0               A             g1    
+#> 3 AGTCT~ SeuratPro~        157           29 0               A             g1    
+#> # i 10 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>,
 #> #   PC_1 <dbl>, PC_2 <dbl>, PC_3 <dbl>, PC_4 <dbl>, PC_5 <dbl>, tSNE_1 <dbl>,
 #> #   tSNE_2 <dbl>
 
 # Use with_ties=FALSE to return exactly n matches
 pbmc_small |> slice_min(nFeature_RNA, n=2, with_ties=FALSE)
-#> # A SingleCellExperiment-tibble abstraction: 2 × 17
+#> # A SingleCellExperiment-tibble abstraction: 2 x 17
 #> # Features=230 | Cells=2 | Assays=counts, logcounts
 #>   .cell  orig.ident nCount_RNA nFeature_RNA RNA_snn_res.0.8 letter.idents groups
 #>   <chr>  <fct>           <dbl>        <int> <fct>           <fct>         <chr> 
-#> 1 CATGA… SeuratPro…         51           26 0               A             g2    
-#> 2 GGCAT… SeuratPro…        172           29 0               A             g1    
-#> # ℹ 10 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>,
+#> 1 CATGA~ SeuratPro~         51           26 0               A             g2    
+#> 2 GGCAT~ SeuratPro~        172           29 0               A             g1    
+#> # i 10 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>,
 #> #   PC_1 <dbl>, PC_2 <dbl>, PC_3 <dbl>, PC_4 <dbl>, PC_5 <dbl>, tSNE_1 <dbl>,
 #> #   tSNE_2 <dbl>
 
 # Or use additional variables to break the tie:
 pbmc_small |> slice_min(tibble::tibble(nFeature_RNA, nCount_RNA), n=2)
-#> # A SingleCellExperiment-tibble abstraction: 2 × 17
+#> # A SingleCellExperiment-tibble abstraction: 2 x 17
 #> # Features=230 | Cells=2 | Assays=counts, logcounts
 #>   .cell  orig.ident nCount_RNA nFeature_RNA RNA_snn_res.0.8 letter.idents groups
 #>   <chr>  <fct>           <dbl>        <int> <fct>           <fct>         <chr> 
-#> 1 CATGA… SeuratPro…         51           26 0               A             g2    
-#> 2 AGTCT… SeuratPro…        157           29 0               A             g1    
-#> # ℹ 10 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>,
+#> 1 CATGA~ SeuratPro~         51           26 0               A             g2    
+#> 2 AGTCT~ SeuratPro~        157           29 0               A             g1    
+#> # i 10 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>,
 #> #   PC_1 <dbl>, PC_2 <dbl>, PC_3 <dbl>, PC_4 <dbl>, PC_5 <dbl>, tSNE_1 <dbl>,
 #> #   tSNE_2 <dbl>
 
 # Use by for group-wise operations
 pbmc_small |> slice_min(nFeature_RNA, n=5, by=groups)
-#> # A SingleCellExperiment-tibble abstraction: 10 × 17
+#> # A SingleCellExperiment-tibble abstraction: 10 x 17
 #> # Features=230 | Cells=10 | Assays=counts, logcounts
 #>    .cell orig.ident nCount_RNA nFeature_RNA RNA_snn_res.0.8 letter.idents groups
 #>    <chr> <fct>           <dbl>        <int> <fct>           <fct>         <chr> 
-#>  1 CATG… SeuratPro…         51           26 0               A             g2    
-#>  2 GACG… SeuratPro…        202           30 0               A             g2    
-#>  3 GGAA… SeuratPro…        150           30 0               A             g2    
-#>  4 AGGT… SeuratPro…         62           31 0               A             g2    
-#>  5 CTTC… SeuratPro…         41           32 0               A             g2    
-#>  6 GGCA… SeuratPro…        172           29 0               A             g1    
-#>  7 AGTC… SeuratPro…        157           29 0               A             g1    
-#>  8 TGGT… SeuratPro…         64           36 0               A             g1    
-#>  9 GATA… SeuratPro…         52           36 0               A             g1    
-#> 10 TTAC… SeuratPro…        228           39 0               A             g1    
-#> # ℹ 10 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>,
+#>  1 CATG~ SeuratPro~         51           26 0               A             g2    
+#>  2 GACG~ SeuratPro~        202           30 0               A             g2    
+#>  3 GGAA~ SeuratPro~        150           30 0               A             g2    
+#>  4 AGGT~ SeuratPro~         62           31 0               A             g2    
+#>  5 CTTC~ SeuratPro~         41           32 0               A             g2    
+#>  6 GGCA~ SeuratPro~        172           29 0               A             g1    
+#>  7 AGTC~ SeuratPro~        157           29 0               A             g1    
+#>  8 TGGT~ SeuratPro~         64           36 0               A             g1    
+#>  9 GATA~ SeuratPro~         52           36 0               A             g1    
+#> 10 TTAC~ SeuratPro~        228           39 0               A             g1    
+#> # i 10 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>,
 #> #   PC_1 <dbl>, PC_2 <dbl>, PC_3 <dbl>, PC_4 <dbl>, PC_5 <dbl>, tSNE_1 <dbl>,
 #> #   tSNE_2 <dbl>
 
