sorted subcols_axis script to generate correct axis cols for both PS and lig plots

scripts/plotting/barplots_subcolours_aa_PS.R

@@ -1,3 +1,4 @@
+#!/usr/bin/env Rscript   
 getwd()
 setwd("~/git/LSHTM_analysis/scripts/plotting")
 getwd()
@@ -42,14 +43,30 @@ cat(paste0("Variables imported:"
            , "\nAngstrom symbol:", angstroms_symbol))
 
 # clear excess variable
-rm(my_df, upos, dup_muts, my_df_u_lig)
+rm(dup_muts_cols, mut_pos_cols_lig, my_df_cols, my_df_u_cols_lig, upos)
+
 #=======================================================================
+# !!! very important!!!!
 #================
 # Inspecting mut_pos_cols
-# position numbers and colours
+# position numbers and colours and assigning axis colours based on lab_fg
+# of the correct df
 # open file from desktop ("sample_axis_cols") for cross checking
 #================
+# very important!
+#my_axis_colours = mut_pos_cols$lab_fg
 
+if ( nrow(mut_pos_cols) == length(unique(my_df_u_cols$position)) ){
+  print("PASS: lengths checked, assigning axis colours")
+  my_axis_colours = mut_pos_cols$lab_fg
+  cat("length of axis colours:", length(my_axis_colours)
+      , "\nwhich corresponds to the number of positions on the x-axis of the plot")
+}else{
+  print("FAIL:lengths mismatch, could not assign axis colours")
+  quit()
+}
+
+# further sanity checks
 table(mut_pos_cols$lab_bg)
 check_lab_bg = sum( table(mut_pos_cols$lab_bg) ) == nrow(mut_pos_cols) # should  be True
 check_lab_bg    
@@ -70,12 +87,6 @@ if (check_lab_bg && check_lab_bg2 && check_lab_fg) {
   quit()
 }
 
-# very important!
-my_axis_colours = mut_pos_cols$lab_fg
-
-# now clear mut_pos_cols
-rm(mut_pos_cols)
-
 #=======
 # output
 #=======
@@ -89,13 +100,13 @@ plot_bp_aa_subcols_duet = paste0(plotdir, "/", bp_aa_subcols_duet)
 # Data for plots
 #================
 # REASSIGNMENT as necessary
-df  = my_df_u
+df  = my_df_u_cols
 
 # sanity checks
 str(df)
 
 ###########################
-# 2: Plot: DUET scores
+# Plot: DUET scores
 ###########################
 
 #==========================
@@ -137,7 +148,7 @@ snp_count = sort(unique(snpsBYpos_df$snpsBYpos))
 if (is.factor(df$duet_outcome)){
   print("duet_outcome is factor")
 }else{
-  print("convert duet_outcome to factor")
+  print("converting duet_outcome to factor")
   df$duet_outcome = as.factor(df$duet_outcome)
 }
 
@@ -165,25 +176,17 @@ tapply(df$duet_scaled, df$duet_outcome, max)
 u = unique(df$duet_scaled) 
 cat("No. of unique values in normalised data:", length(u))
 
-#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-# Run this section if rounding is to be used
-# specify number for rounding
-#n = 3 
-#df$duet_scaledR = round(df$duet_scaled, n)  
-#ur = unique(df$duet_scaledR)
-
-# create an extra column called group which contains the "gp name and score" 
+# Define group
+# Create an extra column called group which contains the "gp name and score" 
 # so colours can be generated for each unique values in this column
-
-#my_grp = df$duet_scaledR # rounding
 my_grp = df$duet_scaled # no rounding
-#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 df$group <- paste0(df$duet_outcome, "_", my_grp, sep = "") 
 
 # Call the function to create the palette based on the group defined above
 colours <- ColourPalleteMulti(df, "duet_outcome", "my_grp")
 print(paste0("Colour palette generated for: ", length(colours), " colours"))
 my_title = "Protein stability (DUET)"
+cat("No. of axis colours: ", length(my_axis_colours))
 
 #========================
 # plot with axis colours