Changes between Version 5 and Version 6 of SOP/scRNA-seq/Slingshot

Timestamp:

10/20/20 09:50:13 (4 years ago)

Author:

byuan

Comment:

--

SOP/scRNA-seq/Slingshot

@@ -49 +49 @@
 library(ggthemes)
 
+# this define the cluster color. You can change it with different color scheme.
 my_color <- createPalette(length(levels(sce$ident)), c("#010101", "#ff0000"), M=1000)
 names(my_color) <- unique(as.character(sce$ident))
@@ -54 +55 @@
 slingshot_df <- data.frame(colData(sce))
 
-# re-order y-axis for better figure:
-slingshot_df$ident = factor(slingshot_df$ident, levels=c(4,2,1,0,3,5,6))
+# re-order y-axis for better figure: This should be tailored with your own cluster names
+# slingshot_df$ident = factor(slingshot_df$ident, levels=c(4,2,1,0,3,5,6))
 
 ggplot(slingshot_df, aes(x = slingPseudotime_1, y = ident,