all barplots generated for ps and lig

scripts/plotting/basic_barplots_LIG.R

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+#!/usr/bin/env Rscript  
+#########################################################
+# TASK: producing barplots
+# 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 and directories
+# 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)
+
+#=======================================================================
+#=======
+# output
+#=======
+# plot 1
+basic_bp_ligand = "basic_barplot_LIG.svg"
+plot_basic_bp_ligand  =  paste0(plotdir,"/", basic_bp_ligand)
+
+# plot 2
+pos_count_ligand = "position_count_LIG.svg"
+plot_pos_count_ligand = paste0(plotdir, "/", pos_count_ligand)
+
+#=======================================================================
+#================
+# Data for plots
+#================
+# REASSIGNMENT as necessary
+df  = my_df_u_lig
+rm(my_df_u, my_df, upos, dup_muts)
+
+# sanity checks
+str(df)
+#=====================================================================
+#****************
+# Plot 1:Count of stabilising and destabilsing muts
+#****************
+
+#svg("basic_barplots_LIG.svg")
+svg(plot_basic_bp_ligand)
+print(paste0("plot1 filename:", basic_bp_ligand))
+
+my_ats = 25 # axis text size
+my_als = 22 # axis label size
+
+theme_set(theme_grey())
+
+#--------------
+# start plot 1
+#--------------
+g = ggplot(df, aes(x = ligand_outcome))
+outPlot = g + geom_bar(aes(fill = ligand_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="ligand_outcome"
+      ) + 
+  scale_fill_discrete(name = "Ligand Outcome"
+                      , labels = c("Destabilising", "Stabilising"))
+
+print(outPlot)
+dev.off()
+
+table(df$ligand_outcome)
+#=======================================================================
+#****************
+# Plot 2: frequency of positions
+#****************
+df_ncols = ncol(df)
+df_nrows = nrow(df)
+
+cat(paste0("original df dimensions:"
+    , "\nNo. of rows:", df_nrows
+    , "\nNo. of cols:", df_ncols
+    , "\nNow adding column: frequency of mutational positions"))
+
+#setDT(df)[, .(pos_count := .N), by = .(position)] 
+setDT(df)[, pos_count := .N, by = .(position)]
+
+rm(df_nrows, df_ncols) 
+
+df_nrows = nrow(df)
+df_ncols = ncol(df)
+
+cat(paste0("revised df dimensions:"
+           , "\nNo. of rows:", df_nrows
+           , "\nNo. of cols:", df_ncols))
+
+# this is cummulative
+table(df$pos_count)
+
+# use group by on this
+snpsBYpos_df <- df %>%
+  group_by(position) %>%
+  summarize(snpsBYpos = mean(pos_count))
+
+table(snpsBYpos_df$snpsBYpos)
+
+#!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+# FIXME, get this mutation_info, perhaLIG useful!
+foo = select(df, mutationinformation
+             , wild_pos
+             , wild_type
+             , mutant_type
+             #, mutation_info # comes from meta data, notused yet
+             , position
+             , pos_count)
+
+#write.csv(foo, "/pos_count_freq.csv")
+#!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+#--------------
+# start plot 2
+#--------------
+#svg("position_count_LIG.svg")
+svg(plot_pos_count_ligand)
+print(paste0("plot filename:", plot_pos_count_ligand))
+
+my_ats = 25 # axis text size
+my_als = 22 # axis label size
+
+# to make x axis display all positions
+# not sure if to use with sort or directly
+my_x = sort(unique(snpsBYpos_df$snpsBYpos)) 
+
+g = ggplot(snpsBYpos_df, aes(x = snpsBYpos))
+outPlot_pos = g + geom_bar(aes (alpha = 0.5)
+                         , show.legend = FALSE) +
+  scale_x_continuous(breaks = unique(snpsBYpos_df$snpsBYpos)) +
+  #scale_x_continuous(breaks = my_x) +
+  geom_label(stat = "count", aes(label = ..count..)
+             , color = "black"
+             , size = 10) +
+  theme(axis.text.x = element_text(size = my_ats
+                                   , angle = 0)
+        , axis.text.y = element_text(size = my_ats
+                                     , angle = 0
+                                     , hjust = 1)
+        , axis.title.x = element_text(size = my_als)
+        , axis.title.y = element_text(size = my_als)
+        , plot.title = element_blank()) +
+  
+  labs(x = "Number of SNPs"
+       , y = "Number of Sites")
+
+print(outPlot_pos)
+dev.off()
+########################################################################
+#               			end of lig barplots         			   
+########################################################################
+