From a3bbb46bd9ab891b6abc01ee665a9fc1c6d9b7cf Mon Sep 17 00:00:00 2001 From: aadamk Date: Wed, 9 Oct 2024 10:33:05 -0400 Subject: [PATCH] Update 04-survival-curves_os.R --- .../post_clustering_associations/04-survival-curves_os.R | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/analyses/post_clustering_associations/04-survival-curves_os.R b/analyses/post_clustering_associations/04-survival-curves_os.R index 51d3182..9a495f8 100644 --- a/analyses/post_clustering_associations/04-survival-curves_os.R +++ b/analyses/post_clustering_associations/04-survival-curves_os.R @@ -33,6 +33,7 @@ dir.create(output_dir, showWarnings = F, recursive = T) mm_clusters <- read_tsv(file = opt$cluster_file) # combine Multi-modal clusters with RNA-derived molecular subtypes +cat('Joining multi-omic cluster annotations with histologic data') histology_file <- opt$histology_file anno_file_rna <- read_tsv(file = histology_file) %>% dplyr::select( @@ -84,6 +85,7 @@ custom_table_theme <- theme_survminer(base_size = 12) + theme(axis.title.x = element_blank(), axis.title.y = element_blank()) # survival curves stratified by RNA-derived molecular subtype +cat('Generating Kaplan Meier survival plots by molecular subtypes') surv_data$molecular_subtype <- factor(surv_data$molecular_subtype, levels = sort(unique(surv_data$molecular_subtype))) fit <- survival::survfit(formula = Surv(as.numeric(OS_days), OS_status) ~ molecular_subtype, data = surv_data) @@ -114,6 +116,7 @@ print(p) dev.off() # survival curves stratified by Methylation-derived molecular subtype (v11) +cat('Generating Kaplan Meier survival plots by DKFZ v11 subtypes') surv_data$dkfz_v11_methylation_subclass <- factor(surv_data$dkfz_v11_methylation_subclass, levels = sort(unique( surv_data$dkfz_v11_methylation_subclass ))) @@ -165,6 +168,7 @@ print(p) dev.off() # survival curves stratified by Methylation-derived molecular subtype (v12) +cat('Generating Kaplan Meier survival plots by DKFZ v12 subtypes') surv_data$dkfz_v12_methylation_subclass <- factor(surv_data$dkfz_v12_methylation_subclass, levels = sort(unique( surv_data$dkfz_v12_methylation_subclass ))) @@ -225,6 +229,7 @@ print(p) dev.off() # survival curves stratified by Multi-modal subtypes +cat('Generating Kaplan Meier survival plots by multi-omic subtypes') surv_data$mm_cluster <- factor(surv_data$mm_cluster, levels = sort(as.numeric(unique( surv_data$mm_cluster ))))