moved subcols script to redundant

scripts/plotting/redundant/barplots_subcolours_PS.R

@@ -0,0 +1,168 @@
+getwd()
+setwd("~/git/LSHTM_analysis/scripts/plotting")
+getwd()
+
+#########################################################
+# TASK: output barplot by position with each bar coloured by 
+# its stability value and NO coloured positions indicated
+#########################################################
+#=======================================================================
+
+############################################################
+# 1: Installing and loading required packages and functions
+#############################################################
+
+#source("Header_TT.R")
+library(ggplot2)
+library(data.table)
+source("barplot_colour_function.R")
+source("plotting_data.R")
+
+# should return the following dfs, directories and variables
+# mut_pos_cols
+# my_df
+# my_df_u
+# my_df_u_lig
+# dup_muts
+
+cat(paste0("Directories imported:"
+           , "\ndatadir:", datadir
+           , "\nindir:", indir
+           , "\noutdir:", outdir
+           , "\nplotdir:", plotdir))
+
+cat(paste0("Variables imported:"
+           , "\ndrug:", drug
+           , "\ngene:", gene
+           , "\ngene_match:", gene_match
+           , "\nLength of upos:", length(upos)
+           , "\nAngstrom symbol:", angstroms_symbol))
+
+# clear excess variable
+rm(my_df, upos, dup_muts, my_df_u_lig)
+########################################################
+
+#=======
+# output
+#=======
+print(paste0("plot will be in:", plotdir))
+bp_subcols_duet = "barplot_coloured_PS.svg"
+plot_bp_subcols_duet = paste0(plotdir, "/", bp_subcols_duet)
+
+#===================
+# Data for plots
+#===================
+# REASSIGNMENT as necessary
+df  = my_df_u
+
+# sanity checks
+str(df)
+upos = unique(df$position)
+
+# should be a factor
+if (is.factor(df$duet_outcome)){
+  print("duet_outcome is factor")
+}else{
+  print("convert duet_outcome to factor")
+  df$duet_outcome = as.factor(df$duet_outcome)
+}
+
+is.factor(df$duet_outcome)
+
+table(df$duet_outcome)
+
+# should be -1 and 1
+min(df$duet_scaled)
+max(df$duet_scaled)
+
+tapply(df$duet_scaled, df$duet_outcome, min)
+tapply(df$duet_scaled, df$duet_outcome, max)
+
+#******************
+# generate plot
+#******************
+#==========================
+# Barplot with scores (unordered)
+# corresponds to duet_outcome
+# Stacked Barplot with colours: duet_outcome @ position coloured by 
+# stability scores. This is a barplot where each bar corresponds 
+# to a SNP and is coloured by its corresponding DUET stability value.
+# Normalised values (range between -1 and 1 ) to aid visualisation
+# NOTE: since barplot plots discrete values, colour = score, so number of
+# colours will be equal to the no. of unique normalised scores 
+# rather than a continuous scale
+# will require generating the colour scale separately.
+#============================
+
+# My colour FUNCTION: based on group and subgroup
+# in my case;
+# df = df
+# group = duet_outcome
+# subgroup = normalised score i.e duet_scaled
+
+# check unique values in normalised data
+u = unique(df$duet_scaled) 
+
+#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+# Run this section if rounding is to be used
+n = 3 
+df$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" 
+# 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)"
+
+# axis label size
+my_xaxls = 13
+my_yaxls = 15
+
+# axes text size
+my_xaxts = 15
+my_yaxts = 15
+
+#******************
+# generate plot: NO axis colours
+#******************
+print(paste0("plot name:", plot_bp_subcols_duet))
+
+svg(plot_bp_subcols_duet, width = 26, height = 4)
+
+g = ggplot(df, aes(factor(position, ordered = T)))
+outPlot = g + 
+  geom_bar(aes(fill = group), colour = "grey") +
+  scale_fill_manual( values = colours
+                     , guide = "none") +
+  theme( axis.text.x = element_text(size = my_xaxls
+                                    , angle = 90
+                                    , hjust = 1
+                                    , vjust = 0.4)
+         , axis.text.y = element_text(size = my_yaxls 
+                                      , angle = 0
+                                      , hjust = 1
+                                      , vjust = 0)
+         , axis.title.x = element_text(size = my_xaxts)
+         , axis.title.y = element_text(size = my_yaxts ) ) +
+  labs(title = ""
+       #title = my_title
+       , x = "position"
+       , y = "Frequency")
+       
+print(outPlot)
+dev.off()
+# for sanity and good practice
+rm(df)
+#======================= end of plot
+# axis colours labels
+# https://stackoverflow.com/questions/38862303/customize-ggplot2-axis-labels-with-different-colors
+# https://stackoverflow.com/questions/56543485/plot-coloured-boxes-around-axis-label