Commit bbdeaa4b by Carine Rey

### fix error if preview

parent 0009f51e
 ... ... @@ -405,7 +405,20 @@ df_auc = subset(df_auc, methode %in% condensed_meths) df_auc\$auc_rank = unlist(tapply(df_auc\$auc,df_auc\$couple, function(x){rank(-x)})) df_auc\$auc2_rank = unlist(tapply(df_auc\$auc2,df_auc\$couple, function(x){rank(-x)})) df_auc\$best_R_90_P_rank = unlist(tapply(df_auc\$best_R_90_P,df_auc\$couple,function(x){rank(-x)})) print(df_auc) df_auc\$string_auc = paste0(df_auc\$auc_rank, " (", round(df_auc\$auc,3),")") df_auc\$string_auc2 = paste0(df_auc\$auc_rank, " (", round(df_auc\$auc2,3),")") df_auc\$string_best_R_90_P = paste0(df_auc\$best_R_90_P_rank, " (", round(df_auc\$best_R_90_P,3),")") df_only_auc = dcast(df_auc, methode ~ couple, value.var="string_auc" ) colnames(df_only_auc)[1] = "methode\auc" df_only_auc2 = dcast(df_auc, methode ~ couple, value.var="string_auc2" ) colnames(df_only_auc2)[1] = "methode\auc2" df_only_string_best_R_90_P = dcast(df_auc, methode ~ couple, value.var="string_best_R_90_P" ) colnames(df_only_string_best_R_90_P)[1] = "methode\best_R_90_P" print(df_only_auc) ######################################################################## ... ... @@ -471,7 +484,7 @@ plot_out = function(df_out, df_d , df_recall_sup09_per_meth, meths = NULL, suffi ) print("plot recall_precision") if (length(meths) <= 9) { if (length(meths) <= 9 & all(c("H0/HaPC NeG1","H0/HaPC NeG2","H0/HaPC NeG4","H0/H0 NeG4/NeG4_NeC_1","H0/H0 NeG1/NeG1_NeC_4", "H0/HaPC NeG4_NeC_1","H0/HaPC NeG1_NeC_4") %in% df_out\$couple)) { couple_i = c("H0/HaPC NeG1","H0/HaPC NeG2","H0/HaPC NeG3","H0/HaPC NeG4","H0/HaPC NeG5","H0/H0 NeG5/NeG5_NeC_1","H0/H0 NeG1/NeG1_NeC_5", "H0/HaPC NeG5_NeC_1","H0/HaPC NeG1_NeC_5","H0/H0 NeG5/NeG4_NeC_1","H0/H0 NeG3/NeG1_NeC_4", "H0/HaPC NeG4_NeC_1","H0/HaPC NeG1_NeC_4") plot = ggplot(subset(df_out, couple %in% couple_i), aes(x=sensitivity, y=precision98_02, col = methode)) plot = plot + theme_bw() ... ... @@ -862,8 +875,8 @@ plot_out(df_out, df_d, df_recall_sup09_per_meth, meths=condensed_meths, suffix= write.table(df_d, file=paste0(opt\$out,".complete_d.tsv"), row.names=FALSE, quote=F, sep = "\t") write.table(df_out, file=paste0(opt\$out,".complete.tsv"), row.names=FALSE, quote=F, sep = "\t") write.table(df_auc, file=paste0(opt\$out,".auc.tsv"), row.names=FALSE, quote=F, sep = "\t") write.table(subset(df_auc, methode %in% condensed_meths), file=paste0(opt\$out,".auc_condensed.tsv"), row.names=FALSE, quote=F, sep = "\t") write.table(df_auc, file=paste0(opt\$out,".auc_condensed.tsv"), row.names=FALSE, quote=F, sep = "\t") write.table(df_only_auc2, append = FALSE, file=paste0(opt\$out,".auc_condensed.tsv"), row.names=FALSE, quote=F, sep = "\t") write.table(df_only_auc, append = T,file=paste0(opt\$out,".auc_condensed.tsv"), row.names=FALSE, quote=F, sep = "\t") write.table(df_only_string_best_R_90_P, append = T,file=paste0(opt\$out,".auc_condensed.tsv"), row.names=FALSE, quote=F, sep = "\t") write.table(df_max_mcc_per_method, file=paste0(opt\$out,".max_MCC_per_meth.tsv"), row.names=FALSE, quote=F, sep = "\t") write.table(df_recall_sup09_per_meth, file=paste0(opt\$out,".recall09_per_meth.tsv"), row.names=FALSE, quote=F, sep = "\t")
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