Merge branch 'release/v2.1.0' into main

Author: dputhier

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: scigenex
 Type: Package
 Title: The scigenex package (Single-Cell Informative GENe Explorer)
-Version: 2.0.14
+Version: 2.1.0
 Date: 2020-07-22
 Author: J. Bavais, Sebastien Nin, Lionel Spinelli and Denis Puthier
 Maintainer: J. Bavais <julie.bavais@yahoo.fr>

Makefile

@@ -1,5 +1,5 @@
 MAKEFILE=Makefile
-VERSION=2.0.14
+VERSION=2.1.0
 
 .PHONY: help
 

R/gm_report.R

@@ -41,6 +41,7 @@
 #' Reduce this number if you have a large dataset (e.g. > 10000 cells/spots). Otherwise the dataset will be too large to be handled by the web browser.
 #' @param plot_heatmap_params Some parameters for plot_heatmap() function.
 #' @param cnetplot_params Some parameters for enrichplot:::cnetplot.enrichResult() function.
+#' @param vlnPlot_params The parameters for Seurat::VlnPlot().
 #' @param rm_tmpdir Whether to delete temporary directory.
 #' @param section Which section to activate/deactivate.
 #' @param quiet Whether to run bookdown::render_book() quietly.
@@ -73,8 +74,8 @@
 #'                 bioc_org_db="org.Hs.eg.db",
 #'                 api_key=NULL,
 #'                 is_spatial_exp=TRUE,
-#'                 SpatialFeaturePlot_params=list(pt.size.factor = 3000),
-#'                 SpatialDimPlot_params=list(pt.size.factor = 3000)) # Object was created with an older seurat version
+#'                 SpatialFeaturePlot_params=list(pt.size.factor = 3000), # adapt the point size as
+#'                 SpatialDimPlot_params=list(pt.size.factor = 3000))     # the object was created with an older seurat version
 #' set_verbosity(3)
 #' markers <- Seurat::FindAllMarkers(lymph_node_tiny_2, only.pos = TRUE)
 #' cs <- cluster_set_from_seurat(lymph_node_tiny_2, markers, p_val_adj=0.001, assay="Spatial")
@@ -89,7 +90,9 @@
 #'                 sample_gg_heatmap=TRUE,
 #'                 subsample_by_ident_params=list(nbcell=20),
 #'                 bioc_org_db="org.Hs.eg.db",
-#'                 api_key=NULL) # Object was created with an older seurat version
+#'                 SpatialFeaturePlot_params=list(pt.size.factor = 3000), # adapt the point size as
+#'                 SpatialDimPlot_params=list(pt.size.factor = 3000),     # the object was created with an older seurat version
+#'                 api_key=NULL) 
 #' @importFrom fs path_home
 #' @importFrom bookdown render_book
 #' @importFrom xaringanExtra use_panelset
@@ -151,7 +154,11 @@ gm_report <- function(cluster_set = NULL,
                             plot_profiles_params=list(to_lin=TRUE, averaged = TRUE),
                             plot_multi_profiles_params=list(legend_name="Gene\nModule",
                                                             center=FALSE),
-                            FeaturePlot_params=list(cols=RColorBrewer::brewer.pal(3, "BuPu")),
+                            FeaturePlot_params=list(cols=RColorBrewer::brewer.pal(3, "BuPu"), 
+                                                    label = TRUE,
+                                                    label.size = 4,
+                                                    repel = TRUE,
+                                                    split.by = "orig.ident"),
                             SpatialFeaturePlot_params=list(pt.size.factor = 1.7),
                             SpatialDimPlot_params=list(pt.size.factor = 1.7),
                             DimPlot_params=list(label = TRUE,  
@@ -172,6 +179,7 @@ gm_report <- function(cluster_set = NULL,
                                                  showCategory = 6, 
                                                  cex.params = list(category_label = 0.6, 
                                                                    gene_label = 0.7)),
+                            vlnPlot_params=list(split.by = "orig.ident"),
                             rm_tmpdir = TRUE,
                             section=c("exp_info",
                                       "exp_metadata",
@@ -197,7 +205,9 @@ gm_report <- function(cluster_set = NULL,
                                       "module_heatmap",
                                       "module_iheatmap",
                                       "module_umap",
+                                      "module_umap_by_ori",
                                       "module_violin",
+                                      "module_violin_by_ori",
                                       "module_genes",
                                       "module_cell_annot_IA",
                                       "module_term_network",
@@ -264,11 +274,18 @@ gm_report <- function(cluster_set = NULL,
 
