From 4609757efb913a1b27944ab6ddcb66f2753ff87f Mon Sep 17 00:00:00 2001
From: Tanushree Tunstall <tanu@tunstall.in>
Date: Sat, 13 Aug 2022 21:19:19 +0100
Subject: [PATCH] added appendix tables script

---
 .../plotting_thesis/appendix_tables.R         | 144 ++++++++++++++++++
 1 file changed, 144 insertions(+)
 create mode 100644 scripts/plotting/plotting_thesis/appendix_tables.R

diff --git a/scripts/plotting/plotting_thesis/appendix_tables.R b/scripts/plotting/plotting_thesis/appendix_tables.R
new file mode 100644
index 0000000..0ffe158
--- /dev/null
+++ b/scripts/plotting/plotting_thesis/appendix_tables.R
@@ -0,0 +1,144 @@
+#!/usr/bin/env Rscript       
+#source("~/git/LSHTM_analysis/config/alr.R")
+source("~/git/LSHTM_analysis/config/embb.R")
+#source("~/git/LSHTM_analysis/config/katg.R")
+#source("~/git/LSHTM_analysis/config/gid.R")
+#source("~/git/LSHTM_analysis/config/pnca.R")
+#source("~/git/LSHTM_analysis/config/rpob.R")
+
+# get plottting dfs 
+source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
+
+source("~/git/LSHTM_analysis/scripts/plotting/plotting_colnames.R")
+#=======
+# output
+#=======
+outdir_images = paste0("~/git/Writing/thesis/images/results/", tolower(gene), "/")
+outdir_stats = paste0(outdir_images,"stats/") 
+
+###################################################################
+# FIXME: ADD distance to NA when SP replies
+
+geneL_normal  = c("pnca")
+geneL_na      = c("gid", "rpob")
+geneL_ppi2    = c("alr", "embb", "katg", "rpob")
+
+# LigDist_colname # from globals used
+# ppi2Dist_colname #from globals used 
+# naDist_colname #from globals used
+
+df3 = merged_df3
+
+# Add adjusted P-values
+df3$p_adj_fdr = p.adjust(df3$pval_fisher, method = "fdr")
+df3$signif_fdr = df3$p_adj_fdr
+df3 = dplyr::mutate(df3
+                    , signif_fdr = case_when(signif_fdr == 0.05 ~ "."
+                                             , signif_fdr <=0.0001 ~ '****'
+                                             , signif_fdr <=0.001 ~ '***'
+                                             , signif_fdr <=0.01 ~ '**'
+                                             , signif_fdr <0.05 ~ '*'
+                                             , TRUE ~ 'ns'))
+
+
+
+
+####################################
+# Appendix: ligand affinity
+####################################
+df_lig = df3[df3[[LigDist_colname]]<DistCutOff,]
+
+
+cols_to_output_lig = c("mutationinformation"
+                   , "position"
+                   , LigDist_colname
+                   , "ligand_affinity_change"
+                   , "ligand_outcome"
+                   , "mmcsm_lig"
+                   , "mmcsm_lig_outcome"
+                   , "or_mychisq"
+                   , "p_adj_fdr"
+                   , "signif_fdr")
+
+# counting
+
+Out_df_lig = df_lig[, cols_to_output_lig]
+Out_df_ligS = Out_df_lig[order(Out_df_lig$or_mychisq, decreasing = T), ]
+
+delta_symbol = "\u0394"; delta_symbol
+
+Out_df_ligS$or_mychisq = round(Out_df_ligS$or_mychisq,2)
+Out_df_ligS$p_adj_fdr = round(Out_df_ligS$p_adj_fdr,2)
+Out_df_ligS
+
+colsNames_to_output_lig = c("Mutation"
+                   , "position"
+                   , paste0("Lig-Dist (", angstroms_symbol, ")")
+                   , "mCSM-ligand affinity"
+                   , "mCSM ligand_outcome"
+                   , "mmCSM-ligand affinity"
+                   , "mmCSM ligand_outcome"
+                   , "Odds Ratio"
+                   , "Adj P-value"
+                   , "P-value significance")
+
+colnames(Out_df_ligS) = colsNames_to_output_lig
+Out_df_ligS
+#--------------------
+# write output file: KS test within grpup
+#----------------------
+Out_ligT = paste0(outdir_stats
+                    , tolower(gene)
+                    , "_lig_muts.csv")
+
+cat("Output of Ligand muts:", Out_ligT )
+write.csv(Out_df_ligS, Out_ligT, row.names = FALSE)
+
+########################################################################
+####################################
+# Appendix: PPi2 affinity
+####################################
+
+df_ppi2 = df3[df3[[ppi2Dist_colname]]<DistCutOff,]
+
+
+cols_to_output_ppi2 = c("mutationinformation"
+                        , "position"
+                        , ppi2Dist_colname
+                        , "mcsm_ppi2_affinity"
+                        , "mcsm_ppi2_outcome"
+                        , "or_mychisq"
+                        , "p_adj_fdr"
+                        , "signif_fdr")
+
+# extract output cols
+Out_df_ppi2 = df_ppi2[, cols_to_output_ppi2]
+Out_df_ppi2S = Out_df_ppi2[order(Out_df_ppi2$or_mychisq, decreasing = T), ]
+
+delta_symbol = "\u0394"; delta_symbol
+
+Out_df_ppi2S$or_mychisq = round(Out_df_ppi2S$or_mychisq,2)
+Out_df_ppi2S$p_adj_fdr = round(Out_df_ppi2S$p_adj_fdr,2)
+Out_df_ppi2S
+
+colsNames_to_output_ppi2 = c("Mutation"
+                             , "position"
+                             , paste0("PPI2-Dist (", angstroms_symbol, ")")
+                             , paste0("mCSM-PPI2 (", delta_symbol, ")")
+                             , "mCSM-PPI2 outcome"
+                             , "Odds Ratio"
+                             , "Adj P-value"
+                             , "P-value significance")
+
+colnames(Out_df_ppi2S) = colsNames_to_output_ppi2
+Out_df_ppi2S
+#--------------------
+# write output file: KS test within grpup
+#----------------------
+Out_ppi2T = paste0(outdir_stats
+                   , tolower(gene)
+                   , "_ppi2_muts.csv")
+
+cat("Output of PPI2 muts:", Out_ppi2T )
+write.csv(Out_df_ppi2S, Out_ppi2T, row.names = FALSE)
+