Cna tab

DESCRIPTION

@@ -5,7 +5,8 @@ Version: 0.99.3
 Date: 2021-03-16
 Authors@R: c(
     person(given = "Arsenij", family = "Ustjanzew", email = "[email protected]", role = c("aut", "cre", "cph"), comment = c(ORCID = "0000-0002-1014-4521")),
-    person("Federico", "Marini", role = "aut", email = "[email protected]", comment = c(ORCID = '0000-0003-3252-7758')))
+    person("Federico", "Marini", role = "aut", email = "[email protected]", comment = c(ORCID = '0000-0003-3252-7758')),
+    person(given = "Charlotte", family = "Reuschel", email = "[email protected]", role = "aut", comment = c(ORCID = "0000-0003-2722-279X")))
 Description: This R package provides an R Shiny application that enables the user to generate, 
     manage, and edit data and metadata files suitable for the import in cBioPortal for Cancer Genomics. 
     Create cancer studies and edit its metadata. Upload mutation data of a patient that will be concatenated to the data_mutation_extended.txt file of the study. 

NAMESPACE

@@ -14,6 +14,7 @@ importFrom(basilisk,basiliskStart)
 importFrom(basilisk,basiliskStop)
 importFrom(dplyr,bind_rows)
 importFrom(dplyr,mutate)
+importFrom(htmltools,HTML)
 importFrom(htmltools,tagList)
 importFrom(jsonlite,fromJSON)
 importFrom(magrittr,"%<>%")
@@ -52,6 +53,7 @@ importFrom(shiny,selectInput)
 importFrom(shiny,shinyApp)
 importFrom(shiny,showModal)
 importFrom(shiny,showNotification)
+importFrom(shiny,splitLayout)
 importFrom(shiny,tags)
 importFrom(shiny,textInput)
 importFrom(shiny,uiOutput)

R/cbpManager-pkg.R

@@ -6,7 +6,7 @@
 #' @author Arsenij Ustjanzew \email{arsenij.ustjanzew@@gmail.com}
 #'
 #' @importFrom magrittr %>% %<>%
-#' @importFrom shiny actionButton column dateInput fluidRow icon invalidateLater
+#' @importFrom shiny actionButton column dateInput fluidRow icon invalidateLater splitLayout
 #' modalButton modalDialog NS numericInput observeEvent reactive reactiveValues
 #' reactiveValuesToList removeModal renderText renderUI runApp selectInput
 #' shinyApp showModal showNotification textInput uiOutput updateSelectInput
@@ -17,7 +17,7 @@
 #' @importFrom dplyr bind_rows mutate
 #' @importFrom jsonlite fromJSON
 #' @importFrom vroom vroom
-#' @importFrom htmltools tagList
+#' @importFrom htmltools tagList HTML
 #' @importFrom shinydashboard box dashboardBody dashboardHeader dashboardPage
 #' dashboardSidebar menuItem sidebarMenu tabBox tabItem tabItems
 #' @importFrom DT renderDT styleEqual DTOutput datatable formatStyle renderDataTable

R/functions.R

@@ -534,3 +534,30 @@ Please try reinstalling cbpManager and basilisk or contact the support at https:
     }
   })
 }
+
+#' Read a metafile line by line into a data frame. 
+#'
+#' @param filepath Filepath with filename of metafile. 
+#' @return data.frame
+#' @examples 
+#' cbpManager:::read_meta(system.file("study", "testpatient", "meta_CNA.txt", package = "cbpManager"))
+#' 
+read_meta <- function(filepath) {
+  meta_df <- data.frame(attribute = character(), value = character())
+  con = file(filepath, "r")
+  while (TRUE) {
+    line = readLines(con, n = 1)
+    if (length(line) == 0) {
+      break
+    }
+    splited_line <- stringr::str_split(line, ": ", n = 2)
+    meta_df <-
+      rbind(meta_df,
+            list(
+              attribute = splited_line[[1]][1], 
+              value = splited_line[[1]][2])
+      )
+  }
+  close(con)
+  return(meta_df)
+}

R/global.R

@@ -3,6 +3,7 @@ source(system.file("tabs", "studyTab.R", package = "cbpManager"), local = TRUE)
 source(system.file("tabs", "patientTab.R", package = "cbpManager"), local = TRUE)
 source(system.file("tabs", "sampleTab.R", package = "cbpManager"), local = TRUE)
 source(system.file("tabs", "mutationsTab.R", package = "cbpManager"), local = TRUE)
+source(system.file("tabs", "cnaTab.R", package = "cbpManager"), local = TRUE)
 source(system.file("tabs", "timelineTab.R", package = "cbpManager"), local = TRUE)
 source(system.file("tabs", "resourceTab.R", package = "cbpManager"), local = TRUE)
 source(system.file("tabs", "validationTab.R", package = "cbpManager"), local = TRUE)

