mikejiang authored on 15/04/2016 21:24:31
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+Package: CytoML |
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+Type: Package |
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+Title: GatingML interface for openCyto |
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+Version: 0.1 |
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+Date: 2016-04-15 |
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+Author: Mike Jiang |
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+Maintainer: Mike Jiang <wjiang2@fhcrc.org> |
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+Description: This package is designed to use GatingML2.0 as the standard format to exchange the gated data with other software platform. |
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+License: Artistic-2.0 |
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+LazyData: TRUE |
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+Imports: |
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+ flowCore, |
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+ flowWorkspace, |
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+ XML, |
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+ data.table, |
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+ flowUtils (>= 1.35.7), |
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+ jsonlite, |
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+ RBGL, |
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+ graph, |
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+ base64enc |
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+biocViews: FlowCytometry, DataImport, DataRepresentation |
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+Suggests: |
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+ testthat, |
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+ flowWorkspaceData, |
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+ knitr, |
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+ ggcyto |
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+VignetteBuilder: knitr |
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+RoxygenNote: 5.0.1 |
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+# Generated by roxygen2 (4.1.0): do not edit by hand |
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+ |
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+S3method(extend,ellipsoidGate) |
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+S3method(extend,polygonGate) |
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+S3method(extend,rectangleGate) |
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+export(GatingSet2GatingML) |
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+export(compare.counts) |
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+export(extend) |
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+export(parse.gatingML) |
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+export(read.gatingML.cytobank) |
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+exportClasses(graphGML) |
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+exportMethods(compensate) |
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+exportMethods(gating) |
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+exportMethods(getChildren) |
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+exportMethods(getCompensationMatrices) |
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+exportMethods(getGate) |
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+exportMethods(getNodes) |
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+exportMethods(getParent) |
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+exportMethods(getTransformations) |
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+exportMethods(plot) |
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+exportMethods(show) |
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+import(data.table) |
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+importClassesFrom(Biobase,AssayData) |
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+importClassesFrom(graph,graph) |
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+importClassesFrom(graph,graphBase) |
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+importClassesFrom(graph,graphNEL) |
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+importClassesFrom(methods,ANY) |
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+importClassesFrom(methods,character) |
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+importClassesFrom(methods,data.frame) |
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+importClassesFrom(methods,environment) |
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+importClassesFrom(methods,list) |
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+importClassesFrom(methods,logical) |
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+importClassesFrom(methods,matrix) |
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+importClassesFrom(methods,missing) |
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+importClassesFrom(methods,numeric) |
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+importClassesFrom(methods,oldClass) |
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+importFrom(RBGL,tsort) |
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+importFrom(Rgraphviz,layoutGraph) |
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+importFrom(Rgraphviz,renderGraph) |
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+importFrom(XML,"xmlAttrs<-") |
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+importFrom(XML,addChildren) |
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+importFrom(XML,getNodeSet) |
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+importFrom(XML,newXMLNode) |
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+importFrom(XML,saveXML) |
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+importFrom(XML,xmlAttrs) |
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+importFrom(XML,xmlChildren) |
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+importFrom(XML,xmlElementsByTagName) |
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+importFrom(XML,xmlGetAttr) |
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+importFrom(XML,xmlName) |
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+importFrom(XML,xmlNode) |
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+importFrom(XML,xmlRoot) |
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+importFrom(XML,xmlTree) |
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+importFrom(XML,xmlTreeParse) |
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+importFrom(XML,xmlValue) |
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+importFrom(base64enc,base64decode) |
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+importFrom(base64enc,base64encode) |
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+importFrom(flowCore,"parameters<-") |
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+importFrom(flowCore,colnames) |
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+importFrom(flowCore,compensate) |
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+importFrom(flowCore,ellipsoidGate) |
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+importFrom(flowCore,eval) |
