diff --git a/README.Rmd b/README.Rmd index 89fedb7..a9aff10 100644 --- a/README.Rmd +++ b/README.Rmd @@ -53,13 +53,8 @@ Installation should take less than three minutes. 1. Installation of `leidenAlg` has non-zero exit status -- Refer to the [package website](https://github.com/kharchenkolab/leidenAlg#installation) for -*leidenAlg* installation details. Otherwise, users may also install a separate branch -of *Banksy* with - -```{r, eval=F} -remotes::install_github("prabhakarlab/Banksy@feat-igraph-leiden") -``` +- Refer to the [`leidenAlg` package website](https://github.com/kharchenkolab/leidenAlg#installation) for +installation details. ## Documentation @@ -90,10 +85,11 @@ usage, along with several vignettes which detail different use cases: *Banksy* is also interoperable with [Seurat](https://satijalab.org/seurat/) via *SeuratWrappers*. Documentation on how to run BANKSY on Seurat objects can be -found [here](https://github.com/satijalab/seurat-wrappers/blob/master/docs/banksy.md). -For installation of *SeuratWrappers* with the latest BANKSY version, run +found [here](https://github.com/jleechung/seurat-wrappers/blob/feat-aft/docs/banksy.md). +For installation of *SeuratWrappers* with BANKSY version `>= 0.1.4`, run + ```{r, eval=F} -remotes::install_github('jleechung/seurat-wrappers') +remotes::install_github('jleechung/seurat-wrappers@feat-aft') ``` ## Quick start diff --git a/README.md b/README.md index 6a72363..a55024d 100644 --- a/README.md +++ b/README.md @@ -45,14 +45,9 @@ Installation should take less than three minutes. 1. Installation of `leidenAlg` has non-zero exit status -- Refer to the [package +- Refer to the [`leidenAlg` package website](https://github.com/kharchenkolab/leidenAlg#installation) - for *leidenAlg* installation details. Otherwise, users may also - install a separate branch of *Banksy* with - -``` r -remotes::install_github("prabhakarlab/Banksy@feat-igraph-leiden") -``` + for installation details. ## Documentation @@ -95,11 +90,11 @@ detail different use cases: *Banksy* is also interoperable with [Seurat](https://satijalab.org/seurat/) via *SeuratWrappers*. Documentation on how to run BANKSY on Seurat objects can be found -[here](https://github.com/satijalab/seurat-wrappers/blob/master/docs/banksy.md). -For installation of *SeuratWrappers* with the latest BANKSY version, run +[here](https://github.com/jleechung/seurat-wrappers/blob/feat-aft/docs/banksy.md). +For installation of *SeuratWrappers* with BANKSY version `>= 0.1.4`, run ``` r -remotes::install_github('jleechung/seurat-wrappers') +remotes::install_github('jleechung/seurat-wrappers@feat-aft') ``` ## Quick start @@ -252,7 +247,7 @@ plotSpatialFeatures(bank, by = features, type = feature.types, main = main, pt.size = 1.5, main.size = 15, nrow = 1, ncol = 2) ``` - + For clarity, we can visualise each of the clusters separately with `wrap = TRUE`: @@ -263,14 +258,14 @@ plotSpatialFeatures(bank, by = features, type = feature.types, main = main, wrap = TRUE) ``` - +
Runtime for analysis - #> Time difference of 1.918232 mins + #> Time difference of 38.77595 secs
@@ -295,7 +290,7 @@ sessionInfo() #> [1] stats graphics grDevices utils datasets methods base #> #> other attached packages: -#> [1] Banksy_0.1.4 +#> [1] Banksy_0.1.5 #> #> loaded via a namespace (and not attached): #> [1] bitops_1.0-7 matrixStats_0.62.0 @@ -316,7 +311,7 @@ sessionInfo() #> [31] dichromat_2.0-0.1 pkgconfig_2.0.3 #> [33] htmltools_0.5.4 MatrixGenerics_1.10.0 #> [35] highr_0.10 fastmap_1.1.0 -#> [37] maps_3.4.1 rlang_1.0.6 +#> [37] maps_3.4.1 rlang_1.1.1 #> [39] GlobalOptions_0.1.2 pals_1.7 #> [41] rstudioapi_0.14 farver_2.1.1 #> [43] shape_1.4.6 generics_0.1.3 @@ -326,7 +321,7 @@ sessionInfo() #> [51] Rcpp_1.0.9 munsell_0.5.0 #> [53] S4Vectors_0.36.0 fansi_1.0.3 #> [55] lifecycle_1.0.3 stringi_1.7.8 -#> [57] leidenAlg_1.0.5 yaml_2.3.6 +#> [57] leidenAlg_1.1.0 yaml_2.3.6 #> [59] ggalluvial_0.12.3 SummarizedExperiment_1.28.0 #> [61] zlibbioc_1.44.0 plyr_1.8.8 #> [63] grid_4.2.1 parallel_4.2.1 diff --git a/docs/articles/banksy-object.html b/docs/articles/banksy-object.html index 40d7bf6..7c07111 100644 --- a/docs/articles/banksy-object.html +++ b/docs/articles/banksy-object.html @@ -325,7 +325,7 @@

