added plotting_globals and text file with info on how to run plotting scripst

scripts/plotting/plotting_globals.R

@@ -0,0 +1,54 @@
+#!/usr/bin/env Rscript             
+#########################################################
+# TASK: importing dir str 
+# create a function that takes 'drug' and 'gene' as args, 
+# This script is sourced by plotting.R to import dir str
+# for various plots, etc.
+#########################################################
+import_dirs <- function(drug, gene) {
+  gene_match = paste0(gene,"_p.")
+  cat(gene_match)
+  
+  #=============
+  # directories and variables
+  #=============
+  datadir        <<- paste0("~/git/Data/")
+  indir          <<- paste0(datadir, drug, "/input")
+  outdir         <<- paste0("~/git/Data/", drug, "/output")
+  plotdir        <<- paste0("~/git/Data/", drug, "/output/plots")
+  
+  dr_muts_col    <<- paste0('dr_mutations_', drug)
+  other_muts_col <<- paste0('other_mutations_', drug)
+  resistance_col <<- "drtype"
+  
+}
+
+#==================
+# mcsm ligand distance  cut off
+#==================
+mcsm_lig_cutoff <<- 10
+
+#==================
+# Angstroms symbol
+#==================
+
+angstroms_symbol <<- "\u212b"
+#cat(paste0("There are ", nrow(my_df_u_lig), " sites lying within 10", angstroms_symbol, " of the ligand\n"))
+
+#==================
+# Delta symbol
+#==================
+
+delta_symbol <<- "\u0394"; delta_symbol
+
+###########################
+# variables for my cols
+###########################
+
+mcsm_red2 <<-  "#ae301e" # most negative
+mcsm_red1 <<-  "#f8766d"
+
+mcsm_mid <<- "white" # middle
+
+mcsm_blue1 <<- "#00bfc4"
+mcsm_blue2 <<- "#007d85" # most positive