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+importFrom(flowCore,parameters) |
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+importFrom(flowCore,polygonGate) |
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+importFrom(flowCore,rectangleGate) |
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+importFrom(flowUtils,read.gatingML) |
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+importFrom(flowUtils,write.gatingML) |
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+importFrom(flowWorkspace,GatingSet) |
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+importFrom(flowWorkspace,add) |
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+importFrom(flowWorkspace,asinh_Gml2) |
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+importFrom(flowWorkspace,flow_trans) |
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+importFrom(flowWorkspace,getChildren) |
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+importFrom(flowWorkspace,getCompensationMatrices) |
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+importFrom(flowWorkspace,getGate) |
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+importFrom(flowWorkspace,getNodes) |
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+importFrom(flowWorkspace,getParent) |
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+importFrom(flowWorkspace,getPopStats) |
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+importFrom(flowWorkspace,getTransformations) |
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+importFrom(flowWorkspace,recompute) |
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+importFrom(flowWorkspace,sampleNames) |
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+importFrom(flowWorkspace,transform) |
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+importFrom(flowWorkspace,transformerList) |
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+importFrom(graph,"nodeData<-") |
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+importFrom(graph,"nodeDataDefaults<-") |
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+importFrom(graph,"nodeRenderInfo<-") |
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+importFrom(graph,"nodes<-") |
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+importFrom(graph,addEdge) |
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+importFrom(graph,edges) |
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+importFrom(graph,graphNEL) |
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+importFrom(graph,inEdges) |
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+importFrom(graph,nodeData) |
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+importFrom(graph,removeNode) |
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+importFrom(graphics,plot) |
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+importFrom(jsonlite,fromJSON) |
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+importFrom(jsonlite,toJSON) |
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+importFrom(methods,show) |
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+importFrom(ncdfFlow,read.ncdfFlowSet) |
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+importFrom(openCyto,gating) |
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+#' Convert a GatingSet to gatingML |
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+#' |
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+#' this function retrieves the gates from GatingSet |
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+#' and writes a customed GatingML-2.0 file |
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+#' which can then be imported into cytobank |
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+#' operation: |
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+#' 1. Read in gate geometry, compensation and transformation from gatingSet |
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+#' 2. Rescale gate boundaries with flowJoTrans() so gates show up in flowJo |
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+#' 3. Save gates and hierarchy structure to R environment |
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+#' 4. Write environment out to gatingML using write.GatingML() |
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+#' @importFrom flowUtils write.gatingML |
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+#' @importFrom XML saveXML xmlTreeParse xmlRoot |
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+#' @export |
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+#' @examples |
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+#' \dontrun{
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+#' library(CytoML) |
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+#' dataDir <- system.file("extdata",package="flowWorkspaceData")
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+#' gs <- load_gs(list.files(dataDir, pattern = "gs_manual",full = TRUE)) |
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+#' outFile <- tempfile(fileext = ".xml") |
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+#' GatingSet2GatingML(gs, outFile) |
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+#' } |
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+GatingSet2GatingML <- function(gs, outFile, showHidden = FALSE, ...){
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+ flowEnv <- GatingSet2Environment(gs, showHidden = showHidden, ...) |
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+ tmp <- tempfile(fileext = ".xml")#ensure correct file extension for xmlTreeParse to work |
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+ flowUtils::write.gatingML(flowEnv, tmp) |
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+ tree <- xmlTreeParse(tmp, trim = FALSE) |
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+ root <- xmlRoot(tree) |
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+ # browser() |
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+ |
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+ root <- addCustomInfo(root, gs, flowEnv, showHidden = showHidden, ...) |
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+ #add pop (GateSet/BooleanAndGate) |
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+ root <- addGateSets(root, gs, flowEnv[["guid_mapping"]], showHidden = showHidden) |
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+ #add experiment info to custom node |
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+ root <- addExperimentInfo(root) |
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+ saveXML(root, file = outFile) |
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+} |
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+ |
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+ |
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+#' extract the trans, comps and gates into GML2 compatible format |
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+#' and save to environment |
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+GatingSet2Environment <- function(gs, cytobank.default.scale = TRUE, showHidden) {
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+ if(cytobank.default.scale) |
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+ warning("With 'cytobank.default.scale' set to 'TRUE', data and gates will be re-transformed with cytobank's default scaling settings, which may affect how gates look like.")