Session information#> [39] dichromat_2.0-0.1 pkgconfig_2.0.3 #> [41] htmltools_0.5.4 MatrixGenerics_1.10.0 #> [43] highr_0.10 maps_3.4.1 -#> [45] fastmap_1.1.0 rlang_1.0.6 +#> [45] fastmap_1.1.0 rlang_1.1.1 #> [47] GlobalOptions_0.1.2 pals_1.7 #> [49] rstudioapi_0.14 farver_2.1.1 #> [51] shape_1.4.6 jquerylib_0.1.4 @@ -335,7 +335,7 @@

Session information#> [59] GenomeInfoDbData_1.2.9 Matrix_1.5-3 #> [61] Rcpp_1.0.9 munsell_0.5.0 #> [63] S4Vectors_0.36.0 fansi_1.0.3 -#> [65] lifecycle_1.0.3 leidenAlg_1.0.5 +#> [65] lifecycle_1.0.3 leidenAlg_1.1.0 #> [67] stringi_1.7.8 yaml_2.3.6 #> [69] ggalluvial_0.12.3 SummarizedExperiment_1.28.0 #> [71] zlibbioc_1.44.0 plyr_1.8.8 diff --git a/docs/articles/banksy-object_files/figure-html/subset3-1.png b/docs/articles/banksy-object_files/figure-html/subset3-1.png index a5776a6..2c09571 100644 Binary files a/docs/articles/banksy-object_files/figure-html/subset3-1.png and b/docs/articles/banksy-object_files/figure-html/subset3-1.png differ diff --git a/docs/articles/dlpfc-analysis.html b/docs/articles/dlpfc-analysis.html index c5a201e..00b93da 100644 --- a/docs/articles/dlpfc-analysis.html +++ b/docs/articles/dlpfc-analysis.html @@ -320,7 +320,7 @@

Session information## [39] pkgconfig_2.0.3 htmltools_0.5.4 ## [41] MatrixGenerics_1.10.0 highr_0.10 ## [43] maps_3.4.1 fastmap_1.1.0 -## [45] rlang_1.0.6 GlobalOptions_0.1.2 +## [45] rlang_1.1.1 GlobalOptions_0.1.2 ## [47] pals_1.7 rstudioapi_0.14 ## [49] farver_2.1.1 shape_1.4.6 ## [51] jquerylib_0.1.4 generics_0.1.3 @@ -330,7 +330,7 @@

Session information## [59] Matrix_1.5-3 Rcpp_1.0.9 ## [61] munsell_0.5.0 S4Vectors_0.36.0 ## [63] fansi_1.0.3 lifecycle_1.0.3 -## [65] leidenAlg_1.0.5 stringi_1.7.8 +## [65] leidenAlg_1.1.0 stringi_1.7.8 ## [67] yaml_2.3.6 ggalluvial_0.12.3 ## [69] SummarizedExperiment_1.28.0 zlibbioc_1.44.0 ## [71] grid_4.2.1 parallel_4.2.1 diff --git a/docs/articles/hippocampus-analysis.html b/docs/articles/hippocampus-analysis.html index d0eb157..90e8bb6 100644 --- a/docs/articles/hippocampus-analysis.html +++ b/docs/articles/hippocampus-analysis.html @@ -195,19 +195,19 @@

Connecting clustershead(meta.data(bank)) #> cell_ID nCount NODG clust_M1_lam0_k50_res0.8 -#> cell_1276 cell_1276 266 51 13 +#> cell_1276 cell_1276 266 51 12 #> cell_691 cell_691 132 36 7 #> cell_396 cell_396 95 27 5 -#> cell_68 cell_68 579 72 13 +#> cell_68 cell_68 579 72 12 #> cell_6954 cell_6954 116 29 8 #> cell_7074 cell_7074 28 17 6 #> clust_M1_lam0_k50_res1.2 clust_M1_lam0.2_k50_res0.8 -#> cell_1276 13 17 +#> cell_1276 12 16 #> cell_691 7 7 -#> cell_396 4 17 -#> cell_68 13 17 +#> cell_396 9 16 +#> cell_68 12 16 #> cell_6954 8 8 #> cell_7074 6 6 #> clust_M1_lam0.2_k50_res1.2 -#> cell_1276 17 +#> cell_1276 16 #> cell_691 7 -#> cell_396 4 -#> cell_68 17 +#> cell_396 9 +#> cell_68 16 #> cell_6954 8 -#> cell_7074 4 +#> cell_7074 6

This updates the meta.data slot with new cluster labels that can be used for visualisation. We can visualise connected output as follows.

