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generated pncA plot for poster for ps_combined

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This commit is contained in:
Tanushree Tunstall 2021-07-07 11:38:07 +01:00
parent cb3a0f71da
commit 59a1213f65
3 changed files with 37 additions and 17 deletions
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14
scripts/plotting/get_plotting_dfs.R
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@ -39,10 +39,10 @@ import_dirs(drug, gene)
#---------------------------
# call: plotting_data()
#---------------------------
#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")
in_filename_params = paste0(tolower(gene), "_comb_afor.csv") # part combined for gid
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)
cat("\nInput file for mcsm comb data not specified, assuming filename: ", infile_params, "\n")
}
@ -62,8 +62,8 @@ dup_muts = pd_df[[4]]
#--------------------------------
# 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")
@ -102,7 +102,7 @@ cols_to_select = c("mutationinformation", "drtype"
, "duet_stability_change", "duet_outcome", "duet_scaled"
, "ligand_affinity_change", "ligand_outcome", "affinity_scaled"
, "ddg", "foldx_scaled", "foldx_outcome"
, "deepddg", "deepddg_outcome"
#, "deepddg", "deepddg_outcome"
, "asa", "rsa", "rd_values", "kd_values"
, "af", "or_mychisq", "pval_fisher"
, "or_fisher", "or_logistic", "pval_logistic"