diff --git a/scripts/plotting/basic_barplots_foldx.R b/scripts/plotting/basic_barplots_foldx.R new file mode 100755 index 0000000..f695cc1 --- /dev/null +++ b/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) +#======================================================================= + + +