renamed file

scripts/plotting/or_plots_combined.R

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+#!/usr/bin/env Rscript
+#########################################################
+# TASK: Basic lineage barplot showing numbers
+
+# Output: Basic barplot with lineage samples and mut count
+
+#=======================================================================
+# working dir and loading libraries
+getwd()
+setwd("~/git/LSHTM_analysis/scripts/plotting/")
+getwd()
+
+
+source("Header_TT.R")
+require(cowplot)
+source("combining_dfs_plotting.R")
+# should return the following dfs, directories and variables
+
+# PS combined: 
+# 1) merged_df2
+# 2) merged_df2_comp
+# 3) merged_df3
+# 4) merged_df3_comp
+
+# LIG combined: 
+# 5) merged_df2_lig
+# 6) merged_df2_comp_lig
+# 7) merged_df3_lig
+# 8) merged_df3_comp_lig
+
+# 9) my_df_u
+# 10) my_df_u_lig
+
+cat(paste0("Directories imported:"
+           , "\ndatadir:", datadir
+           , "\nindir:", indir
+           , "\noutdir:", outdir
+           , "\nplotdir:", plotdir))
+
+cat(paste0("Variables imported:"
+           , "\ndrug:", drug
+           , "\ngene:", gene
+           , "\ngene_match:", gene_match
+           , "\nAngstrom symbol:", angstroms_symbol
+           , "\nNo. of duplicated muts:", dup_muts_nu
+           , "\nNA count for ORs:", na_count
+           , "\nNA count in df2:", na_count_df2
+           , "\nNA count in df3:", na_count_df3))       
+
+#=========================
+#=======
+# output
+#=======
+or_combined = "or_combined_PS_LIG.svg"
+plot_or_combined  =  paste0(plotdir,"/", or_combined)
+
+#or_kin_combined = "or_kin_combined_PS_LIG.svg"
+#plot_or_kin_combined  =  paste0(plotdir,"/", or_kin_combined)
+#=======================================================================
+
+###########################
+# Data for OR and stability plots
+# you need merged_df3_comp
+# since these are matched 
+# to allow pairwise corr
+###########################
+
+ps_df  = merged_df3_comp
+lig_df = merged_df3_comp_lig
+
+# Ensure correct data type in columns to plot: should be TRUE
+is.numeric(ps_df$or_mychisq)
+is.numeric(lig_df$or_mychisq)
+
+# delete variables not required
+rm(merged_df2, merged_df2_comp, merged_df2_lig, merged_df2_comp_lig, my_df_u, my_df_u_lig)
+#%% end of section 1
+
+# sanity check: should be <10
+if (max(lig_df$ligand_distance) < 10){
+  print ("Sanity check passed: lig data is <10Ang")
+}else{
+  print ("Error: data should be filtered to be within 10Ang")
+}
+
+#############
+# Plots: Bubble plot
+# x = Position, Y = stability
+# size of dots = OR
+# col: stability
+#############
+
+#-----------------
+# Plot 1: DUET vs OR by position as geom_points
+#-------------------
+
+my_ats = 20 # axis text size
+my_als = 22 # axis label size
+
+# Spelling Correction: made redundant as already corrected at the source
+#ps_df$duet_outcome[ps_df$duet_outcome=='Stabilizing'] <- 'Stabilising'
+#ps_df$duet_outcome[ps_df$duet_outcome=='Destabilizing'] <- 'Destabilising'
+
+table(ps_df$duet_outcome) ; sum(table(ps_df$duet_outcome))
+
+g1 = ggplot(ps_df, aes(x = factor(position)
+                   , y = duet_scaled))
+
+p1 = g1 + 
+  geom_point(aes(col = duet_outcome
+                 , size = or_mychisq))+
+                 #, size = or_kin)) + # not good, almost like log(or)
+  theme(axis.text.x = element_text(size = my_ats
+                                   , angle = 90
+                                   , hjust = 1
+                                   , vjust = 0.4)
+        , axis.text.y = element_text(size = my_ats
+                                     , angle = 0
+                                     , hjust = 1
+                                     , vjust = 0)
+        , axis.title.x = element_text(size = my_als)
+        , axis.title.y = element_text(size = my_als) 
+        , legend.text = element_text(size = my_als)
+        , legend.title = element_text(size = my_als) ) +
+  #, legend.key.size = unit(1, "cm")) +
+  labs(title = ""
+       , x = "Position"
+       , y = "DUET(PS)"
+       , size = "Odds Ratio"
+       , colour = "DUET Outcome") +
+  guides(colour = guide_legend(override.aes = list(size=4))) 
+
+p1 
+
+#-------------------
+# generate plot 2: Lig vs OR by position as geom_points
+#-------------------
+
+# Spelling Correction: made redundant as already corrected at the source
+
+#lig_df$ligand_outcome[lig_df$ligand_outcome=='Stabilizing'] <- 'Stabilising'
+#lig_df$ligand_outcome[lig_df$ligand_outcome=='Destabilizing'] <- 'Destabilising'
+
+table(lig_df$ligand_outcome)
+
+g2 = ggplot(lig_df, aes(x = factor(position)
+                   , y = affinity_scaled))
+
+p2 = g2 + 
+  geom_point(aes(col = ligand_outcome
+                 , size = or_mychisq))+
+                 #, size = or_kin)) + # not good! almost like log(or)
+  theme(axis.text.x = element_text(size = my_ats
+                                   , angle = 90
+                                   , hjust = 1
+                                   , vjust = 0.4)
+        , axis.text.y = element_text(size = my_ats
+                                     , angle = 0
+                                     , hjust = 1
+                                     , vjust = 0)
+        , axis.title.x = element_text(size = my_als)
+        , axis.title.y = element_text(size = my_als) 
+        , legend.text = element_text(size = my_als)
+        , legend.title = element_text(size = my_als) ) +
+  #, legend.key.size = unit(1, "cm")) +
+  labs(title = ""
+       , x = "Position"
+       , y = "Ligand Affinity"
+       , size = "Odds Ratio"
+       , colour = "Ligand Outcome"
+       ) +
+  guides(colour = guide_legend(override.aes = list(size=4))) 
+
+p2
+
+#======================
+# combine using cowplot
+#======================
+
+svg(plot_or_combined, width = 32, height = 12)
+#svg(plot_or_kin_combined, width = 32, height = 12)
+
+theme_set(theme_gray()) # to preserve default theme
+
+printFile = cowplot::plot_grid(plot_grid(p1, p2
+                             , ncol = 1
+                             , align = 'v'
+                             , labels = c("", "")
+                             , label_size = my_als+5))
+print(printFile)
+dev.off()
+