diff --git a/DESCRIPTION b/DESCRIPTION index d398ac81..cbb9987a 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: UCSCXenaShiny Title: Interactive Analysis of UCSC Xena Data -Version: 1.1.8 +Version: 1.1.9 Authors@R: c(person(given = "Shixiang", family = "Wang", diff --git a/NEWS.md b/NEWS.md index 13535b80..49fd1650 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,8 @@ +# UCSCXenaShiny 1.1.9 + +- Added cancer type control for PCAWG survival analysis. +- Added TCGA batch id from MDA. + # UCSCXenaShiny 1.1.8 - Fixed issue to set mislabelled color in pcawg pan-cancer analysis (#247, Thanks to Tangjian Li). diff --git a/inst/shinyapp/modules/modules-pcawg-survival-analysis.R b/inst/shinyapp/modules/modules-pcawg-survival-analysis.R index 9d9e1573..b4559171 100644 --- a/inst/shinyapp/modules/modules-pcawg-survival-analysis.R +++ b/inst/shinyapp/modules/modules-pcawg-survival-analysis.R @@ -4,6 +4,10 @@ ui.modules_pcawg_sur_plot <- function(id) { fluidPage( fluidRow( column(3, wellPanel( + selectInput( + inputId = ns("dataset"), label = "Choose a dataset:", + choices = unique(pcawg_info$dcc_project_code) + ), shinyWidgets::prettyRadioButtons( inputId = ns("profile"), label = "Select a genomic profile:", choiceValues = c("mRNA", "miRNA_TMM", "miRNA_UQ", @@ -233,6 +237,7 @@ server.modules_pcawg_sur_plot <- function(input, output, session) { val_dat <- data.frame("icgc_specimen_id" = names(val),"val" = as.numeric(val)) dat <- dplyr::inner_join(pcawg_info,val_dat,by="icgc_specimen_id") %>% + dplyr::filter(.data$dcc_project_code %in% input$dataset) %>% dplyr::filter(!is.na(.data$OS.time)) %>% dplyr::select( sampleID = icgc_specimen_id, status = OS , @@ -267,6 +272,7 @@ server.modules_pcawg_sur_plot <- function(input, output, session) { plot_text <- eventReactive(input$go, { paste( + paste("Dataset :", input$dataset), paste("Profile :", input$profile), paste("Item :", input$item_input), paste("Number of cases :", nrow(filter_dat())),