@@ -345,7 +345,7 @@

Session information#> [39] pkgconfig_2.0.3 htmltools_0.5.4 #> [41] MatrixGenerics_1.10.0 highr_0.10 #> [43] maps_3.4.1 fastmap_1.1.0 -#> [45] rlang_1.0.6 GlobalOptions_0.1.2 +#> [45] rlang_1.1.1 GlobalOptions_0.1.2 #> [47] pals_1.7 rstudioapi_0.14 #> [49] farver_2.1.1 shape_1.4.6 #> [51] jquerylib_0.1.4 generics_0.1.3 @@ -355,7 +355,7 @@

Session information#> [59] Matrix_1.5-3 Rcpp_1.0.9 #> [61] munsell_0.5.0 S4Vectors_0.36.0 #> [63] fansi_1.0.3 lifecycle_1.0.3 -#> [65] leidenAlg_1.0.5 stringi_1.7.8 +#> [65] leidenAlg_1.1.0 stringi_1.7.8 #> [67] yaml_2.3.6 ggalluvial_0.12.3 #> [69] SummarizedExperiment_1.28.0 zlibbioc_1.44.0 #> [71] plyr_1.8.8 grid_4.2.1 diff --git a/docs/articles/hippocampus-analysis_files/figure-html/alluv-1.png b/docs/articles/hippocampus-analysis_files/figure-html/alluv-1.png index df4f9a4..7d7e069 100644 Binary files a/docs/articles/hippocampus-analysis_files/figure-html/alluv-1.png and b/docs/articles/hippocampus-analysis_files/figure-html/alluv-1.png differ diff --git a/docs/articles/hippocampus-analysis_files/figure-html/out-1.png b/docs/articles/hippocampus-analysis_files/figure-html/out-1.png index a8ac186..0370a5f 100644 Binary files a/docs/articles/hippocampus-analysis_files/figure-html/out-1.png and b/docs/articles/hippocampus-analysis_files/figure-html/out-1.png differ diff --git a/docs/articles/hippocampus-analysis_files/figure-html/runari-1.png b/docs/articles/hippocampus-analysis_files/figure-html/runari-1.png index 6a15e56..c4eb996 100644 Binary files a/docs/articles/hippocampus-analysis_files/figure-html/runari-1.png and b/docs/articles/hippocampus-analysis_files/figure-html/runari-1.png differ diff --git a/docs/articles/hippocampus-analysis_files/figure-html/wrap-1.png b/docs/articles/hippocampus-analysis_files/figure-html/wrap-1.png index b4b7740..755f32d 100644 Binary files a/docs/articles/hippocampus-analysis_files/figure-html/wrap-1.png and b/docs/articles/hippocampus-analysis_files/figure-html/wrap-1.png differ diff --git a/docs/articles/hypothalamus-analysis.html b/docs/articles/hypothalamus-analysis.html index ebcf1cc..2be3b9d 100644 --- a/docs/articles/hypothalamus-analysis.html +++ b/docs/articles/hypothalamus-analysis.html @@ -163,13 +163,13 @@

Spatial plots#> Done #> Computing neighbors... #> Spatial mode is kNN median -#> Parameters: k_geom = 30 +#> Parameters: k_geom = 15 #> Done #> Computing harmonic m = 0 #> Using 15 neighbors #> Done #> Computing harmonic m = 1 -#> Using 30 neighbors +#> Using 15 neighbors #> Centering #> Done bank <- ScaleBanksy(bank) @@ -314,7 +314,7 @@

Session information#> [41] dichromat_2.0-0.1 pkgconfig_2.0.3 #> [43] htmltools_0.5.4 MatrixGenerics_1.10.0 #> [45] highr_0.10 maps_3.4.1 -#> [47] fastmap_1.1.0 rlang_1.0.6 +#> [47] fastmap_1.1.0 rlang_1.1.1 #> [49] GlobalOptions_0.1.2 pals_1.7 #> [51] rstudioapi_0.14 farver_2.1.1 #> [53] shape_1.4.6 jquerylib_0.1.4 @@ -324,7 +324,7 @@