 data(pbmc_small)
 # Rows with minimum and maximum values of a metadata variable
 pbmc_small |> slice_max(nFeature_RNA, n=5)
-#> # A SingleCellExperiment-tibble abstraction: 5 × 17
+#> # A SingleCellExperiment-tibble abstraction: 5 x 17
 #> # Features=230 | Cells=5 | Assays=counts, logcounts
 #>   .cell  orig.ident nCount_RNA nFeature_RNA RNA_snn_res.0.8 letter.idents groups
 #>   <chr>  <fct>           <dbl>        <int> <fct>           <fct>         <chr> 
-#> 1 GACAT… SeuratPro…        872           96 1               B             g1    
-#> 2 ACGTG… SeuratPro…        709           94 1               B             g2    
-#> 3 TTGAG… SeuratPro…        787           88 0               A             g1    
-#> 4 TTTAG… SeuratPro…        462           86 1               B             g1    
-#> 5 ATTGT… SeuratPro…        745           84 1               B             g2    
-#> # ℹ 10 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>,
+#> 1 GACAT~ SeuratPro~        872           96 1               B             g1    
+#> 2 ACGTG~ SeuratPro~        709           94 1               B             g2    
+#> 3 TTGAG~ SeuratPro~        787           88 0               A             g1    
+#> 4 TTTAG~ SeuratPro~        462           86 1               B             g1    
+#> 5 ATTGT~ SeuratPro~        745           84 1               B             g2    
+#> # i 10 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>,
 #> #   PC_1 <dbl>, PC_2 <dbl>, PC_3 <dbl>, PC_4 <dbl>, PC_5 <dbl>, tSNE_1 <dbl>,
 #> #   tSNE_2 <dbl>
 
diff --git a/reference/summarise.html b/reference/summarise.html
index e4b2ed7..d00ab32 100644
--- a/reference/summarise.html
+++ b/reference/summarise.html
@@ -22,7 +22,7 @@
       
       
         tidySingleCellExperiment
-        1.13.3
+        1.15.1
                @@ -160,7 +160,7 @@

                Examples

                data(pbmc_small)
 pbmc_small |> summarise(mean(nCount_RNA))
 #> tidySingleCellExperiment says: A data frame is returned for independent data analysis.
-#> # A tibble: 1 × 1
+#> # A tibble: 1 x 1
 #>   `mean(nCount_RNA)`
 #>                <dbl>
 #> 1               245.
diff --git a/reference/tbl_format_header.html b/reference/tbl_format_header.html
index 7344256..cdf1f07 100644
--- a/reference/tbl_format_header.html
+++ b/reference/tbl_format_header.html
@@ -26,7 +26,7 @@
       
       
         tidySingleCellExperiment
-        1.13.3
+        1.15.1
                diff --git a/reference/tidy.html b/reference/tidy.html index f24a3ae..f7e2f1e 100644 --- a/reference/tidy.html +++ b/reference/tidy.html @@ -17,7 +17,7 @@ tidySingleCellExperiment - 1.13.3 + 1.15.1 @@ -83,22 +83,22 @@

