diff --git a/scripts/combining_dfs.py b/scripts/combining_dfs.py index 10b10db..634af18 100755 --- a/scripts/combining_dfs.py +++ b/scripts/combining_dfs.py @@ -297,14 +297,14 @@ print('Output filename:', outfile_stab_struc , '\n===================================================================') # write csv -print('Writing file: combined stability and structural parameters') +print('\nWriting file: combined stability and structural parameters') combined_df_clean.to_csv(outfile_stab_struc, index = False) print('\nFinished writing file:' , '\nNo. of rows:', combined_df_clean.shape[0] , '\nNo. of cols:', combined_df_clean.shape[1]) #%%===================================================================== -print('=======================================' - , '\nFifth merge: +print('\n=======================================' + , '\nFifth merge:' , '\ncombined_df_clean + afor_df ' , '\n=======================================') @@ -372,4 +372,4 @@ combined_stab_afor.to_csv(outfile_comb_afor, index = False) print('\nFinished writing file:' , '\nNo. of rows:', combined_stab_afor.shape[0] , '\nNo. of cols:', combined_stab_afor.shape[1]) -#%% end of script \ No newline at end of file +#%% end of script diff --git a/scripts/functions/myaf_or_calcs.R b/scripts/functions/myaf_or_calcs.R index 78acc84..e4c7519 100644 --- a/scripts/functions/myaf_or_calcs.R +++ b/scripts/functions/myaf_or_calcs.R @@ -180,6 +180,12 @@ my_afor <- function ( drug ci_lower_fisher = fisher.test(table(dst, mut))$conf.int[1] ci_upper_fisher = fisher.test(table(dst, mut))$conf.int[2] + #-------------------- + # adding log cols : NEW + #-------------------- + log10_or_mychisq = log10(or_mychisq) + neglog_pval_fisher = -log10(pval_fisher) + #------------------- # chi sq estimates #------------------- @@ -198,9 +204,11 @@ my_afor <- function ( drug , zval_logistic = zval_logistic , ci_low_logistic = ci_lower_logistic , ci_hi_logistic = ci_upper_logistic - , or_mychisq = or_mychisq + , or_mychisq = or_mychisq + , log10_or_mychisq = log10_or_mychisq # NEW , or_fisher = or_fisher , pval_fisher = pval_fisher + , neglog_pval_fisher = neglog_pval_fisher # NEW , ci_low_fisher= ci_lower_fisher , ci_hi_fisher = ci_upper_fisher , est_chisq = est_chisq diff --git a/scripts/functions/plotting_data.R b/scripts/functions/plotting_data.R index d3dff8d..ddda207 100755 --- a/scripts/functions/plotting_data.R +++ b/scripts/functions/plotting_data.R @@ -76,6 +76,14 @@ if ( all(c1 == c2) ){ exit() } +#------------------------------ +# renaming foldx column from +# "ddg" --> "ddg_foldx" +#------------------------------ + +# change name to foldx +colnames(df)[n] <- "ddg_foldx" + #================================== # extract unique mutation entries #================================== diff --git a/scripts/plotting/get_plotting_dfs.R b/scripts/plotting/get_plotting_dfs.R index 0babc1a..a9e78e9 100644 --- a/scripts/plotting/get_plotting_dfs.R +++ b/scripts/plotting/get_plotting_dfs.R @@ -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====================================================") \ No newline at end of file