Session information#> [61] GenomeInfoDbData_1.2.9 Matrix_1.5-3 #> [63] Rcpp_1.0.9 munsell_0.5.0 #> [65] S4Vectors_0.36.0 fansi_1.0.3 -#> [67] lifecycle_1.0.3 leidenAlg_1.0.5 +#> [67] lifecycle_1.0.3 leidenAlg_1.1.0 #> [69] stringi_1.7.8 yaml_2.3.6 #> [71] ggalluvial_0.12.3 SummarizedExperiment_1.28.0 #> [73] zlibbioc_1.44.0 plyr_1.8.8 diff --git a/docs/articles/hypothalamus-analysis_files/figure-html/cluster-1.png b/docs/articles/hypothalamus-analysis_files/figure-html/cluster-1.png index 029499c..c5cd3ed 100644 Binary files a/docs/articles/hypothalamus-analysis_files/figure-html/cluster-1.png and b/docs/articles/hypothalamus-analysis_files/figure-html/cluster-1.png differ diff --git a/docs/articles/hypothalamus-analysis_files/figure-html/heatmap-1.png b/docs/articles/hypothalamus-analysis_files/figure-html/heatmap-1.png index 470f331..26e03c8 100644 Binary files a/docs/articles/hypothalamus-analysis_files/figure-html/heatmap-1.png and b/docs/articles/hypothalamus-analysis_files/figure-html/heatmap-1.png differ diff --git a/docs/articles/hypothalamus-analysis_files/figure-html/pca-1.png b/docs/articles/hypothalamus-analysis_files/figure-html/pca-1.png index a974555..477df4e 100644 Binary files a/docs/articles/hypothalamus-analysis_files/figure-html/pca-1.png and b/docs/articles/hypothalamus-analysis_files/figure-html/pca-1.png differ diff --git a/docs/articles/hypothalamus-analysis_files/figure-html/pca-2.png b/docs/articles/hypothalamus-analysis_files/figure-html/pca-2.png index 76a3232..cc38e66 100644 Binary files a/docs/articles/hypothalamus-analysis_files/figure-html/pca-2.png and b/docs/articles/hypothalamus-analysis_files/figure-html/pca-2.png differ diff --git a/docs/articles/single-cell-exp.html b/docs/articles/single-cell-exp.html index 0240e12..2ae29de 100644 --- a/docs/articles/single-cell-exp.html +++ b/docs/articles/single-cell-exp.html @@ -146,13 +146,13 @@

Running BANKSY#> Done #> Computing neighbors... #> Spatial mode is kNN median -#> Parameters: k_geom = 30 +#> Parameters: k_geom = 15 #> Done #> Computing harmonic m = 0 #> Using 15 neighbors #> Done #> Computing harmonic m = 1 -#> Using 30 neighbors +#> Using 15 neighbors #> Centering #> Done bank <- ScaleBanksy(bank) @@ -264,7 +264,7 @@

Session information#> [31] glue_1.6.2 pals_1.7 #> [33] gtable_0.3.1 zlibbioc_1.44.0 #> [35] XVector_0.38.0 GetoptLong_1.0.5 -#> [37] DelayedArray_0.24.0 leidenAlg_1.0.5 +#> [37] DelayedArray_0.24.0 leidenAlg_1.1.0 #> [39] BiocSingular_1.14.0 shape_1.4.6 #> [41] maps_3.4.1 scales_1.2.1 #> [43] DBI_1.1.3 edgeR_3.40.1 @@ -277,7 +277,7 @@

Session information#> [57] farver_2.1.1 sass_0.4.4 #> [59] uwot_0.1.14 locfit_1.5-9.6 #> [61] utf8_1.2.2 tidyselect_1.2.0 -#> [63] labeling_0.4.2 rlang_1.0.6 +#> [63] labeling_0.4.2 rlang_1.1.1 #> [65] munsell_0.5.0 tools_4.2.1 #> [67] cachem_1.0.6 cli_3.4.1 #> [69] dbscan_1.1-11 generics_0.1.3 diff --git a/docs/articles/single-cell-exp_files/figure-html/unnamed-chunk-5-1.png b/docs/articles/single-cell-exp_files/figure-html/unnamed-chunk-5-1.png index 60ecc9d..535806f 100644 Binary files a/docs/articles/single-cell-exp_files/figure-html/unnamed-chunk-5-1.png and b/docs/articles/single-cell-exp_files/figure-html/unnamed-chunk-5-1.png differ diff --git a/docs/articles/single-cell-exp_files/figure-html/unnamed-chunk-5-2.png b/docs/articles/single-cell-exp_files/figure-html/unnamed-chunk-5-2.png index a574f20..ed6fa96 100644 Binary files a/docs/articles/single-cell-exp_files/figure-html/unnamed-chunk-5-2.png and b/docs/articles/single-cell-exp_files/figure-html/unnamed-chunk-5-2.png differ diff --git a/docs/index.html b/docs/index.html index bcf4f24..efd75a5 100644 --- a/docs/index.html +++ b/docs/index.html @@ -125,10 +125,8 @@

Installationpackage website for leidenAlg installation details. Otherwise, users may also install a separate branch of Banksy with +
  • Refer to the leidenAlg package website for installation details.
    • -
    -remotes::install_github("prabhakarlab/Banksy@feat-igraph-leiden")

    Documentation @@ -142,22 +140,22 @@

    DocumentationMouse hypothalamus MERFISH dataset: Illustrates visualization functionality with a dataset with 3 spatial dimensions.

  • Interoperability with SingleCellExperiment: Illustrates BANKSY interoperability with Bioconductor SingleCellExperiment framework for interfacing with packages like scran or scater.

