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added log10 OR and P values to myaf_or_calcs.R

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Tanushree Tunstall 2021-08-23 20:01:01 +01:00
parent 0c16937b68
commit 1e3670f935
4 changed files with 32 additions and 12 deletions
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18
scripts/plotting/get_plotting_dfs.R
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@ -101,7 +101,7 @@ cols_to_select = c("mutationinformation", "drtype"
, "chain", "ligand_id", "ligand_distance"
, "duet_stability_change", "duet_outcome", "duet_scaled"
, "ligand_affinity_change", "ligand_outcome", "affinity_scaled"
, "ddg", "foldx_scaled", "foldx_outcome"
, "ddg_foldx", "foldx_scaled", "foldx_outcome"
, "deepddg", "deepddg_outcome" # comment out as not available for pnca
, "asa", "rsa", "rd_values", "kd_values"
, "af", "or_mychisq", "pval_fisher"
@ -375,10 +375,10 @@ cat("\n=========================================="
df_ps = merged_df2
#--------------------
# adding log cols
# adding log cols : NEW UNCOMMENT
#--------------------
df_ps$log10_or_mychisq = log10(df_ps$or_mychisq)
df_ps$neglog_pval_fisher = -log10(df_ps$pval_fisher)
#df_ps$log10_or_mychisq = log10(df_ps$or_mychisq)
#df_ps$neglog_pval_fisher = -log10(df_ps$pval_fisher)
##df_ps$log10_or_kin = log10(df_ps$or_kin)
##df_ps$neglog_pwald_kin = -log10(df_ps$pwald_kin)
@ -484,10 +484,10 @@ df_lig = merged_df2_lig
table(df_lig$ligand_outcome)
#--------------------
# adding log cols
# adding log cols : NEW UNCOMMENT
#--------------------
df_lig$log10_or_mychisq = log10(df_lig$or_mychisq)
df_lig$neglog_pval_fisher = -log10(df_lig$pval_fisher)
#df_lig$log10_or_mychisq = log10(df_lig$or_mychisq)
#df_lig$neglog_pval_fisher = -log10(df_lig$pval_fisher)
##df_lig$log10_or_kin = log10(df_lig$or_kin)
##df_lig$neglog_pwald_kin = -log10(df_lig$pwald_kin)
@ -583,3 +583,7 @@ identical(corr_data_ps, corr_ps_df2)
# End of script
########################################################################
rm(foo)
cat("\n===================================================\n"
, "\nSuccessful: get_plotting_dfs.R worked!"
, "\n====================================================")