Visualization

Modules/FindRscript.cmake

@@ -0,0 +1,3 @@
+find_program(RSCRIPT_COMMAND Rscript DOC "Rscript executable.")
+
+find_package_handle_standard_args(Rscript DEFAULT_MSG RSCRIPT_COMMAND)

src/CMakeLists.txt

@@ -4,6 +4,7 @@ include(CheckLibraryExists)
 
 add_subdirectory(lib)
 add_subdirectory(treecall)
+add_subdirectory(mutmap)
 
 include_directories(BEFORE "${CMAKE_CURRENT_BINARY_DIR}")
 

src/mutmap/CMakeLists.txt

@@ -0,0 +1,36 @@
+find_package(Rscript)
+
+set(MUTMAP_DIR ${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_LIBEXECDIR}/mutmap)
+
+configure_file("${CMAKE_CURRENT_SOURCE_DIR}/mutmap.sh.in"
+  "${CMAKE_CURRENT_BINARY_DIR}/mutmap.sh" @ONLY)
+
+configure_file("${CMAKE_CURRENT_SOURCE_DIR}/build.R"
+  "${CMAKE_CURRENT_BINARY_DIR}/build.R" @ONLY)
+
+configure_file("${CMAKE_CURRENT_SOURCE_DIR}/bundle.js"
+  "${CMAKE_CURRENT_BINARY_DIR}/bundle.js" @ONLY)
+
+configure_file("${CMAKE_CURRENT_SOURCE_DIR}/index.html"
+  "${CMAKE_CURRENT_BINARY_DIR}/index.html" @ONLY)
+
+configure_file("${CMAKE_CURRENT_SOURCE_DIR}/pedigree_and_layout.R"
+  "${CMAKE_CURRENT_BINARY_DIR}/pedigree_and_layout.R" @ONLY)
+
+install (DIRECTORY DESTINATION ${MUTMAP_DIR})
+
+install (PROGRAMS "${CMAKE_CURRENT_BINARY_DIR}/mutmap.sh"
+  DESTINATION ${CMAKE_INSTALL_LIBEXECDIR} RENAME dng-mutmap)
+
+install (FILES "${CMAKE_CURRENT_BINARY_DIR}/build.R"
+  DESTINATION ${MUTMAP_DIR})
+
+install (FILES "${CMAKE_CURRENT_BINARY_DIR}/bundle.js"
+  DESTINATION ${MUTMAP_DIR})
+
+install (FILES "${CMAKE_CURRENT_BINARY_DIR}/index.html"
+  DESTINATION ${MUTMAP_DIR})
+
+install (FILES "${CMAKE_CURRENT_BINARY_DIR}/pedigree_and_layout.R"
+  DESTINATION ${MUTMAP_DIR})
+

src/mutmap/build.R

@@ -0,0 +1,108 @@
+#!/usr/bin/env Rscript
+
+parseArguments <- function() {
+
+    library(argparser, quietly=TRUE)
+
+    argParser <- arg_parser("Visualization for DeNovoGear")
+    argParser <- add_argument(argParser, "sourceDirectory",
+                              help="Source directory for input files",
+                              type="character")
+    argParser <- add_argument(argParser, "pedFilePath",
+                              help="Path to pedigree file", type="character")
+    argParser <- add_argument(argParser, "dngOutputFilePath",
+                              help="DeNovoGear output VCF", type="character")
+    argParser <- add_argument(argParser, "outputFilePath",
+                              help="Where to write the output",
+                              type="character")
+    argv <- parse_args(argParser)
+    return(argv)
+}
+
+computeLayout <- function(pedFilePath) {
+
+    library(kinship2, quietly=TRUE)
+    library(jsonlite, quietly=TRUE)
+
+    data <- read.table(pedFilePath, header=FALSE)
+
+    ped <- pedigree(id=data[,2], dadid=data[,3], momid=data[,4], sex=data[,5],
+                    famid=data[,1])
+
+    ped1 <- ped['1']
+    outData <- list()
+    outData$layout <- align.pedigree(ped1)
+    pedigree <- list()
+    pedigree$id <- ped1$id
+    pedigree$famid <- ped1$famid
+    pedigree$sex <- ped1$sex
+    pedigree$findex <- ped1$findex
+    pedigree$mindex <- ped1$mindex
+    outData$pedigree <- pedigree
+
+    jsonOut <- (toJSON(outData, pretty=TRUE, digits=NA))
+    return(jsonOut)
+}
+
+readFile <- function(filePath) {
+    return(readChar(filePath, file.info(filePath)$size))
+}
+
+escapeAsciiForJavaScript <- function(string) {
+    return(gsub('\n', '\\\\x0A', gsub('"', '\\\\x22', string)))
+}
+
+build <- function(sourceDirectory, pedFilePath, dngOutputFilePath,
+                  outputFilePath) {
+
+    pedFileText <- escapeAsciiForJavaScript(readFile(pedFilePath))
+    bundleFilePath <- file.path(sourceDirectory, 'bundle.js')
+    bundleFileText <- readFile(bundleFilePath)
+
+    templateFilePath <- file.path(sourceDirectory, 'index.html')
+    templateFileText <- readFile(templateFilePath)
+    outputText <- sub("<!--BUNDLE_JS_PLACEHOLDER-->", bundleFileText,
+                      templateFileText, fixed=TRUE)
+
+    outputText <- sub("/*PEDIGREE_FILE_TEXT_PLACEHOLDER*/",
+                      paste("var pedigreeFileText = \"", pedFileText, "\";",
+                            sep=""),
+                      outputText, fixed=TRUE)
+
+    layoutData <- computeLayout(pedFilePath)
+    outputText <- sub("/*LAYOUT_DATA_PLACEHOLDER*/",
+                      paste("var layoutData = ", layoutData, ";", sep=""),
+                      outputText, fixed=TRUE)
+
+    dngOutputFileText <- escapeAsciiForJavaScript(readFile(dngOutputFilePath))
+    outputText <- sub("/*DNG_VCF_DATA_PLACEHOLDER*/",
+                      paste("var dngOutputFileText = \"", dngOutputFileText,
+                            "\";", sep=""),
+                      outputText, fixed=TRUE)
+
+    write(outputText, outputFilePath)
+}
+
+test <- function() {
+    sourceDirectory <- file.path('dist')
+    pedFilePath <- file.path('test', 'data', 'test.ped')
+    dngOutputFilePath <- file.path('test', 'data', 'dng_test_output.vcf')
+    outputFilePath <- file.path('mutmap.html')
+
+    build(sourceDirectory, pedFilePath, dngOutputFilePath, outputFilePath)
+}
+
+main <- function() {
+    argv <- parseArguments()
+    sourceDirectory <- argv$sourceDirectory
+    pedFilePath <- argv$pedFilePath
+    dngOutputFilePath <- argv$dngOutputFilePath
+    outputFilePath <- argv$outputFilePath
+
+    build(sourceDirectory, pedFilePath, dngOutputFilePath, outputFilePath)
+}
+
+if (!interactive()) {
+    main()
+}
+