R/shinyAppServer.R

@@ -112,10 +112,12 @@ shinyAppServer <- function(input, output, session) {
   source(system.file("reactives", "reactivesSampleTab.R", package = "cbpManager"), local = TRUE)
   # Tab 4 Mutations ---------------------------------------------------------------
   source(system.file("reactives", "reactivesMutationsTab.R", package = "cbpManager"), local = TRUE)
-  # Tab 5 Timelines  ---------------------------------------------------------------
+  # Tab 5 Copy Number Data ---------------------------------------------------------
+  source(system.file("reactives", "reactivesCnaTab.R", package = "cbpManager"), local = TRUE)
+  # Tab 6 Timelines  ---------------------------------------------------------------
   source(system.file("reactives", "reactivesTimelineTab.R", package = "cbpManager"), local = TRUE)
-  # Tab 6 Resource data  ---------------------------------------------------------------
+  # Tab 7 Resource data  ---------------------------------------------------------------
   source(system.file("reactives", "reactivesResourceTab.R", package = "cbpManager"), local=TRUE)
-  # Tab 7 Validation  ---------------------------------------------------------------
+  # Tab 8 Validation  ---------------------------------------------------------------
   source(system.file("reactives", "reactivesValidationTab.R", package = "cbpManager"), local=TRUE)
 }

R/shinyAppUI.R

@@ -60,6 +60,7 @@ shinyAppUI <- dashboardPage(
       menuItem("Patient", tabName = "patient"),
       menuItem("Sample", tabName = "sample"),
       menuItem("Mutations", tabName = "mutations"),
+      menuItem("Copy Number Data", tabName = "cna"),
       menuItem("Timelines", tabName = "timelines"),
       menuItem("Resources", tabName = "resource"),
       menuItem("Validation", tabName = "validation")
@@ -98,6 +99,9 @@ shinyAppUI <- dashboardPage(
 
       # Tab 4 Mutations - mutationsTab.R
       mutationsTab,
+
+      # Tab Copy Number Data - cnaTab.R
+      cnaTab,
 
       # Tab 5 Timelines - timelineTab.R
       timelineTab,

inst/apphelp/descriptionCnaTab.md

@@ -0,0 +1,23 @@
+**Load a valid copy number data file.** This file is used in cBioPortal for the copy number data panel (see image on the right.)
+
+---
+
+#### Description of a valid copy number alteration data file:
+
+The user can currently upload the file **"all_thresholded.by_genes.txt"** derived from GISTIC 2.0 or a **tab-separated file** containing the following columns:
+
+One or both of:
+
+- **Hugo_Symbol (Required)**: A HUGO gene symbol.
+- **Entrez_Gene_Id (Optional, but recommended)**: An Entrez Gene identifier.
+
+**For each sample in the dataset an additional column is required using the sample ID as column header.** Please make sure that all of the sample IDs have been added to the loaded study via the Sample tab before upload the file.
+
+The discrete copy number data file contains for each gene-sample combination a copy number level. By default the following applies:
+- "-2" is a deep loss, possibly a homozygous deletion
+- "-1" is a single-copy loss (heterozygous deletion)
+- "0" is diploid
+- "1" indicates a low-level gain
+- "2" is a high-level amplification
+
+The information "profile_name" and "profile_description" listed in the metafile can be adapted to the uploaded file (see "Change metadata of copy number alteration" below). It is recommended to provide the source and a brief characterization of the data under "profile_name" and to define the interpretation of the copy number level in the "profile_description". 

inst/apphelp/tour_cna.txt

@@ -0,0 +1,9 @@
+element;intro
+#Welcome;Welcome to the interactive tour for <code>cbpManager</code>!<br><br>In the <b>Copy Number Data</b> tab, you can add copy number alteration data to samples by uploading a file in the appropriate format. In the following you will learn how to do this in detail.
+#cna_description;This box contains a description of the <b>Copy Number Data</b> tab.
+#cna_img;Here you can see an example image how the copy number data will look later in cBioPortal.
+#cna_metadata; Here you have the opportunity of changing the information that is saved in the metafile of the copy number data under "profile_name" and "profile_description". Please refer to the description above for more information.    
+#CNAdata;If the loaded study already has copy number data, it would be shown in this table.
+#chooseCNADiv;Upload a copy number data file to the study. This file will be concatenated to the existing copy number data. Please have a look at the description box for the correct file format! If the upload was successful, the new copy number data is added to the table on the right.
+#saveCNA;Make the changes persistent by saving the file!
+#Thanks;Thank you for taking the <b>Copy Number Data</b> tab tour of <code>cbpManager</code>!