`resolved ambiguous muts and generated clean output. Also seaprated dir.R

scripts/data_extraction.py

@@ -1170,7 +1170,7 @@ del(out_filename_metadata_poscounts)
 
 #%% Write file: gene_metadata (i.e gene_LF1)
 # where each row has UNIQUE mutations NOT unique sample ids
-out_filename_metadata = gene.lower() + '_metadata.csv'
+out_filename_metadata = gene.lower() + '_metadata_raw.csv'
 outfile_metadata = outdir + '/' + out_filename_metadata
 print('Writing file: LF formatted data'
       , '\nFile:', outfile_metadata

scripts/plotting/combining_dfs_plotting.R

@@ -156,6 +156,7 @@ other_muts = foo2[foo2$mutation_info == other_muts_col,]
 
 common_muts = dr_muts[dr_muts$mutation%in%other_muts$mutation,]
 #write.csv(common_muts, 'common_muts.csv')
+rm(common_muts)
 
 # FIXME read properly
 # "ambiguous_mut_names.csv"
@@ -165,11 +166,45 @@ ambiguous_muts_names = ambiguous_muts$mutation
 
 common_muts_all = gene_metadata[gene_metadata$mutation%in%ambiguous_muts_names,]
 
-gene_metadata2 = gene_metadata
-
 if (gene_metadata$mutation_info[gene_metadata$mutation%in%ambiguous_muts_names] == other_muts_col){
   print('change me')
 }
+
+# make a copy
+gene_metadata2 = gene_metadata
+table(gene_metadata$mutation_info)
+count_check = as.data.frame(cbind(table(gene_metadata$mutationinformation, gene_metadata$mutation_info)))
+#count_check$checks = ifelse(count_check$dr_mutations_pyrazinamide&&count_check$other_mutations_pyrazinamide>0, "ambi", "pass")
+table(count_check$checks)
+
+
+poo = c("V180F", "G132A", "D49G")
+poo2 = count_check[rownames(count_check)%in%poo,]
+poo2[[dr_muts_col]]&& poo2[[other_muts_col]]>0
+poo2$checks = ifelse(poo2$checkspoo2[[dr_muts_col]]&& poo2[[other_muts_col]]>0, "ambi", "pass")
+
+# remove common_muts_all
+ids = gene_metadata$mutation%in%common_muts_all$mutation; table(ids)
+gene_metadata_unambiguous = gene_metadata2[!ids,]
+
+# sanity checks: should be true
+table(gene_metadata_unambiguous$mutation%in%common_muts_all$mutation)[[1]] == nrow(gene_metadata_unambiguous)
+nrow(gene_metadata_unambiguous) + nrow(common_muts_all) == nrow(gene_metadata)
+
+# correct common muts
+table(common_muts_all$mutation_info)
+common_muts_all$mutation_info = as.factor(common_muts_all$mutation_info)
+
+# change the other_muts to dr_muts
+common_muts_all$mutation_info[common_muts_all$mutation_info==other_muts_col] <- dr_muts_col
+
+table(common_muts_all$mutation_info)
+common_muts_all$mutation_info = factor(common_muts_all$mutation_info)
+table(common_muts_all$mutation_info)
+
+# add it back to 
+gene_meta_data
+
 ###################################################################
 #                           combining: PS
 ###################################################################

scripts/plotting/opp_mcsm_muts.R

@@ -39,6 +39,7 @@ rm(my_df, upos, dup_muts)
 #in_file1: output of plotting_data.R
 # my_df_u
 
+#===========
 # output
 #===========
 # mutations with opposite effects

scripts/plotting/plotting_data.R

@@ -15,7 +15,10 @@ library(ggplot2)
 library(data.table)
 library(dplyr)
 
+source("dirs.R")
+
 require("getopt", quietly = TRUE) #cmd parse arguments
+
 #========================================================
 # command line args
 #spec = matrix(c(
@@ -31,19 +34,6 @@ require("getopt", quietly = TRUE) #cmd parse arguments
 #  stop("Missing arguments: --drug and --gene must both be specified (case-sensitive)")
 #}
 #========================================================
-#%% variable assignment: input and output paths & filenames
-drug = "pyrazinamide"
-gene = "pncA"
-gene_match = paste0(gene,"_p.")
-cat(gene_match)
-
-#=============
-# directories
-#=============
-datadir = paste0("~/git/Data")
-indir = paste0(datadir, "/", drug, "/input")
-outdir = paste0("~/git/Data", "/", drug, "/output")
-plotdir = paste0("~/git/Data", "/", drug, "/output/plots")
 #======
 # input
 #======
@@ -53,15 +43,14 @@ infile_params = paste0(outdir, "/", in_filename_params)
 cat(paste0("Input file 1:", infile_params) )
 
 
-dr_muts_col = paste0('dr_mutations_', drug)
-dr_muts_col  = paste0('other_mutations_', drug)
-
-cat('Extracting columns based on variables:\n'
+cat('columns based on variables:\n'
       , drug
       , '\n'
       , dr_muts_col
       , '\n'
       , other_muts_col
+      , "\n"
+      , resistance_col
       , '\n===============================================================')
 
 #%%===============================================================
@@ -74,9 +63,6 @@ my_df = read.csv(infile_params, header = T)
 
 cat("\nInput dimensions:", dim(my_df)) 
 
-# quick checks
-#colnames(my_df)
-#str(my_df)
 
 ###########################
 # extract unique mutation entries

scripts/plotting/running_plot_scripts

@@ -1,6 +1,10 @@
 #========
 # plotting
 #========
+FIXME:
+
+#dirs.R: imports dir structure
+change this to cmd so you can pass in drug and gene name
 
 #=======================
 plotting_data.R