    • -

    Banksy is also interoperable with Seurat via SeuratWrappers. Documentation on how to run BANKSY on Seurat objects can be found here. For installation of SeuratWrappers with the latest BANKSY version, run

    -
    -remotes::install_github('jleechung/seurat-wrappers')
    +

    Banksy is also interoperable with Seurat via SeuratWrappers. Documentation on how to run BANKSY on Seurat objects can be found here. For installation of SeuratWrappers with BANKSY version >= 0.1.4, run

    +
    +remotes::install_github('jleechung/seurat-wrappers@feat-aft')

    Quick start

    Banksy takes as input an expression matrix and cell centroids. Example datasets are provided with the package:

    -
    +
     library(Banksy)
 
 data(hippocampus)
 expr <- hippocampus$expression
 locs <- hippocampus$locations
    
 
    The gene expression matrix for cells should be a matrix:
    
-
    +
     class(expr)
 #> [1] "matrix" "array"
 head(expr[,1:5])
@@ -169,7 +167,7 @@ 
    Quick start#> Atp1a2          0         0        4        3         0
 #> Tnc             0         0        0        0         0
    
 
    while cell locations should be supplied as a data.frame:
    
-
    +
     class(locs)
 #> [1] "data.frame"
 head(locs)
@@ -181,7 +179,7 @@ 
    Quick start#> cell_9818   11308.101 15846.37
 #> cell_11310  14894.101 15810.37
    
 
    Next, create a BanksyObject with the expression matrix and cell locations.
    
-
    +
     bank <- BanksyObject(own.expr = expr,
                      cell.locs = locs)
 
@@ -213,11 +211,11 @@ 
    Quick start#> cell_396   cell_396     95   27
 #> cell_9818 cell_9818     10    5
    
 
    Apply basic QC by keeping only cells with total counts within the 5th and 98th percentile:
    
-
    +
     bank <- SubsetBanksy(bank, metadata = nCount > quantile(nCount, 0.05) &
                                       nCount < quantile(nCount, 0.98))
    
 
    We first normalize the expression matrix, compute the neighbor matrix, and scale the resulting matrices.
    
-
    +
     bank <- NormalizeBanksy(bank)
 bank <- ComputeBanksy(bank, k_geom = c(15, 30))
 #> Computing neighbors...
@@ -237,7 +235,7 @@ 
    Quick start#> Done
 bank <- ScaleBanksy(bank)
    
 
    Run PCA on the BANKSY matrix for lambda=0 (no spatial information) and lambda=0.2.
    
-
    +
     bank <- RunBanksyPCA(bank, lambda = c(0, 0.2))
 #> Running PCA for M=1 lambda=0
 #> BANKSY matrix with own.expr, F0, F1
@@ -246,33 +244,33 @@ 
    Quick start#> BANKSY matrix with own.expr, F0, F1
 #> Squared lambdas: 0.8, 0.1333, 0.0667
    
 
    Next, we obtain cluster assignments using graph-based clustering with the Leiden algorithm on the first 20 PCs.
    
-
    +
     set.seed(42)
 bank <- ClusterBanksy(bank, lambda = c(0, 0.2), pca = TRUE, npcs = 20,
                       method = 'leiden', resolution = 1.2)
    
 
    Different clustering runs can be harmonised with ConnectClusters:
    
-
    +
     bank <- ConnectClusters(bank, map.to = clust.names(bank)[1])
    
 
    Visualise the clustering output for non-spatial clustering (lambda=0) and BANKSY clustering (lambda=0.2).
    
-
    +
     features <- clust.names(bank)
 feature.types <- rep('discrete', 2)
 main <- c('Non-spatial', 'BANKSY')
 plotSpatialFeatures(bank, by = features, type = feature.types, main = main, 
                     pt.size = 1.5, main.size = 15, nrow = 1, ncol = 2)
    
-
    
+
    
 
    For clarity, we can visualise each of the clusters separately with wrap = TRUE:
    
-
    +
     plotSpatialFeatures(bank, by = features, type = feature.types, main = main, 
                     pt.size = 1, main.size = 15, nrow = 1, ncol = 2, 
                     wrap = TRUE)
    
-
    
+
    
 
    
 Runtime for analysis
-
    #> Time difference of 1.918232 mins
    
+
    #> Time difference of 38.77595 secs
    
 
    
