From 48050752db0db8aaf2ecfca6a0c7ccbd92671ac8 Mon Sep 17 00:00:00 2001
From: Tanushree Tunstall <tanu@tunstall.in>
Date: Wed, 23 Sep 2020 19:23:34 +0100
Subject: [PATCH] added more analysis in extreme_muts.R to be tidied later

---
 scripts/plotting/extreme_muts.R | 100 +++++++++++++++++++++++++++++++-
 1 file changed, 99 insertions(+), 1 deletion(-)

diff --git a/scripts/plotting/extreme_muts.R b/scripts/plotting/extreme_muts.R
index 053fde9..12ffcab 100644
--- a/scripts/plotting/extreme_muts.R
+++ b/scripts/plotting/extreme_muts.R
@@ -139,15 +139,45 @@ bar = merged_df3 %>% group_by(position) %>% count()
 all(table(foo$n) == table(bar$n))
 table(foo$n)
 
-
 n_budding_sites = table(foo$n)[[2]]
 n_mult_muts_sites = sum(table(foo$n)) - (table(foo$n)[[1]] - table(foo$n)[[2]])
 
 cat("No of budding hotspots (sites with 2 mutations):", n_budding_sites
     , "\nNo. of sites with mutiple (>2) mutations:", n_mult_muts_sites)
 
+#====================
+# budding hotspots: dr muts
+#====================
+merged_df3_dr = merged_df3[merged_df3$mutation_info == dr_muts_col,]
+
+bar = merged_df3_dr %>% group_by(position) %>% count()
+table(bar$n)
+
+n_budding_sites_dr = table(bar$n)[[2]]
+n_mult_muts_sites_dr = sum(table(bar$n)) - (table(bar$n)[[1]] - table(bar$n)[[2]])
+
+cat("No of budding hotspots (sites with 2 mutations) for dr muts:", n_budding_sites_dr
+    , "\nNo. of sites with mutiple (>2) mutations for dr muts:", n_mult_muts_sites_dr)
+
 #==========================================================================
 
+#==============================
+# wild_pos count: This tells you 
+# how many muts associated with each
+# wild-type postion: handy!
+#==============================
+wild_pos_count_filename = paste0(outdir, "/"
+, tolower(gene), "_wild_pos_count.csv")
+
+
+head(merged_df3$position)
+# order by position
+merged_df3_s = merged_df3[order(merged_df3$position),]
+head(merged_df3_s$position)
+
+wild_pos_count = as.data.frame(table(merged_df3_s$wild_pos))
+write.csv(wild_pos_count, wild_pos_count_filename)
+
 #==============================
 # agreement of foldx and DUET
 #==============================
@@ -166,3 +196,71 @@ agreement = 100 - disagreement
 cat("There is", agreement, "% between mcsm and foldx predictions")
 
 ##############################################################################
+
+# plots
+
+plot(density(merged_df3$duet_stability_change))
+plot(density(merged_df3$ddg))
+
+plot(density(merged_df3$duet_scaled))
+plot(density(merged_df3$foldx_scaled))
+
+hist(merged_df3$duet_scaled)
+hist(merged_df3$foldx_scaled)
+
+
+#========================================
+#layout(matrix(c(1,1,2,3), 2, 2, byrow = TRUE))
+par(mfrow=c(3,1)) 
+
+#----------
+# OR
+#----------
+# raw
+plot(density(merged_df3$or_mychisq, na.rm = T))
+hist(merged_df3$or_mychisq)
+
+# log10
+plot(density(log10(merged_df3$or_mychisq), na.rm = T))
+hist(log10(merged_df3$or_mychisq))
+
+
+
+
+#----------
+# adjusted OR
+#----------
+# raw
+plot(density(merged_df3$or_kin, na.rm = T))
+hist(merged_df3$or_kin)
+
+# log
+plot(density(log10(merged_df3$or_kin), na.rm = T))
+hist(log10(merged_df3$or_kin))
+
+
+# overlay
+#par(yaxs="i",las=1)
+d = density(log10(merged_df3$or_mychisq), na.rm = T)
+ylim = max(d$y); ylim
+
+hist(log10(merged_df3$or_mychisq)
+     , prob = TRUE
+     , col = "grey"
+     , border= "black"
+     , ylim = c(0, ylim)
+     , xlab = "Adjusted OR (Log10)"
+     , main = "Adjusted OR")
+
+box(bty="l")
+
+lines(density(log10(merged_df3$or_mychisq)
+              , na.rm = T
+              , bw = "nrd0") # default
+      , col = "black"
+      , lwd = 2)
+
+#grid(nx=NA,ny=NULL,lty=1,lwd=1,col="gray")
+
+#===============================
+par(mfrow=c(2,2))