- Ajout du choix de la palette de couleur pour les plots de classes (dans visualization et compare)

- Optimisations du code (+ fonctions dans fichiers séparés)

config.R

@@ -88,3 +88,13 @@ presets.listgenes.grid <- function(shiny_session, input.presets) {
     updateSelectizeInput(shiny_session, "genes_list_grid", selected=c("CD3D","CD8A","CD4","NCAM1","FCGR3A","CD14","HLA-DRA","ITGAX","ITGAM","CD79A","CD19","MS4A1","SDC1","IRF8","IL3RA","FCER1A","HBA1"))
   } 
 }
+
+## Color palettes ----
+color.palettes <- function(inputname) {
+  selectInput(inputId = as.character(inputname),
+              label="Choose a color palette :",
+              choices = list(`Ggplot` = c("Dark2", "Set1", "Set2", "Set3", "Pastel1", "Pastel2", "Paired", "Accent", "Spectral"),
+                             `Ggpubr` = c("npg", "aaas", "lancet", "jco", "ucscgb"),
+                             `Misc` = c("simpsons", "rickandmorty")),
+              selected = "npg")
+}

install.R

@@ -19,6 +19,8 @@ install.packages("RColorBrewer")
 install.packages("data.table")
 install.packages("devtools")
 install.packages("BiocManager")
+install.packages("ggpubr")
+install.packages("colourpicker")
 BiocManager::install("clusterProfiler")
 BiocManager::install("MAST")    
 BiocManager::install("org.Hs.eg.db")

utils.R

@@ -9,11 +9,19 @@
 assign.colors <- function(obj, ident, palette){
   ident <- as.factor(ident)
   nr.groups <- length(levels(ident))
-  colors <- colorRampPalette(brewer.pal(8, palette))(nr.groups)
+  colors <- colorRampPalette(get_palette(palette, 8))(nr.groups)
   colors.df <- data.frame(group=levels(ident), color=colors)
   return(colors.df)
 }
 
+## Function which use assign.colors to give a color for each group of each class ----
+all.class.colors <- function(obj, palette) {
+coldf <- lapply(obj@meta.data[,sapply(obj@meta.data, class) %in% c("factor","character")],
+                assign.colors,
+                obj = obj, 
+                palette = palette)
+return(coldf)
+}
 
 ## Uptade Gene lists function ----
 update.geneslist <- function(obj, shiny_session, genes_list, inputname, selected_choice = "IGKC") {