   print_msg("Computing module scores...", msg_type = "INFO")
   add_module_score_used_params <- as.list(formals(Seurat:::AddModuleScore.Seurat))
+  for(i in names(add_module_score_used_params)){
+    if(is.null(add_module_score_used_params[[i]]) || as.character(add_module_score_used_params[[i]])[1] == "deprecated"){
+      add_module_score_used_params <- add_module_score_used_params[names(add_module_score_used_params) != i]
+    }
+  }
 
   for(i in names(add_module_score_params)){
     add_module_score_used_params[[i]] <- add_module_score_params[[i]]
   }
 
+  print_msg("Calling AddModuleScore()...", msg_type = "DEBUG")
+  
   add_module_score_used_params$object <- seurat_object
   add_module_score_used_params$features <- lapply(cluster_set@gene_clusters, gsub, pattern = "~[0-9]+$", replacement = "_")
   add_module_score_used_params$name <- "MOD_"

inst/rmarkdown/index.Rmd

@@ -50,7 +50,7 @@ DT::datatable(NULL)
 ```
 
 ```{r, section_gen_info_1, eval="exp_info" %in% section, echo=FALSE, results = "asis"} 
-knitr::asis_output("# All Modules ")
+knitr::asis_output("# General information")
 ``` 
 
 ```{r, section_gen_info_2, eval="exp_info" %in% section, echo=FALSE, results = "asis"} 
@@ -135,7 +135,7 @@ if(nrow(workflow_params) > 0)
 
 
 ```{r, section_gen_info_14, eval=TRUE, echo=FALSE, results = "asis"} 
-knitr::asis_output("## Experiment information {.panelset}") 
+knitr::asis_output("## Cell/spot populations {.panelset}") 
 ``` 
 
 ```{r, section_gen_info_14a, eval="exp_pca" %in% section, echo=FALSE, results = "asis"} 
@@ -172,6 +172,12 @@ knitr::asis_output("A UMAP showing the cell/spot classes.")
 
