added shorter scripts for each different processing for plots to make it wasire to read code

scripts/plotting/corr_data.R

@@ -0,0 +1,67 @@
+#!/usr/bin/env Rscript  
+#########################################################
+# TASK: Script to format data for corr plots
+#########################################################
+
+#=================================================
+#         Data for Corrplots
+#=================================================
+cat("\n=========================================="
+    , "\nCORR PLOTS data: ALL params"
+    , "\n=========================================")
+
+# use data
+#merged_df2
+
+#----------------------------
+# columns for corr plots:PS
+#----------------------------
+# NOTE: you can add mcsm_ppi column as well, and it will only select what it can find!
+big_df_colnames = data.frame(names(merged_df2))
+
+corr_cols_select <- c("mutationinformation", drug, "mutation_info_labels"
+                   , "duet_stability_change", "ligand_affinity_change", "ddg_foldx", "asa", "rsa"
+                   , "rd_values", "kd_values", "log10_or_mychisq", "neglog_pval_fisher","af"
+                   , "deepddg", "ddg_dynamut", "ddg_dynamut2", "mcsm_na_affinity"
+                   , "ddg_encom", "dds_encom", "ddg_mcsm", "ddg_sdm", "ddg_duet", "ligand_distance")
+
+#===========================
+# Corr data for plots: PS
+# big_df ps: ~ merged_df2
+#===========================
+
+corr_df_m2 = merged_df2[,colnames(merged_df2)%in%corr_cols_select]
+
+#===========================
+# Corr data for plots: PS
+# short_df ps: ~merged_df3
+#===========================
+
+corr_df_m3 = corr_df_m2[!duplicated(corr_df_m2$mutationinformation),]
+
+na_or = sum(is.na(corr_df_m3$log10_or_mychisq))
+check1 = nrow(corr_df_m3) - na_or; check1
+
+if (nrow(corr_df_m3) == nrow(merged_df3) && nrow(merged_df3_comp) == check1) {
+  cat( "\nPASS: No. of rows for corr_df_m3 match"
+       , "\nPASS: No. of OR values checked: " , check1)
+} else {
+  cat("\nFAIL: Numbers  mismatch:"
+      , "\nExpected nrows: ", nrow(merged_df3)
+      , "\nGot: ", nrow(corr_df_m3)
+      , "\nExpected OR values: ", nrow(merged_df3_comp)
+      , "\nGot: ", check1)
+}
+
+cat("\nCorr Data created:"
+, "\n==================================="
+, "\ncorr_df_m2: created from merged_df2"
+, "\n==================================="
+, "\nnrows:", nrow(corr_df_m2)
+, "\nncols:", ncol(corr_df_m2)
+, "\n==================================="
+, "\ncorr_df_m3: created from merged_df3"
+, "\n==================================="
+, "\nnrows:", nrow(corr_df_m3)
+, "\nncols:", ncol(corr_df_m3)
+)