                Value

                Examples

                data(pbmc_small)
 pbmc_small
-#> # A SingleCellExperiment-tibble abstraction: 80 × 17
+#> # A SingleCellExperiment-tibble abstraction: 80 x 17
 #> # Features=230 | Cells=80 | Assays=counts, logcounts
 #>    .cell orig.ident nCount_RNA nFeature_RNA RNA_snn_res.0.8 letter.idents groups
 #>    <chr> <fct>           <dbl>        <int> <fct>           <fct>         <chr> 
-#>  1 ATGC… SeuratPro…         70           47 0               A             g2    
-#>  2 CATG… SeuratPro…         85           52 0               A             g1    
-#>  3 GAAC… SeuratPro…         87           50 1               B             g2    
-#>  4 TGAC… SeuratPro…        127           56 0               A             g2    
-#>  5 AGTC… SeuratPro…        173           53 0               A             g2    
-#>  6 TCTG… SeuratPro…         70           48 0               A             g1    
-#>  7 TGGT… SeuratPro…         64           36 0               A             g1    
-#>  8 GCAG… SeuratPro…         72           45 0               A             g1    
-#>  9 GATA… SeuratPro…         52           36 0               A             g1    
-#> 10 AATG… SeuratPro…        100           41 0               A             g1    
-#> # ℹ 70 more rows
-#> # ℹ 10 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>,
+#>  1 ATGC~ SeuratPro~         70           47 0               A             g2    
+#>  2 CATG~ SeuratPro~         85           52 0               A             g1    
+#>  3 GAAC~ SeuratPro~         87           50 1               B             g2    
+#>  4 TGAC~ SeuratPro~        127           56 0               A             g2    
+#>  5 AGTC~ SeuratPro~        173           53 0               A             g2    
+#>  6 TCTG~ SeuratPro~         70           48 0               A             g1    
+#>  7 TGGT~ SeuratPro~         64           36 0               A             g1    
+#>  8 GCAG~ SeuratPro~         72           45 0               A             g1    
+#>  9 GATA~ SeuratPro~         52           36 0               A             g1    
+#> 10 AATG~ SeuratPro~        100           41 0               A             g1    
+#> # i 70 more rows
+#> # i 10 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>,
 #> #   PC_1 <dbl>, PC_2 <dbl>, PC_3 <dbl>, PC_4 <dbl>, PC_5 <dbl>, tSNE_1 <dbl>,
 #> #   tSNE_2 <dbl>
 
diff --git a/reference/unite.html b/reference/unite.html
index 30ce1e9..b5f1d01 100644
--- a/reference/unite.html
+++ b/reference/unite.html
@@ -17,7 +17,7 @@
       
       
         tidySingleCellExperiment
-        1.13.3
+        1.15.1
                @@ -114,22 +114,22 @@

