diff --git a/scripts/ml/ml_functions/MultClfs.py b/scripts/ml/ml_functions/MultClfs.py index aa1522a..40f5a78 100755 --- a/scripts/ml/ml_functions/MultClfs.py +++ b/scripts/ml/ml_functions/MultClfs.py @@ -292,7 +292,8 @@ def MultModelsCl(input_df , ('SVC' , SVC(**rs) ) , ('Stochastic GDescent' , SGDClassifier(**rs, **njobs) ) , ('XGBoost' , XGBClassifier(**rs, verbosity = 0, use_label_encoder = False, **njobs) ) - , ('Dummy Classifier' , DummyClassifier(strategy = 'most_frequent') ) + #, ('Dummy Classifier' , DummyClassifier(strategy = 'most_frequent') ) + , ('Dummy Classifier' , DummyClassifier(constant = 1) ) ] mm_skf_scoresD = {} diff --git a/scripts/ml/ml_functions/MultClfs_CVs.py b/scripts/ml/ml_functions/MultClfs_CVs.py index c862c80..6809bca 100755 --- a/scripts/ml/ml_functions/MultClfs_CVs.py +++ b/scripts/ml/ml_functions/MultClfs_CVs.py @@ -276,7 +276,8 @@ def MultModelsCl_CVs(input_df , ('SVC' , SVC(**rs) ) , ('Stochastic GDescent' , SGDClassifier(**rs, **njobs) ) , ('XGBoost' , XGBClassifier(**rs, verbosity = 0, use_label_encoder = False, **njobs) ) - , ('Dummy Classifier' , DummyClassifier(strategy = 'most_frequent') ) + #, ('Dummy Classifier' , DummyClassifier(strategy = 'most_frequent') ) + , ('Dummy Classifier' , DummyClassifier(constant = 1) ) ] mm_skf_scoresD = {} diff --git a/scripts/plotting/plotting_thesis/ORandSNP_results.R b/scripts/plotting/plotting_thesis/ORandSNP_results.R index 8bbef3e..3eb7859 100644 --- a/scripts/plotting/plotting_thesis/ORandSNP_results.R +++ b/scripts/plotting/plotting_thesis/ORandSNP_results.R @@ -2,15 +2,14 @@ #source("~/git/LSHTM_analysis/config/pnca.R") #source("~/git/LSHTM_analysis/config/embb.R") -source("~/git/LSHTM_analysis/config/gid.R") -#source("~/git/LSHTM_analysis/config/alr.R") +#source("~/git/LSHTM_analysis/config/gid.R") +source("~/git/LSHTM_analysis/config/alr.R") #source("~/git/LSHTM_analysis/config/katg.R") #source("~/git/LSHTM_analysis/config/rpob.R") # get plottting dfs source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R") -source("~/git/LSHTM_analysis/scripts/plotting/plotting_colnames.R") #======= # output #======= @@ -210,8 +209,13 @@ if (nrow(bar_or) == nrow(sen1) + nrow(res1) ){ # percent for OR muts pc_orR = nrow(res1)/(nrow(sen1) + nrow(res1)); pc_orR -cat("\nPercentage of muts with OR>1 i.e resistant:" - , pc_orR *100 ) +cat("\nNo.of DST muts:", nrow(bar_or) + , "\nNo of DST (R):", table(bar_or$sensitivity)[[1]] + , "\nNo of DST (S):", table(bar_or$sensitivity)[[2]] + , "\nNumber of R muts with OR >1 (n = ", nrow(res1),")" + , "\nPercentage of muts with OR>1 i.e resistant:" , pc_orR *100 ) + + # muts with highest OR head(bar_or$mutationinformation, 10) diff --git a/scripts/plotting/plotting_thesis/rpob/pe_sens_site_count_rpob.R b/scripts/plotting/plotting_thesis/rpob/pe_sens_site_count_rpob.R index 03ed2ed..6dbe2b4 100644 --- a/scripts/plotting/plotting_thesis/rpob/pe_sens_site_count_rpob.R +++ b/scripts/plotting/plotting_thesis/rpob/pe_sens_site_count_rpob.R @@ -7,7 +7,7 @@ source("/home/tanu/git/LSHTM_analysis/scripts/plotting/plotting_thesis/rpob/sens pe_colour_map = c("DD_lig" = "#f0e68c" # khaki , "SS_lig" = "#ffd700" # gold - , "DD_nucleic_acid"= "#d2b48c" # sandybrown + , "DD_nucleic_acid"= "#d2b48c" # tan or sandybrown , "SS_nucleic_acid"= "#a0522d" # sienna , "DD_ppi2" = "#da70d6" # orchid