update colour for lin & assignment thresh = 0.5

camlab-bioml · May 19, 2021 · 971f092 · 971f092
1 parent 92f95bf
commit 971f092
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Showing 2 changed files with 9 additions and 2 deletions.
diff --git a/R/colours.R b/R/colours.R
@@ -3,16 +3,22 @@
 #' @export
 jackson_basel_colours <- function() {
   pal <- c("#8B5B42", "#AF4EA9", "#FFB60A", "#0AC694", "#0024DD", "#6CC1FF",
-           "#0496FF", "#1DA05B", "#E11E00", "#A78882")
+           "#0496FF", "#1DA05B", "#E11E00", "#A78882", "#BD93D8")
 
   celltype_colours <- c(
     "Stromal" = pal[1],
     "B cells" = pal[2],
+    "Other immune" = pal[2],
     "T cells" = pal[3],
+    "Treg" = pal[3],
     "Macrophage" = pal[4],#
     "Epithelial (basal)" = pal[5],
     "Epithelial (luminal)" = pal[6],
     "Epithelial (other)" = pal[7],
+    "Epithelial" = pal[6],
+    "Epithelial proliferative" = pal[7],
+    "Epithelial immunosuppressive" = pal[5],
+    "Epithelial I-P" = pal[11],
     "Monocyte" = pal[8], #
     "Endothelial" = pal[9],
     "Fibroblasts" = pal[10],
@@ -68,6 +74,7 @@ cohort_colours <- function(){
   cohort_cols <- c(
     "Basel" = pal[1],
     "Zurich1" = pal[2],
+    "Zurich" = pal[2],
     "Wagner" = pal[3],
     "Schapiro" = pal[4]
   )

diff --git a/R/utils.R b/R/utils.R
@@ -66,7 +66,7 @@ to_csv <- function(sce,
 #' Get cell type assignments given probability matrix
 #'
 #' @export
-get_celltypes <- function(prob_mat, thresh = 0.7) {
+get_celltypes <- function(prob_mat, thresh = 0.5) {
   if(is.data.frame(prob_mat)) {
     prob_mat <- as.matrix(prob_mat)
   }