updated running_plotting_scripts.R

scripts/plotting/barplots_subcolours.R

@@ -124,4 +124,4 @@ print(outPlot_bp_lig)
 dev.off()
 ######################################################################=
 #                             End of script
-######################################################################=
+######################################################################=

scripts/plotting/get_plotting_dfs.R

@@ -39,8 +39,8 @@ import_dirs(drug, gene)
 #---------------------------
 # call: plotting_data()
 #---------------------------
-if (!exists("infile_params") && exists("gene")){
-#if (!is.character(infile_params) && exists("gene")){ # when running as cmd
+#if (!exists("infile_params") && exists("gene")){
+if (!is.character(infile_params) && exists("gene")){ # when running as cmd
   #in_filename_params = paste0(tolower(gene), "_all_params.csv") #for pncA
   in_filename_params = paste0(tolower(gene), "_comb_afor.csv") # part combined for gid
   infile_params = paste0(outdir, "/", in_filename_params)
@@ -67,8 +67,8 @@ cat("\nLigand distance cut off, colname:", LigDist_colname
 #--------------------------------
 # call: combining_dfs_plotting()
 #--------------------------------
-if (!exists("infile_metadata") && exists("gene")){
-#if (!is.character(infile_metadata) && exists("gene")){ # when running as cmd
+#if (!exists("infile_metadata") && exists("gene")){
+if (!is.character(infile_metadata) && exists("gene")){ # when running as cmd
   in_filename_metadata = paste0(tolower(gene), "_metadata.csv") # part combined for gid
   infile_metadata = paste0(outdir, "/", in_filename_metadata)
   cat("\nInput file for gene metadata not specified, assuming filename: ", infile_metadata, "\n")

scripts/plotting/lineage_basic_barplots_combined.R

@@ -3,9 +3,10 @@ getwd()
 setwd("~/git/LSHTM_analysis/scripts/plotting/")
 getwd()
 #########################################################
-# TASK: Basic lineage barplot showing numbers
+# TASK: Basic lineage barplots showing numbers
 
 # Output: Basic barplot with lineage samples and mut count
+# + SNP diversity
 
 ##########################################################
 # 				Installing and loading required packages 			 
@@ -16,6 +17,27 @@ source("../functions/bp_lineage.R")
 #===========
 # input
 #===========
+#drug = 'streptomycin'
+#gene = 'gid'
+
+spec = matrix(c(
+    "drug"       , "d",  1, "character",
+    "gene"       , "g",  1, "character",
+    "data_file1" , "fa", 2, "character",
+    "data_file2" , "fb", 2, "character" 
+), byrow = TRUE, ncol = 4)
+
+opt = getopt(spec)
+
+drug            = opt$drug
+gene            = opt$gene
+infile_params   = opt$data_file1
+infile_metadata = opt$data_file2
+
+if(is.null(drug)|is.null(gene)) {
+    stop("Missing arguments: --drug and --gene must both be specified (case-sensitive)")
+}
+
 source ('get_plotting_dfs.R')
 
 cat("Directories imported:"

scripts/plotting/running_plotting_scripts.txt

@@ -113,12 +113,28 @@ note:
  - fb flag has default if not supplied
  
  
-#===================
-# Add LINEAGE ONE
-#=================== 
-# Lineage_bp.R
-creates Count and Diversity plot
+#====================================
+# lineage_basic_barplots_combined.R
+#====================================
+#-----------------------------------------------------------------------
+./lineage_basic_barplots_combined.R-d streptomycin -g gid
+#-----------------------------------------------------------------------
 
+It replaces
+ ## lineage_basic_barplot.R
+These have been moved to redundant/
+
+
+sources:
+ ## get_plotting_dfs.R
+ ## functions//bp_lineage.R"
+
+ outputs: 1 svg in the plotdir
+ ## basic_lineage_barplots_combined.svg
+ 
+note: 
+ - fa flag has default if not supplied 
+ - fb flag has default if not supplied
  
 ########################################################################
 # TODO