 ```{r section_gen_info_17, echo=FALSE, eval="exp_umap" %in% section, echo=FALSE, results = "asis"}
 DimPlot_used_params <- as.list(formals(Seurat::DimPlot))
+for(i in names(DimPlot_used_params)){
+  if(is.null(DimPlot_used_params[[i]]) || as.character(DimPlot_used_params[[i]])[1] == "deprecated"){
+    DimPlot_used_params <- DimPlot_used_params[names(DimPlot_used_params) != i]
+  }
+}
+
 for(i in names(DimPlot_params)){
   DimPlot_used_params[[i]] <- DimPlot_params[[i]]}
 DimPlot_used_params$object <- seurat_object
@@ -191,6 +197,12 @@ knitr::asis_output("A UMAP showing the cell/spot classes according to origin.")
 
 ```{r section_gen_info_17_1, echo=FALSE, eval="exp_umap" %in% section, echo=FALSE, results = "asis"}
 DimPlot_used_params <- as.list(formals(Seurat::DimPlot))
+for(i in names(DimPlot_used_params)){
+  if(is.null(DimPlot_used_params[[i]]) || as.character(DimPlot_used_params[[i]])[1] == "deprecated"){
+    DimPlot_used_params <- DimPlot_used_params[names(DimPlot_used_params) != i]
+  }
+}
+
 for(i in names(DimPlot_params)){
   DimPlot_used_params[[i]] <- DimPlot_params[[i]]}
 DimPlot_used_params$object <- seurat_object
@@ -293,12 +305,13 @@ colnames(df) <- c("Origin", "Cell_Identity")
 df$Origin <- factor(df$Origin)
 df$Cell_Identity <- factor(df$Cell_Identity)
 Cell_Identity <- Origin <- Count <- NULL
-ggplot2::ggplot(df, mapping = ggplot2::aes(x=Cell_Identity, fill=Origin)) +
+ggplot2::ggplot(df, mapping = ggplot2::aes(x=Cell_Identity, fill=Origin, by = Cell_Identity)) +
               ggplot2::geom_bar(position="fill") +
-              ggplot2::labs(x="Cell Identity", y="Count") +
+              ggplot2::labs(x="Cell Identity", y="Fraction") +
               ggplot2::theme_minimal() +
               ggplot2::coord_flip() +
-              ggplot2::theme(legend.position = "none") 
+              ggplot2::theme(legend.position = "none") +
+  ggplot2::geom_text(stat = ggstats::StatProp, position = ggplot2::position_fill(.5), size=2)
 
 df <-  as.data.frame(cbind(seurat_object@meta.data$orig.ident, Idents(seurat_object)))
 colnames(df) <- c("Origin", "Cell_Identity")
@@ -307,24 +320,23 @@ df$Cell_Identity <- factor(df$Cell_Identity)
 Cell_Identity <- Origin <- Count <- NULL
 ggplot2::ggplot(df, mapping = ggplot2::aes(x=Origin, fill=Cell_Identity, by = Origin)) +
               ggplot2::geom_bar(position="fill") +
-              ggplot2::labs(x="fill", y="Cell_Identity") +
+              ggplot2::labs(x="Origin", y="Cell_Identity") +
               ggplot2::theme_minimal() +
   ggplot2::geom_text(stat = ggstats::StatProp, position = ggplot2::position_fill(.5), size=2)
 ```
 
 
 
-```{r, section_gen_info_17d_1, eval="exp_pop_table_by_ori" %in% section, echo=FALSE, results = "asis"} 
+```{r, section_gen_info_17d_2, eval="exp_pop_table_by_ori" %in% section, echo=FALSE, results = "asis"} 
 knitr::asis_output("### Population table by origin") 
 ``` 
 
-```{r, section_gen_info_17e_1, eval="exp_pop_table_by_ori" %in% section, echo=FALSE, results = "asis"} 
+```{r, section_gen_info_17e_2, eval="exp_pop_table_by_ori" %in% section, echo=FALSE, results = "asis"} 
 knitr::asis_output("The size of each cell population according to the corresponding sample/origin. Raw counts") 
 ``` 
 
-```{r section_gen_info_17f_1, echo=FALSE, eval="exp_pop_table_by_ori" %in% section, echo=FALSE, results = "asis"}
-df <-  as.data.frame(cbind(seurat_object@meta.data$orig.ident, Idents(seurat_object)))
-colnames(df) <- c("Origin", "Cell_Identity")
+```{r section_gen_info_17f_2, echo=FALSE, eval="exp_pop_table_by_ori" %in% section, echo=FALSE, results = "asis"}
+df <-  data.frame(Origin=seurat_object@meta.data$orig.ident, Cell_Identity=Idents(seurat_object))
 df <- table(df$Cell_Identity, df$Origin)
 DT::datatable(
     df,
@@ -339,9 +351,6 @@ DT::datatable(
 
 
 
-
-
-
 ```{r, section_gen_info_18, eval="exp_spatial_dist" %in% section, echo=FALSE, results = "asis"} 
 knitr::asis_output("### Spatial distribution") 
 ``` 
@@ -351,11 +360,8 @@ knitr::asis_output("The spatial distribution of counts and features.")
 ``` 
 
 ```{r section_gen_info_20, echo=FALSE, eval="exp_spatial_dist" %in% section, echo=FALSE, results = "asis"}
-SpatialFeaturePlot_used_params <- as.list(formals(Seurat::SpatialFeaturePlot))
-for(i in names(SpatialFeaturePlot_params)){
-  SpatialFeaturePlot_used_params[[i]] <- SpatialFeaturePlot_params[[i]]}
 