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+ flowEnv <- new.env(parent = emptyenv()) |
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+ |
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+ #parse comp and channel names |
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+ comp <- gs@compensation |
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+ if(is.null(comp)){
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+ #(assume it is identical across samples) |
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+ comp.obj <- flowWorkspace:::.cpp_getCompensation(gs@pointer, sampleNames(gs)[1]) |
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+ if(is.null(comp.obj)){
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+ #no compensation and channel names in transformation are not prefixed |
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+ chnls <- colnames(getData(gs)) |
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+ }else{
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+ #parsed from flowJo and channel names are usually prefixed |
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+ #thus get the raw channel names from here |
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+ chnls <- comp.obj[["parameters"]] |
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+ comp <- compensation(matrix(comp.obj$spillOver |
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+ ,nrow=length(chnls) |
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+ ,ncol=length(chnls) |
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+ ,byrow=TRUE |
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+ ,dimnames=list(chnls,chnls) |
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+ ) |
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+ ) |
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+ |
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+ } |
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+ }else{
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+ #compensation was added in R |
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+ #channel names are not prefixed |
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+ chnls <- as.vector(parameters(comp)) |
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+ |
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+ } |
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+ |
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+ #add comp |
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+ if(!is.null(comp)){
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+ #prefix the channels since cytobank expect that |
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+ prefix_chnls <- paste0("Comp_", chnls)
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+ rownames(comp@spillover) <- prefix_chnls #change fluorochromes and leave detector(colnames) unchanged |
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+ comp <- compensation(comp@spillover) |
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+ |
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+ compId <- identifier(comp) |
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+ compId <- paste("Spill", compId, sep = "_")
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+ identifier(comp) <- compId |
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+ |
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+ flowEnv[[compId]] <- comp |
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+ }else |
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+ prefix_chnls <- chnls |
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+ |
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+ |
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+ |
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+ #add trans (assume it is identical across samples) |
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+ trans <- getTransformations(gs[[1]], only.function = FALSE) |