                Examples

                pbmc_small |> unite( col="new_col", c("orig.ident", "groups")) -#> # A SingleCellExperiment-tibble abstraction: 80 × 16 +#> # A SingleCellExperiment-tibble abstraction: 80 x 16 #> # Features=230 | Cells=80 | Assays=counts, logcounts #> .cell new_col nCount_RNA nFeature_RNA RNA_snn_res.0.8 letter.idents #> <chr> <chr> <dbl> <int> <fct> <fct> -#> 1 ATGCCAGAACGACT SeuratP… 70 47 0 A -#> 2 CATGGCCTGTGCAT SeuratP… 85 52 0 A -#> 3 GAACCTGATGAACC SeuratP… 87 50 1 B -#> 4 TGACTGGATTCTCA SeuratP… 127 56 0 A -#> 5 AGTCAGACTGCACA SeuratP… 173 53 0 A -#> 6 TCTGATACACGTGT SeuratP… 70 48 0 A -#> 7 TGGTATCTAAACAG SeuratP… 64 36 0 A -#> 8 GCAGCTCTGTTTCT SeuratP… 72 45 0 A -#> 9 GATATAACACGCAT SeuratP… 52 36 0 A -#> 10 AATGTTGACAGTCA SeuratP… 100 41 0 A -#> # ℹ 70 more rows -#> # ℹ 10 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>, +#> 1 ATGCCAGAACGACT SeuratP~ 70 47 0 A +#> 2 CATGGCCTGTGCAT SeuratP~ 85 52 0 A +#> 3 GAACCTGATGAACC SeuratP~ 87 50 1 B +#> 4 TGACTGGATTCTCA SeuratP~ 127 56 0 A +#> 5 AGTCAGACTGCACA SeuratP~ 173 53 0 A +#> 6 TCTGATACACGTGT SeuratP~ 70 48 0 A +#> 7 TGGTATCTAAACAG SeuratP~ 64 36 0 A +#> 8 GCAGCTCTGTTTCT SeuratP~ 72 45 0 A +#> 9 GATATAACACGCAT SeuratP~ 52 36 0 A +#> 10 AATGTTGACAGTCA SeuratP~ 100 41 0 A +#> # i 70 more rows +#> # i 10 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>, #> # PC_1 <dbl>, PC_2 <dbl>, PC_3 <dbl>, PC_4 <dbl>, PC_5 <dbl>, tSNE_1 <dbl>, #> # tSNE_2 <dbl> diff --git a/reference/unnest.html b/reference/unnest.html index 31df69a..82b8da3 100644 --- a/reference/unnest.html +++ b/reference/unnest.html @@ -17,7 +17,7 @@ tidySingleCellExperiment - 1.13.3 + 1.15.1 @@ -197,22 +197,22 @@

                Examples

                pbmc_small |> nest(data=-groups) |> unnest(data) -#> # A SingleCellExperiment-tibble abstraction: 80 × 17 +#> # A SingleCellExperiment-tibble abstraction: 80 x 17 #> # Features=230 | Cells=80 | Assays=counts, logcounts #> .cell orig.ident nCount_RNA nFeature_RNA RNA_snn_res.0.8 letter.idents #> <chr> <fct> <dbl> <int> <fct> <fct> -#> 1 ATGCCAGAACG… SeuratPro… 70 47 0 A -#> 2 GAACCTGATGA… SeuratPro… 87 50 1 B -#> 3 TGACTGGATTC… SeuratPro… 127 56 0 A -#> 4 AGTCAGACTGC… SeuratPro… 173 53 0 A -#> 5 AGGTCATGAGT… SeuratPro… 62 31 0 A -#> 6 GGGTAACTCTA… SeuratPro… 101 41 0 A -#> 7 CATGAGACACG… SeuratPro… 51 26 0 A -#> 8 TACGCCACTCC… SeuratPro… 99 45 0 A -#> 9 GTAAGCACTCA… SeuratPro… 67 33 0 A -#> 10 TACATCACGCT… SeuratPro… 109 41 0 A -#> # ℹ 70 more rows -#> # ℹ 11 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>, +#> 1 ATGCCAGAACG~ SeuratPro~ 70 47 0 A +#> 2 GAACCTGATGA~ SeuratPro~ 87 50 1 B +#> 3 TGACTGGATTC~ SeuratPro~ 127 56 0 A +#> 4 AGTCAGACTGC~ SeuratPro~ 173 53 0 A +#> 5 AGGTCATGAGT~ SeuratPro~ 62 31 0 A +#> 6 GGGTAACTCTA~ SeuratPro~ 101 41 0 A +#> 7 CATGAGACACG~ SeuratPro~ 51 26 0 A +#> 8 TACGCCACTCC~ SeuratPro~ 99 45 0 A +#> 9 GTAAGCACTCA~ SeuratPro~ 67 33 0 A +#> 10 TACATCACGCT~ SeuratPro~ 109 41 0 A +#> # i 70 more rows +#> # i 11 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>, #> # groups <chr>, PC_1 <dbl>, PC_2 <dbl>, PC_3 <dbl>, PC_4 <dbl>, PC_5 <dbl>, #> # tSNE_1 <dbl>, tSNE_2 <dbl>