 Session information
-
    +
     sessionInfo()
 #> R version 4.2.1 (2022-06-23 ucrt)
 #> Platform: x86_64-w64-mingw32/x64 (64-bit)
@@ -289,7 +287,7 @@ 
    Quick start#> [1] stats     graphics  grDevices utils     datasets  methods   base     
 #> 
 #> other attached packages:
-#> [1] Banksy_0.1.4
+#> [1] Banksy_0.1.5
 #> 
 #> loaded via a namespace (and not attached):
 #>  [1] bitops_1.0-7                matrixStats_0.62.0         
@@ -310,7 +308,7 @@ 
    Quick start#> [31] dichromat_2.0-0.1           pkgconfig_2.0.3            
 #> [33] htmltools_0.5.4             MatrixGenerics_1.10.0      
 #> [35] highr_0.10                  fastmap_1.1.0              
-#> [37] maps_3.4.1                  rlang_1.0.6                
+#> [37] maps_3.4.1                  rlang_1.1.1                
 #> [39] GlobalOptions_0.1.2         pals_1.7                   
 #> [41] rstudioapi_0.14             farver_2.1.1               
 #> [43] shape_1.4.6                 generics_0.1.3             
@@ -320,7 +318,7 @@ 
    Quick start#> [51] Rcpp_1.0.9                  munsell_0.5.0              
 #> [53] S4Vectors_0.36.0            fansi_1.0.3                
 #> [55] lifecycle_1.0.3             stringi_1.7.8              
-#> [57] leidenAlg_1.0.5             yaml_2.3.6                 
+#> [57] leidenAlg_1.1.0             yaml_2.3.6                 
 #> [59] ggalluvial_0.12.3           SummarizedExperiment_1.28.0
 #> [61] zlibbioc_1.44.0             plyr_1.8.8                 
 #> [63] grid_4.2.1                  parallel_4.2.1             
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index f6dcb8a..df8cbf9 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -7,7 +7,7 @@ articles:
   hippocampus-analysis: hippocampus-analysis.html
   hypothalamus-analysis: hypothalamus-analysis.html
   single-cell-exp: single-cell-exp.html
-last_built: 2023-06-06T09:28Z
+last_built: 2023-08-01T17:42Z
 urls:
   reference: https://prabhakarlab.github.io/Banksy/reference
   article: https://prabhakarlab.github.io/Banksy/articles
diff --git a/docs/reference/ClusterBanksy.html b/docs/reference/ClusterBanksy.html
index f9d756a..36b4534 100644
--- a/docs/reference/ClusterBanksy.html
+++ b/docs/reference/ClusterBanksy.html
@@ -171,13 +171,13 @@ 
    Examples
    
 #> Done
 #> Computing neighbors...
 #> Spatial mode is kNN median
-#> Parameters: k_geom = 30
+#> Parameters: k_geom = 15
 #> Done
 #> Computing harmonic m = 0
 #> Using 15 neighbors
 #> Done
 #> Computing harmonic m = 1
-#> Using 30 neighbors
+#> Using 15 neighbors
 #> Centering
 #> Done
 bank <-     ScaleBanksy(bank)
diff --git a/docs/reference/ComputeBanksy.html b/docs/reference/ComputeBanksy.html
index c6d8e56..03bb2c0 100644
--- a/docs/reference/ComputeBanksy.html
+++ b/docs/reference/ComputeBanksy.html
@@ -165,13 +165,13 @@ 
    Examples
    
 #> Done
 #> Computing neighbors...
 #> Spatial mode is kNN median
-#> Parameters: k_geom = 30
+#> Parameters: k_geom = 15
 #> Done
 #> Computing harmonic m = 0
 #> Using 15 neighbors
 #> Done
 #> Computing harmonic m = 1
-#> Using 30 neighbors
+#> Using 15 neighbors
 #> Centering
 #> Done
 
diff --git a/docs/reference/ConnectClusters.html b/docs/reference/ConnectClusters.html
index baacf8d..1e3b8b3 100644
--- a/docs/reference/ConnectClusters.html
+++ b/docs/reference/ConnectClusters.html
@@ -109,13 +109,13 @@ 
    Examples
    
 #> Done
 #> Computing neighbors...
 #> Spatial mode is kNN median
-#> Parameters: k_geom = 30
+#> Parameters: k_geom = 15
 #> Done
 #> Computing harmonic m = 0
 #> Using 15 neighbors
 #> Done
 #> Computing harmonic m = 1
-#> Using 30 neighbors
+#> Using 15 neighbors
 #> Centering
 #> Done
 bank <- RunBanksyPCA(bank, lambda = 0.2)
diff --git a/docs/reference/Rplot002.png b/docs/reference/Rplot002.png
index 019757a..8595e3e 100644
Binary files a/docs/reference/Rplot002.png and b/docs/reference/Rplot002.png differ
diff --git a/docs/reference/RunBanksyPCA.html b/docs/reference/RunBanksyPCA.html
index d688d00..ae8457d 100644
--- a/docs/reference/RunBanksyPCA.html
+++ b/docs/reference/RunBanksyPCA.html
@@ -121,13 +121,13 @@ 
    Examples
    
 #> Done
 #> Computing neighbors...
 #> Spatial mode is kNN median
-#> Parameters: k_geom = 30
+#> Parameters: k_geom = 15
 #> Done
 #> Computing harmonic m = 0
 #> Using 15 neighbors
 #> Done
 #> Computing harmonic m = 1
-#> Using 30 neighbors
+#> Using 15 neighbors
 #> Centering
 #> Done
 bank <- RunBanksyPCA(bank, lambda = 0.2)
diff --git a/docs/reference/RunBanksyUMAP.html b/docs/reference/RunBanksyUMAP.html
index d47aa1b..2f2b069 100644
--- a/docs/reference/RunBanksyUMAP.html
+++ b/docs/reference/RunBanksyUMAP.html
@@ -162,13 +162,13 @@ 
    Examples
    