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+ |
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+ if(length(trans) == 0) |
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+ stop("no transformation is found in GatingSet!")
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+ trans.Gm2objs <- list() |
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+ rescale.gate <- FALSE |
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+ for(transName in names(trans)){
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+ trans.obj <- trans[[transName]] |
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+ type <- trans.obj[["name"]] |
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+ ind <- sapply(chnls, grepl, x = transName, USE.NAMES = FALSE) |
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+ nMatched <- sum(ind) |
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+ if(nMatched > 1) |
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+ stop("More than one channels matched to transformation: ", transName)
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+ else if(nMatched == 1){
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+ trans.func <- trans.obj[["transform"]] |
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+ chnl <- chnls[ind] |
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+ prefix_chnl <- prefix_chnls[ind] |
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+ param.obj <- compensatedParameter(prefix_chnl |
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+ , spillRefId = compId |
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+ , searchEnv = flowEnv |
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+ , transformationId = prefix_chnl) |
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+ |
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+ if(type == "asinhtGml2"){
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+ #extract parameters |
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+ env <- environment(trans.func) |
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+ transID <- paste0("Tr_Arcsinh_", prefix_chnl)
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+ flowEnv[[transID]] <- asinhtGml2(parameters = param.obj |
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+ , M = env[["m"]] |
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+ , T = env[["t"]] |
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+ , A = env[["a"]] |
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+ , transformationId = transID |
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+ ) |
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+ }else if(type == "logicleGml2"){
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+ #extract parameters |
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+ env <- environment(trans.func) |
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+ transID <- paste0("Tr_logicleGml2_", prefix_chnl)
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+ flowEnv[[transID]] <- logicletGml2(parameters = param.obj |
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+ , M = env[["M"]] |
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+ , T = env[["T"]] |
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+ , A = env[["A"]] |
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+ , W = env[["W"]] |
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+ , transformationId = transID |
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+ ) |
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+ }else if(type == "logicle"){
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+ #extract parameters |
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+ env <- environment(trans.func) |
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+ transID <- paste0("Tr_logicle_", prefix_chnl)
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+ flowEnv[[transID]] <- logicletGml2(parameters = param.obj |
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+ , M = env[["m"]] |