-SpatialFeaturePlot_used_params$object <- seurat_object
+SpatialFeaturePlot_params$object <- seurat_object
 
 if(length(grep("^[Mm][Tt]-", rownames(seurat_object))) > 0 )
   seurat_object[["pctMito"]] <- PercentageFeatureSet(seurat_object, pattern = "^[Mm][Tt]-")
@@ -366,8 +372,8 @@ if(length(grep("^[Rr][Pp][Ll]", rownames(seurat_object))) > 0)
 var_qc <- grep("(^nFeature)|(^nCount)|(^pctMito)|(^pctRibo)", colnames(seurat_object@meta.data), perl = TRUE, value = TRUE)
 
 for(feat in var_qc){
-  SpatialFeaturePlot_used_params$features <- feat
-  tryerror <- try(base::do.call(Seurat::SpatialFeaturePlot, SpatialFeaturePlot_used_params)) # got some Error in `FetchData()`...
+  SpatialFeaturePlot_params$features <- feat
+  tryerror <- try(base::do.call(Seurat::SpatialFeaturePlot, SpatialFeaturePlot_params)) # got some Error in `FetchData()`...
     if(!inherits(tryerror, "try-error")){
       print(tryerror)
   }
@@ -387,15 +393,10 @@ identities <- grep("seurat_clusters",
                       colnames(seurat_object@meta.data), perl=TRUE, val=TRUE)
 
 if(length(identities)){
-    SpatialDimPlot_used_params <- as.list(formals(Seurat::SpatialDimPlot))
-    
-  for(i in names(SpatialDimPlot_params)){
-    SpatialDimPlot_used_params[[i]] <- SpatialDimPlot_params[[i]]
-  }
   
-  SpatialDimPlot_used_params$object <- seurat_object
+  SpatialDimPlot_params$object <- seurat_object
   
-  print(base::do.call(Seurat::SpatialDimPlot, SpatialDimPlot_used_params))
+  print(base::do.call(Seurat::SpatialDimPlot, SpatialDimPlot_params))
   
 }
 
@@ -433,7 +434,6 @@ knitr::asis_output("### Module genes")
 ``` 
 
 
-
 ```{r, section_gen_info_30, eval="exp_genes" %in% section, echo=FALSE, results = "asis"} 
 knitr::asis_output("This section provides information about gene contained in modules.") 
 ``` 
@@ -497,14 +497,10 @@ knitr::asis_output("Mean expression of gene across cell/spot populations for eac
 
 ```{r section_gen_info_38, echo=FALSE, eval="exp_mean_1" %in% section}
 
-plot_multi_profiles_used_params <- as.list(formals(plot_multi_profiles))
-for(i in names(plot_multi_profiles_params))
-  plot_multi_profiles_used_params[[i]] <- plot_multi_profiles_params[[i]]
+plot_multi_profiles_params$data <- cluster_set
+plot_multi_profiles_params$ident <- Idents(seurat_object)
 
-plot_multi_profiles_used_params$data <- cluster_set
-plot_multi_profiles_used_params$ident <- Idents(seurat_object)
-
-print(base::do.call(plot_multi_profiles, plot_multi_profiles_used_params))
+print(base::do.call(plot_multi_profiles, plot_multi_profiles_params))
 ```
 
 ```{r, section_gen_info_39, eval="exp_mean_2" %in% section, echo=FALSE, results = "asis"} 
@@ -516,10 +512,8 @@ knitr::asis_output("Mean expression of gene across cell/spot populations for eac
 ``` 
 
 ```{r section_gen_info_41, echo=FALSE, eval="exp_mean_2" %in% section}
-plot_profiles_used_params <- as.list(formals(plot_profiles))
-for(i in names(plot_profiles_params))
-  plot_profiles_used_params[[i]] <- plot_profiles_params[[i]]
-plot_profiles_used_params$data <- cluster_set
-plot_profiles_used_params$ident <- Idents(seurat_object)
-print(base::do.call(plot_profiles, plot_profiles_used_params))
+
+plot_profiles_params$data <- cluster_set
+plot_profiles_params$ident <- Idents(seurat_object)
+print(base::do.call(plot_profiles, plot_profiles_params))
 ```