Approved v2.0.0 update.

Author: enblacar

CRAN-SUBMISSION

@@ -1,3 +1,3 @@
-Version: 1.1.2
-Date: 2023-01-17 13:07:52 UTC
-SHA: 466fe9e44f1ccda22062425774a4743a38045a40
+Version: 2.0.0
+Date: 2023-08-09 13:21:38 UTC
+SHA: aa0e071e38d4c36ab1357304b698d72ffac20e44

DESCRIPTION

@@ -1,81 +1,87 @@
-Package: SCpubr
 Type: Package
-Title: Generate Publication Ready Visualizations of Single Cell Transcriptomics Data
-Version: 2.0.0.9000
-Authors@R: person("Enrique", "Blanco-Carmona", email = "[email protected]", role = c("cre", "aut"), comment = c(ORCID = "0000-0002-1208-1691"))
-Description: A system that provides a streamlined way of generating publication ready plots for known Single-Cell transcriptomics data in a “publication ready” format. This is, the goal is to automatically generate plots with the highest quality possible, that can be used right away or with minimal modifications for a research article.
+Package: SCpubr
+Title: Generate Publication Ready Visualizations of Single Cell
+    Transcriptomics Data
+Version: 2.0.0
+Authors@R: 
+    person("Enrique", "Blanco-Carmona", , "[email protected]", role = c("cre", "aut"),
+           comment = c(ORCID = "0000-0002-1208-1691"))
+Description: A system that provides a streamlined way of generating
+    publication ready plots for known Single-Cell transcriptomics data in
+    a “publication ready” format. This is, the goal is to automatically
+    generate plots with the highest quality possible, that can be used
+    right away or with minimal modifications for a research article.
 License: GPL-3
-Encoding: UTF-8
-LazyData: true
-LazyDataCompression: xz
-Depends: R (>= 4.0.0)
-Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.1
-URL: https://github.com/enblacar/SCpubr/, https://enblacar.github.io/SCpubr-book/
+URL: https://github.com/enblacar/SCpubr/,
+    https://enblacar.github.io/SCpubr-book/
 BugReports: https://github.com/enblacar/SCpubr/issues/
+Depends: 
+    R (>= 4.0.0)
 Suggests:
+    AnnotationDbi,
     assertthat,
+    AUCell,
     circlize,
+    cli,
+    cluster,
+    clusterProfiler,
     colorspace,
-    covr,
     ComplexHeatmap,
+    covr,
+    decoupleR,
     dplyr (>= 1.1.0),
+    enrichplot,
+    forcats,
+    ggalluvial,
     ggbeeswarm,
     ggdist,
     ggExtra,
     ggh4x,
+    ggnewscale,
     ggplot2 (>= 3.4.0),
     ggplotify,
     ggrastr,
     ggrepel,
     ggridges,
     ggsignif,
     graphics,
+    infercnv,
+    knitr,
+    labeling,
     magrittr,
+    MASS,
+    Matrix,
     methods,
     Nebulosa,
+    org.Hs.eg.db,
     patchwork,
     pheatmap,
     plyr,
-    rlang,
-    scales,
-    scattermore,
-    Seurat,
-    SeuratObject,
-    tibble,
-    tidyr,
-    forcats,
-    infercnv,
-    knitr,
-    Matrix,
     purrr,
     qpdf,
+    RColorBrewer,
     rgdal,
     rjags,
+    rlang,
     rmarkdown,
+    scales,
+    scattermore,
+    Seurat,
+    SeuratObject,
     stringr,
     svglite,
-    ggalluvial,
     testthat (>= 3.0.0),
-    viridis,
+    tibble,
+    tidyr,
     UCell,
-    AUCell,
-    clusterProfiler,
-    enrichplot,
-    ggnewscale,
-    AnnotationDbi,
-    org.Hs.eg.db,
-    labeling,
-    MASS,
-    RColorBrewer,
-    cluster,
-    decoupleR,
-    cli,
-    withr,
-    liana (>= 0.1.6)
-VignetteBuilder: knitr
+    viridis,
+    withr
+VignetteBuilder: 
+    knitr
+biocViews: Software, SingleCell, Visualization
 Config/testthat/edition: 3
-biocViews: 
-    Software, SingleCell, Visualization
-Remotes: 
-    saezlab/liana
+Encoding: UTF-8
+LazyData: true
+LazyDataCompression: xz
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.2.1