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+ , T = env[["t"]] |
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+ , A = env[["a"]] |
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+ , W = env[["w"]] |
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+ , transformationId = transID |
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+ ) |
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+ rescale.gate <- TRUE |
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+ }else if(type %in% c("flowJo_biexp", "flowJo_fasinh")){
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+ transID <- paste0("Tr_Arcsinh_", prefix_chnl)
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+ #use asinhtGml2 with cytobank default setting |
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+ flowEnv[[transID]] <- asinhtGml2(parameters = param.obj |
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+ , M = 0.43429448190325176 |
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+ , T = 176.2801790465702 |
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+ , A = 0.0 |
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+ , transformationId = transID |
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+ ) |
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+ rescale.gate <- TRUE |
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+ }else{
|
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+ # browser() |
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+ stop("unsupported trans: ", type)
|
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+ } |
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+ |
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+ |
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+ } |
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+ |
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+ if(cytobank.default.scale){
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+ rescale.gate <- TRUE |
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+ #overwrite the customed scale with default one |
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+ flowEnv[[transID]] <- asinhtGml2(parameters = param.obj |
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+ , M = 0.43429448190325176 |
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+ , T = 176.2801790465702 |
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+ , A = 0.0 |
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| 172 |
+ , transformationId = transID) |
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+ } |
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+ |
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| 175 |
+ #save another copy of trans.obj in the list |
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+ trans.Gm2objs[[chnl]] <- flowEnv[[transID]] |
|
| 177 |
+ } |
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+ |
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| 179 |
+ #add gates and pops(as GateSets) |
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| 180 |
+ nodePaths <- getNodes(gs, showHidden = showHidden)[-1] |
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| 181 |
+ fcs_names <- pData(gs)[["name"]] |
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| 182 |
+ rng <- range(getData(gs[[1]], use.exprs = FALSE)) |
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| 183 |
+ for(gate_id in seq_along(nodePaths)){
|
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| 184 |
+ nodePath <- nodePaths[gate_id] |
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| 185 |
+ gates <- getGate(gs, nodePath) |
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| 186 |
+ popName <- basename(nodePath) |
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| 187 |
+ for(fcs_id in seq_along(fcs_names)){
|
|
| 188 |
+ sn <- fcs_names[fcs_id] |
|
| 189 |
+ gate <- gates[[sn]] |
|
| 190 |
+# browser() |
|
| 191 |
+ #cytobank does not support negated gate |
|
| 192 |
