added corr plot TODO for lineage counts

scripts/functions/corr_plot_data.R

@@ -18,9 +18,12 @@
 # RETURNS: DF
     # containing all the columns required for generating downstream correlation plots
 
-# TO DO: SHINY
+# TODO: ADD
-    #1) Corr type?
+#lineage_count_all
-    #2)
+#lineage_count_unique
+#my_df['lineage_proportion']      = my_df['lineage_count_unique']/my_df['lineage_count_all']
+#my_df['dist_lineage_proportion'] = my_df['lineage_count_unique']/total_mtblineage_uc
+
 ##################################################################
 # LigDist_colname   #from globals: plotting_globals.R
 # ppi2Dist_colname  #from globals: plotting_globals.R

scripts/plotting/plotting_thesis/corr_plots_thesis.R

@@ -1,10 +1,30 @@
+#!/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")
+####################################################
+#=======
+# output
+#=======
+outdir_images = paste0("~/git/Writing/thesis/images/results/", tolower(gene), "/")
+
+#=======
+# Input
+#=======
 merged_df3 = as.data.frame(merged_df3)
 corr_plotdf = corr_data_extract(merged_df3
                                 , gene = gene
                                 , drug = drug
                                 , extract_scaled_cols = F)
 colnames(corr_plotdf)
-
+colnames(corr_df_m3_f)
+corr_plotdf = corr_df_m3_f  # for downstream code
 #================
 # stability
 #================
@@ -179,7 +199,7 @@ corr_end = end-ncol_omit
 #----------------------------
 corr_consP =  paste0(outdir_images
                      ,tolower(gene)
-                     ,"_corr_ppi2.svg" )
+                     ,"_corr_conservation.svg" )
 
 cat("Corr plot conservation coloured dots:", corr_consP)
 svg(corr_consP, width = 10, height = 10)
@@ -191,9 +211,9 @@ my_corr_pairs(corr_data_all = corr_df_cons
               , categ_colour =  c("red", "blue")
               , density_show = F
               , hist_col = "coral4"
-              , dot_size = 2
+              , dot_size =1.1
               , ats = 1.5
-              , corr_lab_size = 3
+              , corr_lab_size = 2.5
               , corr_value_size = 1)
 
 dev.off()