Merge branch 'release/v2.0.10' into main

Author: dputhier

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: scigenex
 Type: Package
 Title: The scigenex package (Single-Cell Informative GENe Explorer)
-Version: 2.0.9
+Version: 2.0.10
 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=2.0.9
+VERSION=2.0.10
 
 .PHONY: help
 

R/gm_report.R

@@ -143,7 +143,10 @@ gm_report <- function(cluster_set = NULL,
                             plot_multi_profiles_params=list(legend_name="Gene\nModule"),
                             FeaturePlot_params=list(cols=RColorBrewer::brewer.pal(3, "BuPu")),
                             SpatialFeaturePlot_params=list(pt.size.factor = 1.7),
-                            SpatialDimPlot_params=list(pt.size.factor = 1.7),
+                            SpatialDimPlot_params=list(pt.size.factor = 1.7, 
+                                                       label = T, 
+                                                       repel = T, 
+                                                       label.size = 4),
                             plot_ggheatmap_params=list(use_top_genes=FALSE, 
                                                        hide_gene_name=TRUE,
                                                        xlab = "Cells/Spots",

inst/rmarkdown/index.Rmd

@@ -20,8 +20,9 @@ params:
 ---
 
 
-<!-- UPPERCASE variable are text to be replaced. -->
-<!-- There are several global variables obtained from st_report() function. -->
+<!-- Some UPPERCASE (e.g MODULE_NUMBER) variables are text to be replaced (see st_report() function). -->
+<!-- NB: This code contains several global variables derived from gm_report() function arguments. -->
+
 
 ```{r start, include=FALSE, echo=FALSE, eval=TRUE}
 library(knitr)
@@ -184,8 +185,14 @@ knitr::asis_output("Seurat provides a convenient framework for exploring quality
 ``` 
 
 ```{r section_gen_info_17c, echo=FALSE, eval="exp_metrics" %in% section, echo=FALSE, results = "asis"}
-seurat_object[["percent.mt"]] <- Seurat::PercentageFeatureSet(seurat_object, pattern = "^[Mm][Tt]-")
-seurat_object[["percent.ribo"]] <- Seurat::PercentageFeatureSet(seurat_object, pattern = "^[Rr][Pp][LlSs][0-9]+")
+if(length(grep("^[Mm][Tt]-", rownames(seurat_object))) > 0 ){
+    seurat_object[["percent.mt"]] <- Seurat::PercentageFeatureSet(seurat_object, pattern = "^[Mm][Tt]-")
+}
+
+if(length(grep("^[Rr][Pp][LlSs][0-9]+", rownames(seurat_object))) > 0 ){
+  seurat_object[["percent.ribo"]] <- Seurat::PercentageFeatureSet(seurat_object, pattern = "^[Rr][Pp][LlSs][0-9]+")
+}
+
 var_qc <- grep("(^nFeature)|(nCount)|(percent.mt)|(percent.ribo)", colnames(seurat_object@meta.data), perl = TRUE, value = TRUE)
 for(qc in var_qc){
   print(Seurat::VlnPlot(seurat_object, features = qc, ncol = 1))

inst/rmarkdown/module.Rmd

@@ -1,6 +1,6 @@
 
-<!-- UPPERCASE variable are text to be replaced (see st_report() function). -->
-<!-- NB: The code contains several global variables derived from gm_report() function arguments. -->
+<!-- Some UPPERCASE (e.g FIG_PATH, and MODULE_NUMBER) variables are text to be replaced (see st_report() function). -->
+<!-- NB: This code contains several global variables derived from gm_report() function arguments. -->