 #> Done
 #> Computing neighbors...
 #> Spatial mode is kNN median
-#> Parameters: k_geom = 30
+#> Parameters: k_geom = 15
 #> Done
 #> Computing harmonic m = 0
 #> Using 15 neighbors
 #> Done
 #> Computing harmonic m = 1
-#> Using 30 neighbors
+#> Using 15 neighbors
 #> Centering
 #> Done
 bank <- RunBanksyPCA(bank, lambda = 0.2)
diff --git a/docs/reference/figures/README-unnamed-chunk-14-1.png b/docs/reference/figures/README-unnamed-chunk-14-1.png
index 5c3844a..5e34dcd 100644
Binary files a/docs/reference/figures/README-unnamed-chunk-14-1.png and b/docs/reference/figures/README-unnamed-chunk-14-1.png differ
diff --git a/docs/reference/figures/README-unnamed-chunk-15-1.png b/docs/reference/figures/README-unnamed-chunk-15-1.png
index 0dd01a6..944ca20 100644
Binary files a/docs/reference/figures/README-unnamed-chunk-15-1.png and b/docs/reference/figures/README-unnamed-chunk-15-1.png differ
diff --git a/docs/reference/figures/README-unnamed-chunk-16-1.png b/docs/reference/figures/README-unnamed-chunk-16-1.png
index 9371f01..ac8843a 100644
Binary files a/docs/reference/figures/README-unnamed-chunk-16-1.png and b/docs/reference/figures/README-unnamed-chunk-16-1.png differ
diff --git a/docs/reference/getARI.html b/docs/reference/getARI.html
index b533c01..2e05902 100644
--- a/docs/reference/getARI.html
+++ b/docs/reference/getARI.html
@@ -109,13 +109,13 @@ 
    Examples
    
 #> Done
 #> Computing neighbors...
 #> Spatial mode is kNN median
-#> Parameters: k_geom = 30
+#> Parameters: k_geom = 15
 #> Done
 #> Computing harmonic m = 0
 #> Using 15 neighbors
 #> Done
 #> Computing harmonic m = 1
-#> Using 30 neighbors
+#> Using 15 neighbors
 #> Centering
 #> Done
 bank <- RunBanksyPCA(bank, lambda = 0.2)
@@ -127,9 +127,9 @@ 
    Examples
    
 ari
 #>                            clust_M1_lam0.2_k50_res0.5
 #> clust_M1_lam0.2_k50_res0.5                      1.000
-#> clust_M1_lam0.2_k50_res1.5                      0.245
+#> clust_M1_lam0.2_k50_res1.5                      0.259
 #>                            clust_M1_lam0.2_k50_res1.5
-#> clust_M1_lam0.2_k50_res0.5                      0.245
+#> clust_M1_lam0.2_k50_res0.5                      0.259
 #> clust_M1_lam0.2_k50_res1.5                      1.000
 
 
    
diff --git a/docs/reference/getBanksyMatrix.html b/docs/reference/getBanksyMatrix.html
index 16044c4..e0ac3e5 100644
--- a/docs/reference/getBanksyMatrix.html
+++ b/docs/reference/getBanksyMatrix.html
@@ -114,13 +114,13 @@ 
    Examples
    
 #> Done
 #> Computing neighbors...
 #> Spatial mode is kNN median
-#> Parameters: k_geom = 30
+#> Parameters: k_geom = 15
 #> Done
 #> Computing harmonic m = 0
 #> Using 15 neighbors
 #> Done
 #> Computing harmonic m = 1
-#> Using 30 neighbors
+#> Using 15 neighbors
 #> Centering
 #> Done
 bm <- getBanksyMatrix(bank)
diff --git a/docs/reference/plotARI-1.png b/docs/reference/plotARI-1.png
index 89ebe97..44332d1 100644
Binary files a/docs/reference/plotARI-1.png and b/docs/reference/plotARI-1.png differ
diff --git a/docs/reference/plotARI.html b/docs/reference/plotARI.html
index 76ca58e..90140c6 100644
--- a/docs/reference/plotARI.html
+++ b/docs/reference/plotARI.html
@@ -121,13 +121,13 @@ 
    Examples
    
