added basic_barplots_foldx.R for supp figure

scripts/plotting/basic_barplots_foldx.R

@@ -0,0 +1,103 @@
+#!/usr/bin/env Rscript  
+#########################################################
+# TASK: producing barplots for foldx
+# basic barplots with count of mutations
+# basic barplots with frequency of count of mutations
+#########################################################
+#=======================================================================
+# working dir and loading libraries
+getwd()
+setwd("~/git/LSHTM_analysis/scripts/plotting")
+getwd()
+
+#source("Header_TT.R")
+library(ggplot2)
+library(data.table)
+library(dplyr)
+source("plotting_data.R")
+
+# should return the following dfs, directories and variables
+# 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
+#=======
+# plot 1
+basic_bp_foldx = "basic_barplot_foldx.svg"
+plot_basic_bp_foldx  =  paste0(plotdir,"/", basic_bp_foldx)
+#=======================================================================
+#================
+# Data for plots
+#================
+# REASSIGNMENT as necessary
+df  = my_df_u
+
+# sanity checks
+str(df)
+#=======================================================================
+#****************
+# Plot 1:Count of stabilising and destabilsing muts
+#****************
+
+svg(plot_basic_bp_foldx)
+print(paste0("plot1 filename:", plot_basic_bp_foldx))
+
+my_ats = 25 # axis text size
+my_als = 22 # axis label size
+
+theme_set(theme_grey())
+
+#--------------
+# start plot 1
+#--------------
+g = ggplot(df, aes(x = foldx_outcome))
+OutPlot_count = g + geom_bar(aes(fill = foldx_outcome)
+                         , show.legend = TRUE) + 
+  geom_label(stat = "count"
+             , aes(label = ..count..)
+             , color = "black"
+             , show.legend = FALSE
+             , size = 10) + 
+  theme(axis.text.x = element_blank()
+        , axis.title.x = element_blank()
+        , axis.title.y = element_text(size=my_als)
+        , axis.text.y = element_text(size = my_ats)
+        , legend.position = c(0.73,0.8)
+        , legend.text = element_text(size=my_als-2)
+        , legend.title = element_text(size=my_als)
+        , plot.title = element_blank()) + 
+  labs(title = ""
+       , y = "Number of SNPs"
+      #, fill="FoldX Outcome"
+      ) + 
+  scale_fill_discrete(name = "FoldX Outcome"
+                      , labels = c("Destabilising", "Stabilising"))
+
+print(OutPlot_count)
+dev.off()
+
+table(df$foldx_outcome)
+#=======================================================================
+
+
+