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

scripts/plotting/plotting_globals.R

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+#!/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

scripts/plotting/running_plotting_scripts.txt

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+#========
+# basic_barplots_PS.R: 
+#========
+Rscript basic_barplots_PS.R
+# Calls 'plotting_data.R' --> calls 'dirs.R'
+ 'Plotting_data.R':
+#drug = opt$drug
+#gene = opt$gene
+
+# hardcoding when not using cmd
+drug = "streptomycin"
+gene = "gid"
+
+#TODO
+making such that cmd line agrs are passed to basic_barplots_PS.R for gene, drug and maybe input file
+and then these call functions
+
+Delete: dirs.R
+after grepping
+barplots_subcolours_aa_combined.R:source("dirs.R")
+basic_barplots_PS.R:source("dirs.R")
+resolving_ambiguous_muts.R:source("dirs.R")
+
+#=======================================================================