 #> Done
 #> Computing neighbors...
 #> Spatial mode is kNN median
-#> Parameters: k_geom = 30
+#> Parameters: k_geom = 15
 #> Done
 #> Computing harmonic m = 0
 #> Using 15 neighbors
 #> Done
 #> Computing harmonic m = 1
-#> Using 30 neighbors
+#> Using 15 neighbors
 #> Centering
 #> Done
 bank <- RunBanksyPCA(bank, lambda = 0.2)
diff --git a/docs/reference/plotAlluvia-1.png b/docs/reference/plotAlluvia-1.png
index 608dd5e..4102230 100644
Binary files a/docs/reference/plotAlluvia-1.png and b/docs/reference/plotAlluvia-1.png differ
diff --git a/docs/reference/plotAlluvia-2.png b/docs/reference/plotAlluvia-2.png
index b39aef9..a3507fc 100644
Binary files a/docs/reference/plotAlluvia-2.png and b/docs/reference/plotAlluvia-2.png differ
diff --git a/docs/reference/plotAlluvia.html b/docs/reference/plotAlluvia.html
index 95b6489..c3ea0a5 100644
--- a/docs/reference/plotAlluvia.html
+++ b/docs/reference/plotAlluvia.html
@@ -117,13 +117,13 @@ 
    Examples
    
 #> Done
 #> Computing neighbors...
 #> Spatial mode is kNN median
-#> Parameters: k_geom = 30
+#> Parameters: k_geom = 15
 #> Done
 #> Computing harmonic m = 0
 #> Using 15 neighbors
 #> Done
 #> Computing harmonic m = 1
-#> Using 30 neighbors
+#> Using 15 neighbors
 #> Centering
 #> Done
 bank <- RunBanksyPCA(bank, lambda = 0.2)
diff --git a/docs/reference/plotReduction-1.png b/docs/reference/plotReduction-1.png
index 0d06845..9fd772f 100644
Binary files a/docs/reference/plotReduction-1.png and b/docs/reference/plotReduction-1.png differ
diff --git a/docs/reference/plotReduction.html b/docs/reference/plotReduction.html
index 6aede87..064e946 100644
--- a/docs/reference/plotReduction.html
+++ b/docs/reference/plotReduction.html
@@ -187,13 +187,13 @@ 
    Examples
    
 #> Done
 #> Computing neighbors...
 #> Spatial mode is kNN median
-#> Parameters: k_geom = 30
+#> Parameters: k_geom = 15
 #> Done
 #> Computing harmonic m = 0
 #> Using 15 neighbors
 #> Done
 #> Computing harmonic m = 1
-#> Using 30 neighbors
+#> Using 15 neighbors
 #> Centering
 #> Done
 bank <- RunBanksyPCA(bank, lambda = 0.2)
diff --git a/docs/reference/plotScree-1.png b/docs/reference/plotScree-1.png
index bc5200b..59be990 100644
Binary files a/docs/reference/plotScree-1.png and b/docs/reference/plotScree-1.png differ
diff --git a/docs/reference/plotScree.html b/docs/reference/plotScree.html
index cf83e6c..d106570 100644
--- a/docs/reference/plotScree.html
+++ b/docs/reference/plotScree.html
@@ -113,13 +113,13 @@ 
    Examples
    
 #> Done
 #> Computing neighbors...
 #> Spatial mode is kNN median
-#> Parameters: k_geom = 30
+#> Parameters: k_geom = 15
 #> Done
 #> Computing harmonic m = 0
 #> Using 15 neighbors
 #> Done
 #> Computing harmonic m = 1
-#> Using 30 neighbors
+#> Using 15 neighbors
 #> Centering
 #> Done
 bank <- RunBanksyPCA(bank, lambda = 0.2)
diff --git a/docs/reference/plotSpatialFeatures.html b/docs/reference/plotSpatialFeatures.html
index 678080f..dde93d2 100644
--- a/docs/reference/plotSpatialFeatures.html
+++ b/docs/reference/plotSpatialFeatures.html
@@ -147,13 +147,13 @@ 
    Examples
    
 #> Done
 #> Computing neighbors...
 #> Spatial mode is kNN median
-#> Parameters: k_geom = 30
+#> Parameters: k_geom = 15
 #> Done
 #> Computing harmonic m = 0
 #> Using 15 neighbors
 #> Done
 #> Computing harmonic m = 1
-#> Using 30 neighbors
+#> Using 15 neighbors
 #> Centering
 #> Done
 bank <- RunBanksyPCA(bank, lambda = 0.2)
diff --git a/man/figures/README-unnamed-chunk-14-1.png b/man/figures/README-unnamed-chunk-14-1.png
index 5c3844a..5e34dcd 100644
Binary files a/man/figures/README-unnamed-chunk-14-1.png and b/man/figures/README-unnamed-chunk-14-1.png differ
diff --git a/man/figures/README-unnamed-chunk-15-1.png b/man/figures/README-unnamed-chunk-15-1.png
index 0dd01a6..944ca20 100644
Binary files a/man/figures/README-unnamed-chunk-15-1.png and b/man/figures/README-unnamed-chunk-15-1.png differ
diff --git a/man/figures/README-unnamed-chunk-16-1.png b/man/figures/README-unnamed-chunk-16-1.png
index 9371f01..ac8843a 100644
Binary files a/man/figures/README-unnamed-chunk-16-1.png and b/man/figures/README-unnamed-chunk-16-1.png differ