import commit

mcsm_analysis/pyrazinamide/scripts/plotting/barplots_2colours_LIG.R

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+getwd()
+setwd("~/git/LSHTM_analysis/mcsm_analysis/pyrazinamide/scripts/plotting")
+getwd()
+
+########################################################################
+# 				Installing and loading required packages 			   #
+########################################################################
+
+source("../Header_TT.R")
+
+########################################################################
+#		 Read file: call script for combining df for lig		   	   #
+########################################################################
+
+source("../combining_two_df_lig.R") 
+
+#---------------------- PAY ATTENTION
+# the above changes the working dir
+#[1] "git/LSHTM_analysis/mcsm_analysis/pyrazinamide/scripts"
+#---------------------- PAY ATTENTION
+
+#==========================
+# This will return:
+
+# df with NA:
+# merged_df2
+# merged_df3
+
+# df without NA:
+# merged_df2_comp
+# merged_df3_comp
+#===========================
+
+###########################
+# Data for Lig plots
+# you need merged_df3
+# or
+# merged_df3_comp
+# since these have unique SNPs
+# I prefer to use the merged_df3
+# because using the _comp dataset means
+# we lose some muts and at this level, we should use
+# as much info as available
+###########################
+
+# uncomment as necessary
+#%%%%%%%%%%%%%%%%%%%%%%%%
+# REASSIGNMENT
+my_df  = merged_df3
+#my_df = merged_df3_comp
+#%%%%%%%%%%%%%%%%%%%%%%%%
+
+# delete variables not required
+rm(merged_df2, merged_df2_comp, merged_df3, merged_df3_comp)
+
+# quick checks
+colnames(my_df)
+str(my_df)
+
+#############################
+# Extra sanity check:
+# for mcsm_lig ONLY
+# Dis_lig_Ang should be <10
+#############################
+
+if (max(my_df$Dis_lig_Ang) < 10){
+  print ("Sanity check passed: lig data is <10Ang")
+}else{
+  print ("Error: data should be filtered to be within 10Ang")
+}
+########################################################################
+#               end of data extraction and cleaning for plots          #
+########################################################################
+
+#==========================
+# Plot: Barplot with scores (unordered)
+# corresponds to Lig_outcome
+# Stacked Barplot with colours: Lig_outcome @ position coloured by 
+# Lig_outcome. This is a barplot where each bar corresponds 
+# to a SNP and is coloured by its corresponding Lig_outcome.
+#============================
+
+#===================
+# Data for plots
+#===================
+
+#%%%%%%%%%%%%%%%%%%%%%%%%
+# REASSIGNMENT
+df  = my_df 
+#%%%%%%%%%%%%%%%%%%%%%%%%
+
+rm(my_df)
+
+# sanity checks
+upos = unique(my_df$Position)
+
+# should be a factor
+is.factor(df$Lig_outcome)
+#TRUE
+
+table(df$Lig_outcome)
+
+# should be -1 and 1: may not be in this case because you have filtered the data
+# FIXME: normalisation before or after filtering?
+min(df$ratioPredAff) #
+max(df$ratioPredAff) #
+
+# sanity checks
+tapply(df$ratioPredAff, df$Lig_outcome, min)
+tapply(df$ratioPredAff, df$Lig_outcome, max)
+
+#******************
+# generate plot
+#******************
+
+# set output dir for plots
+getwd()
+setwd("~/git/Data/pyrazinamide/output/plots")
+getwd()
+
+my_title = "Ligand affinity"
+
+# axis label size
+my_xaxls = 13
+my_yaxls = 15
+
+# axes text size
+my_xaxts = 15
+my_yaxts = 15
+
+# no ordering of x-axis
+g = ggplot(df, aes(factor(Position, ordered = T)))
+g + 
+  geom_bar(aes(fill = Lig_outcome), colour = "grey") +
+  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 = my_title
+       , x = "Position"
+       , y = "Frequency")
+
+# 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