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reran plots with current lig dist

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This commit is contained in:
Tanushree Tunstall 2021-06-30 17:35:57 +01:00
parent b679068a5e
commit a6f0832a42
2 changed files with 30 additions and 141 deletions
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22
scripts/plotting/get_plotting_dfs.R
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@ -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")
in_filename_params = paste0(tolower(gene), "_comb_afor.csv") # part combined for gid
infile_params = paste0(outdir, "/", in_filename_params)
@ -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")
@ -95,19 +95,19 @@ merged_df3_comp_lig = all_plot_dfs[[8]]
####################################################################
# can include: mutation, or_kin, pwald, af_kin
cols_to_select = c("mutationinformation", "drtype"
#, "wild_type"
, "wild_type"
, "position"
#, "mutant_type"
, "mutant_type"
, "chain", "ligand_id", "ligand_distance"
, "duet_stability_change", "duet_outcome", "duet_scaled"
, "ligand_affinity_change", "ligand_outcome", "affinity_scaled"
, "ddg", "foldx_scaled", "foldx_outcome"
, "deepddg", "deepddg_outcome"
, "asa", "rsa", "rd_values", "kd_values")
#, "af", "or_mychisq", "pval_fisher"
#, "or_fisher", "or_logistic", "pval_logistic")
#, "wt_prop_water", "mut_prop_water", "wt_prop_polarity", "mut_prop_polarity"
#, "wt_calcprop", "mut_calcprop")
, "asa", "rsa", "rd_values", "kd_values"
, "af", "or_mychisq", "pval_fisher"
, "or_fisher", "or_logistic", "pval_logistic"
, "wt_prop_water", "mut_prop_water", "wt_prop_polarity", "mut_prop_polarity"
, "wt_calcprop", "mut_calcprop")
#=======================
# Data for sub colours