From 71c3dab056adbc7fee4ce0b3c641ce8e21217e3e Mon Sep 17 00:00:00 2001
From: ShixiangWang <wangshx@shanghaitech.edu.cn>
Date: Thu, 8 Dec 2022 21:08:33 +0800
Subject: [PATCH] Add shiny PCAWG cancer type control

---
 DESCRIPTION                                             | 2 +-
 NEWS.md                                                 | 5 +++++
 inst/shinyapp/modules/modules-pcawg-survival-analysis.R | 6 ++++++
 3 files changed, 12 insertions(+), 1 deletion(-)

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())),