diff --git a/scripts/plotting/corr_plots.R b/scripts/plotting/corr_plots.R
new file mode 100755
index 0000000..8ab78ef
--- /dev/null
+++ b/scripts/plotting/corr_plots.R
@@ -0,0 +1,242 @@
+#!/usr/bin/env Rscript
+getwd()
+setwd("~/git/LSHTM_analysis/scripts/plotting")
+getwd()
+source("Header_TT.R")
+
+spec = matrix(c(
+  "drug"       , "d",  1, "character",
+  "gene"       , "g",  1, "character",
+  "data_file1" , "fa", 2, "character",
+  "data_file2" , "fb", 2, "character" 
+), byrow = TRUE, ncol = 4)
+
+opt = getopt(spec)
+
+drug            = opt$drug
+gene            = opt$gene
+infile_params   = opt$data_file1
+infile_metadata = opt$data_file2
+
+if(is.null(drug)|is.null(gene)) {
+  stop("Missing arguments: --drug and --gene must both be specified (case-sensitive)")
+}
+
+#===========
+# Input
+#===========
+
+source("get_plotting_dfs.R")
+
+#===========
+# output
+#===========
+# PS
+corr_ps = "corr_PS.svg"
+plot_corr_ps =  paste0(plotdir,"/", corr_ps)
+
+corr_ps_all = "corr_PS_all.svg"
+plot_corr_ps_all =  paste0(plotdir,"/", corr_ps_all)
+
+
+# LIG
+corr_lig = "corr_LIG.svg"
+plot_corr_lig =  paste0(plotdir,"/", corr_lig)
+
+corr_lig_all = "corr_LIG_all.svg"
+plot_corr_lig_all =  paste0(plotdir,"/", corr_lig_all)
+
+##############################################################################
+foo = corr_ps_df3
+#foo2 = corr_ps_df2
+
+bar = corr_lig_df3
+#bar2 = corr_lig_df2
+
+#================================
+# Data for Correlation plots: PS
+#================================
+# subset data to generate pairwise correlations
+cols_to_select = c("DUET"
+                     , "Foldx"
+                     , "Log (OR)"
+                     , "-Log (P)"
+                     , "MAF"
+                     , "duet_outcome"
+                     , drug)
+corr_data_ps = foo[names(foo)%in%cols_to_select]
+length(cols_to_select)
+
+colnames(corr_data_ps)
+
+start = 1
+end = which(colnames(corr_data_ps) == drug); end # should be the last column
+offset = 1
+
+my_corr_ps = corr_data_ps[start:(end - offset)]
+head(my_corr_ps)
+
+#---------------------
+# Corr plot PS: short
+# data: corr_ps_df3
+# cols: 7
+#---------------------
+cat("Corr plot PS DUET with coloured dots:", plot_corr_ps)
+svg(plot_corr_ps, width = 15, height = 15)
+
+pairs.panels(my_corr_ps[1:(length(my_corr_ps)-1)]
+             , method = "spearman" # correlation method
+             , hist.col = "grey" ##00AFBB
+             , density = TRUE  # show density plots
+             , ellipses = F # show correlation ellipses
+             , stars = T
+             , rug = F
+             , breaks = "Sturges"
+             , show.points = T
+             , bg = c("#f8766d", "#00bfc4")[unclass(factor(my_corr_ps$duet_outcome))] # foldx colours are reveresed
+             , pch = 21 # for bg
+             , jitter = T
+             , alpha = 1
+             , cex = 1.8
+             , cex.axis = 2
+             , cex.labels = 4
+             , cex.cor = 1
+             , smooth = F
+)
+dev.off()
+
+corr_ps_rho = corr.test(my_corr_ps[1:5], method = "spearman")$r
+corr_ps_p = corr.test(my_corr_ps[1:5], method = "spearman")$p
+
+#---------------------
+# Corr plot PS: ALL
+# data: corr_ps_df3
+# cols: 10
+#---------------------
+end_ps_all = which(colnames(foo) == drug); end_ps_all # should be the last column
+
+my_corr_ps_all = foo[start:(end_ps_all - offset)]
+cols_to_drop = "Mutation"
+my_corr_ps_all = my_corr_ps_all[, !(names(my_corr_ps_all)%in%cols_to_drop)]
+head(my_corr_ps_all)
+length(colnames(my_corr_ps_all))
+
+cat("Corr plot PS DUET with coloured dots:", plot_corr_ps_all)
+svg(plot_corr_ps_all, width = 15, height = 15)
+
+pairs.panels(my_corr_ps_all[1:(length(my_corr_ps_all)-1)]
+             , method = "spearman" # correlation method
+             , hist.col = "grey" ##00AFBB