+ #we have to create inverse gate on our end |
|
| 193 |
+ if(flowWorkspace:::isNegated(gs[[sn]], nodePath)){
|
|
| 194 |
+ gate <- inverse(gate, rng) |
|
| 195 |
+ } |
|
| 196 |
+ #transform to raw scale |
|
| 197 |
+ #and attach comp and trans reference to parameters |
|
| 198 |
+ gate <- processGate(gate, trans.Gm2objs, compId, flowEnv, rescale.gate, trans) |
|
| 199 |
+ |
|
| 200 |
+ parent <- getParent(gs, nodePath) |
|
| 201 |
+ if(parent == "root") |
|
| 202 |
+ parent_id <- 0 |
|
| 203 |
+ else |
|
| 204 |
+ parent_id <- match(parent, nodePaths) |
|
| 205 |
+ |
|
| 206 |
+ guid <- paste("gate", gate_id, fcs_id, sep = "_")
|
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| 207 |
+ identifier(gate) <- guid |
|
| 208 |
+ #add gate |
|
| 209 |
+ flowEnv[[guid]] <- gate |
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| 210 |
+ |
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| 211 |
+ } |
|
| 212 |
+ } |
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| 213 |
+ flowEnv |
|
| 214 |
+} |
|
| 215 |
+ |
|
| 216 |
+#' @importFrom base64enc base64encode base64decode |
|
| 217 |
+base64encode_cytobank <- function(x){
|
|
| 218 |
+ x <- base64encode(charToRaw(x)) |
|
| 219 |
+ x <- gsub("=", ".", x)
|
|
| 220 |
+ x <- gsub("\\+", "_", x)
|
|
| 221 |
+ x <- gsub("/", "-", x)
|
|
| 222 |
+ x |
|
| 223 |
+} |
|
| 224 |
+base64decode_cytobank <- function(x){
|
|
| 225 |
+ x <- gsub("\\.", "=", x)
|
|
| 226 |
+ x <- gsub("_", "\\+", x)
|
|
| 227 |
+ x <- gsub("-", "/", x)
|
|
| 228 |
+ base64decode(x) |
|
| 229 |
+} |
|
| 230 |
+ |
|
| 231 |
+setMethod("transform", signature = c("polygonGate"), function(`_data`, ...){
|
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| 232 |
+ .transform.polygonGate(`_data`, ...) |
|
| 233 |
+}) |
|
| 234 |
+.transform.polygonGate <- function(gate, trans.fun, param){
|
|
| 235 |
+ gate@boundaries[, param] <- trans.fun(gate@boundaries[, param]) |
|
| 236 |
+ gate |
|
| 237 |
+} |
|
| 238 |
+ |
|
| 239 |
+setMethod("transform", signature = c("ellipsoidGate"), function(`_data`, ...){
|
|
| 240 |
+ # .transform.ellipsoidGate(`_data`, ...) |
|
| 241 |
+ transform(as(`_data`, "polygonGate"), ...) |
|
| 242 |
+}) |
|
| 243 |
+# somehow ellips shape is not well perseved after transforming the two antipods and mean |
|
| 244 |
+.transform.ellipsoidGate <- function(gate, trans.fun, param){
|
|
| 245 |
+ #convert cov format to antipotal format since cov can not be transformed independently on each param |
|
| 246 |
+ #it is based on 5.3.1 of gatingML2 doc |
|
| 247 |
+ mu <- gate@mean |
|
| 248 |
+ CC <- gate@cov |
|
| 249 |
+ dims <- colnames(CC) |
|
| 250 |
+ x <- dims[1] |
|
| 251 |
+ y <- dims[2] |
|
| 252 |
+ D <- gate@distance |
|
| 253 |
+ |
|
| 254 |
+# term <- sqrt((CC[x, x] - CC[y, y]) ^ 2 + 4 * CC[x, y] ^ 2) |
|
| 255 |
+# lambda <- ((CC[x, x] + CC[y, y]) + c(term, -term)) / 2 |
|
| 256 |
+# |
|
| 257 |
+# if(CC[x,y] == 0){
|
|
| 258 |
+# X1 <- c(1, 0) |
|
| 259 |
+# X2 <- c(0, 1) |
|
| 260 |
+# }else{
|
|
| 261 |
+# X1 <- c(lambda[1] - CC[y, y], CC[x, y]) |
|
| 262 |
+# X2 <- c(lambda[2] - CC[y, y], CC[x, y]) |
|
| 263 |
+# } |
|
| 264 |
+ #compute eigen value (for a, b) and eigen vector (for angle) |
|
| 265 |
+ res <- eigen(CC) |
|
| 266 |
+ lambda <- res[["values"]] |
|
| 267 |
+ X1 <- res[["vectors"]][,1] |
|
| 268 |
+ if(X1[1] == 0){
|
|
| 269 |
+ theta <- pi/2 |
|
| 270 |
+ }else{
|
|
| 271 |
+ theta <- atan(X1[2]/X1[1]) |
|
| 272 |
+ } |
|
| 273 |
+ |
|
| 274 |
+ a <- sqrt(lambda[1] * D ^ 2) |
|
| 275 |
+ b <- sqrt(lambda[2] * D ^ 2) |
|
| 276 |
+ |
|
| 277 |
+ #get coordinates of centred antipodal points |
|
| 278 |
+ antipod1 <- c(a * cos(theta), a * sin(theta)) |
|
| 279 |
+ antipod2 <- c(b * sin(theta), - b * cos(theta)) |
|
| 280 |
+ # browser() |
|
| 281 |
+ #shift to mu |
|
| 282 |
+ antipod1 <- antipod1 + mu |
|
| 283 |
+ antipod2 <- antipod2 + mu |
|
| 284 |
+ names(antipod1) <- dims |
|
| 285 |
+ names(antipod2) <- dims |
|
| 286 |
+ #transform the respective dim of antipods |
|
| 287 |
+ antipod1[param] <- trans.fun(antipod1[param]) |