NAMESPACE

@@ -1,7 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
 export(check_dependencies)
-export(do_AffinityAnalysisPlot)
 export(do_AlluvialPlot)
 export(do_BarPlot)
 export(do_BeeSwarmPlot)
@@ -11,7 +10,6 @@ export(do_ChordDiagramPlot)
 export(do_ColorPalette)
 export(do_CopyNumberVariantPlot)
 export(do_CorrelationPlot)
-export(do_DiffusionMapPlot)
 export(do_DimPlot)
 export(do_DotPlot)
 export(do_EnrichmentHeatmap)
@@ -21,17 +19,11 @@ export(do_FunctionalAnnotationPlot)
 export(do_GeyserPlot)
 export(do_GroupedGOTermPlot)
 export(do_GroupwiseDEPlot)
-export(do_LigandReceptorPlot)
-export(do_LoadingsPlot)
-export(do_MetadataPlot)
 export(do_NebulosaPlot)
 export(do_PathwayActivityPlot)
 export(do_RidgePlot)
-export(do_SCEnrichmentHeatmap)
-export(do_SCExpressionHeatmap)
 export(do_TFActivityPlot)
 export(do_TermEnrichmentPlot)
 export(do_ViolinPlot)
 export(do_VolcanoPlot)
 export(package_report)
-export(save_Plot)

NEWS.md

@@ -19,7 +19,7 @@ Many (except a few selected cases) of the functions that returned list of differ
 -   `SCpubr::do_MetadataPlot()` to generate metadata heatmaps with ease both from Seurat object or from a data frame. Will be first released as part of the `development version` and then released in CRAN as part of future updates. The idea is to gather feedback from users before officially releasing it.
 -   `SCpubr::do_SCExpressionHeatmap()` to generate heatmaps of expression of genes across all cells in the dataset. Will be first released as part of the `development version` and then released in CRAN as part of future updates. The idea is to gather feedback from users before officially releasing it.
 -   `SCpubr::do_SCEnrichementHeatmap()` to generate heatmaps of enrichment of genes across all cells in the dataset. Will be first released as part of the `development version` and then released in CRAN as part of future updates. The idea is to gather feedback from users before officially releasing it.
--   `SCpubr::do_AffinityAnalysisPlot()` to assess the affinity of gene sets to subset of cells in the Seurat objects using the weighted means algorithms from [DecoupleR](https://saezlab.github.io/decoupleR/). Will be first released as part of the `development version` and then released in CRAN as part of future updates. The idea is to gather feedback from users before officially releasing it.
+-   `SCpubr::do_AffinityAnalysisPlot()` to assess the affinity of gene sets to subset of cells in the Seurat objects using the weighted means algorithms from DecoupleR. Will be first released as part of the `development version` and then released in CRAN as part of future updates. The idea is to gather feedback from users before officially releasing it.
 -   `SCpubr::do_LoadingsPlot()` to generate a summary heatmap of the PCA loadings (top and bottom scored genes for each PC) together with a expression heatmap of the same genes. Will be first released as part of the `development version` and then released in CRAN as part of future updates. The idea is to gather feedback from users before officially releasing it.
 -   `SCpubr::do_DiffusionMapPlot()` to analyze the output of a diffusion map analysis on the context of enrichment in gene sets used for the generation of the diffusion map. Will be first released as part of the `development version` and then released in CRAN as part of future updates. The idea is to gather feedback from users before officially releasing it.
 -   `SCpubr::check_dependencies()` to generate a per-function summary of the needed packages to run the function. The report has been enhanced with `cli` package and now clearly illustrates what is missing to run the function.