+             , density = TRUE  # show density plots
+             , ellipses = F # show correlation ellipses
+             , stars = T
+             , rug = F
+             , breaks = "Sturges"
+             , show.points = T
+             , bg = c("#f8766d", "#00bfc4")[unclass(factor(my_corr_ps_all$duet_outcome))] # foldx colours are reveresed
+             , pch = 21 # for bg
+             , jitter = T
+             , alpha = 1
+             , cex = 1.5
+             , cex.axis = 2
+             , cex.labels = 2.5
+             , cex.cor = 1
+             , smooth = F
+)
+dev.off()
+
+#==================================
+# Data for Correlation plots: LIG
+#==================================
+cols_to_select_lig = c("Ligand Affinity"
+                     , "Log (OR)"
+                     , "-Log (P)"
+                     , "MAF"
+                     , "ligand_outcome"
+                     , drug)
+
+corr_data_lig = bar[names(bar)%in%cols_to_select_lig]
+length(cols_to_select_lig)
+
+colnames(corr_data_lig)
+
+start_lig = 1
+end_lig = which(colnames(corr_data_lig) == drug); end_lig # should be the last column
+offset_lig = 1
+
+my_corr_lig = corr_data_lig[start_lig:(end_lig-offset_lig)]
+head(my_corr_lig)
+
+#---------------------
+# Corr plot LIG: short
+# data: corr_lig_df3
+# cols: 7
+#---------------------
+cat("Corr LIG plot with coloured dots:", plot_corr_lig)
+svg(plot_corr_lig, width = 15, height = 15)
+
+pairs.panels(my_corr_lig[1:(length(my_corr_lig)-1)]
+             , method = "spearman" # correlation method
+             , hist.col = "grey" ##00AFBB
+             , density = TRUE  # show density plots
+             , ellipses = F # show correlation ellipses
+             , stars = T
+             , rug = F
+             , breaks = "Sturges"
+             , show.points = T
+             , bg = c("#f8766d", "#00bfc4")[unclass(factor(my_corr_lig$ligand_outcome))] 
+             , pch = 21 # for bg
+             , jitter = T
+             , cex = 2
+             , cex.axis = 2
+             , cex.labels = 4
+             , cex.cor = 1
+             , smooth = F
+)
+
+dev.off()
+
+corr_lig_rho = corr.test(my_corr_lig[1:4], method = "spearman")$r
+corr_lig_p = corr.test(my_corr_lig[1:4], method = "spearman")$p
+
+#---------------------
+# Corr plot LIG: ALL
+# data: corr_lig_df3
+# cols: 9
+#---------------------
+end_lig_all = which(colnames(bar) == drug); end_lig_all # should be the last column
+
+my_corr_lig_all = bar[start_lig:(end_lig_all - offset_lig)]
+cols_to_drop = "Mutation"
+my_corr_lig_all = my_corr_lig_all[, !(names(my_corr_lig_all)%in%cols_to_drop)]
+head(my_corr_lig_all)
+length(colnames(my_corr_lig_all))
+
+cat("Corr plot LIG with coloured dots:", plot_corr_lig_all)
+svg(plot_corr_lig_all, width = 15, height = 15)
+
+pairs.panels(my_corr_lig_all[1:(length(my_corr_lig_all)-1)]
+             , method = "spearman" # correlation method
+             , hist.col = "grey" ##00AFBB
+             , density = TRUE  # show density plots
+             , ellipses = F # show correlation ellipses
+             , stars = T
+             , rug = F
+             , breaks = "Sturges"
+             , show.points = T
+             , bg = c("#f8766d", "#00bfc4")[unclass(factor(my_corr_lig_all$ligand_outcome))] # foldx colours are reveresed
+             , pch = 21 # for bg
+             , jitter = T
+             , alpha = 1
+             , cex = 1.5
+             , cex.axis = 2
+             , cex.labels = 2.2
+             , cex.cor = 1
+             , smooth = F
+)
+dev.off()
+
+
+######################################################################=
+#                             End of script
+######################################################################=
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