|
| 288 |
+ antipod2[param] <- trans.fun(antipod2[param]) |
|
| 289 |
+ |
|
| 290 |
+ # transform to get new mu |
|
| 291 |
+ mu[param] <- trans.fun(mu[param]) |
|
| 292 |
+ #shift to new center |
|
| 293 |
+ antipod1 <- antipod1 - mu |
|
| 294 |
+ antipod2 <- antipod2 - mu |
|
| 295 |
+ #compute the new a, b |
|
| 296 |
+ a <- sqrt(sum(antipod1 ^ 2)) |
|
| 297 |
+ b <- sqrt(sum(antipod2 ^ 2)) |
|
| 298 |
+ #convert it back to the inverse covaiance mat |
|
| 299 |
+ |
|
| 300 |
+ CC.inv <- CC |
|
| 301 |
+ CC.inv[x, x] <- cos(theta) ^ 2 / a ^ 2 + sin(theta) ^ 2 / b ^ 2 |
|
| 302 |
+ CC.inv[y, y] <- sin(theta) ^ 2 / a ^ 2 + cos(theta) ^ 2 / b ^ 2 |
|
| 303 |
+ CC.inv[x, y] <- CC.inv[y, x] <- sin(theta) * cos(theta) * (1/a^2 - 1/b^2) |
|
| 304 |
+ CC <- solve(CC.inv) |
|
| 305 |
+ |
|
| 306 |
+ |
|
| 307 |
+ gate1 <- gate |
|
| 308 |
+ gate1@cov <- CC |
|
| 309 |
+ gate1@mean <- mu |
|
| 310 |
+ # browser() |
|
| 311 |
+ gate1 |
|
| 312 |
+ |
|
| 313 |
+} |
|
| 314 |
+ |
|
| 315 |
+setMethod("transform", signature = c("rectangleGate"), function(`_data`, ...){
|
|
| 316 |
+ .transform.rectangleGate(`_data`, ...) |
|
| 317 |
+}) |
|
| 318 |
+.transform.rectangleGate <- function(gate, trans.fun, param){
|
|
| 319 |
+ |
|
| 320 |
+ min <- gate@min[[param]] |
|
| 321 |
+ if(!is.infinite(min)) |
|
| 322 |
+ gate@min[[param]] <- trans.fun(min) |
|
| 323 |
+ |
|
| 324 |
+ max <- gate@max[[param]] |
|
| 325 |
+ if(!is.infinite(max)) |
|
| 326 |
+ gate@max[[param]] <- trans.fun(max) |
|
| 327 |
+ |
|
| 328 |
+ gate |
|
| 329 |
+ |
|
| 330 |
+} |
|
| 331 |
+#' @importFrom flowCore eval |
|
| 332 |
+processGate <- function(gate, gml2.trans, compId, flowEnv, rescale.gate = FALSE, orig.trans){
|
|
| 333 |
+ |
|
| 334 |
+ params <- as.vector(parameters(gate)) |
|
| 335 |
+ chnls <- names(gml2.trans) |
|
| 336 |
+ |
|
| 337 |
+ for(i in seq_along(params)){
|
|
| 338 |
+ param <- params[i] |
|
| 339 |
+ ind <- sapply(chnls, function(chnl)grepl(chnl, param), USE.NAMES = FALSE) |
|
| 340 |
+ nMatched <- sum(ind) |
|
| 341 |
+ if(nMatched == 0){
|
|
| 342 |
+ |
|
| 343 |
+ chnl <- gate@parameters[[i]]@parameters |
|
| 344 |
+ gate@parameters[[i]] <- compensatedParameter(chnl |
|
| 345 |
+ , spillRefId = "uncompensated"#compId |
|
| 346 |
+ , searchEnv = flowEnv |
|
| 347 |
+ , transformationId = chnl |
|
| 348 |
+ ) |
|
| 349 |
+ }else if(nMatched == 1){
|
|
| 350 |
+ chnl <- chnls[ind] |
|
| 351 |
+ orig.trans.obj <- orig.trans[[which(ind)]] |
|
| 352 |
+ gml2.trans.obj <- gml2.trans[[chnl]] |
|
| 353 |
+ if(rescale.gate){
|
|
| 354 |
+ inv.fun <- orig.trans.obj[["inverse"]] |
|
| 355 |
+ trans.fun <- eval(gml2.trans.obj) |
|
| 356 |
+ #rescale |
|
| 357 |
+ gate <- transform(gate, inv.fun, param) |
|
| 358 |
+ gate <- transform(gate, trans.fun, param) |
|
| 359 |
+ } |
|
| 360 |
+ |
|
| 361 |
+ |
|
| 362 |
+ #attach trans reference |
|
| 363 |
+ gate@parameters[[i]] <- gml2.trans.obj |
|
| 364 |
+ }else if(nMatched > 1) |
|
| 365 |
+ stop("multiple trans matched to :", param)
|
|
| 366 |
+ } |
|
| 367 |
+ |
|
| 368 |
+ # round |
|
| 369 |
+ gate |
|
| 370 |
+ |
|
| 371 |
+} |
|
| 372 |
+ |
|
| 373 |
+#' @importFrom XML xmlTree |
|
| 374 |
+addGateSets <- function(root, gs, showHidden, ...) |
|
| 375 |
+{
|
|
| 376 |
+ |
|
| 377 |
+ nodePaths <- getNodes(gs, showHidden = showHidden)[-1] |
|
| 378 |
+ # browser() |
|
| 379 |
+ newNodes <- lapply(seq_along(nodePaths), function(gate_id){
|
|
| 380 |
+ nodePath <- nodePaths[gate_id] |
|
| 381 |
+ curNode <- nodePath |
|
| 382 |
+ pop_name <- basename(nodePath) |
|
| 383 |
+ gate_id_path <- gate_id |
|
| 384 |
+ # browser() |
|
| 385 |
+ repeat{
|
|
| 386 |
+ curNode <- getParent(gs, curNode) |
|
| 387 |
+ if(curNode == "root") |
|
| 388 |
+ break |
|
| 389 |
+ else{
|
|
| 390 |
+ cur_parent_id <- match(curNode, nodePaths) |
|
| 391 |
+ gate_id_path <- c(cur_parent_id, gate_id_path) |
|
| 392 |
+ } |
|
| 393 |
+ |
|
| 394 |
+ } |
|
| 395 |
+ GateSetNode(gate_id, pop_name, gate_id_path, nodePaths, ...) |
|
| 396 |
+ }) |
|
| 397 |
+ |
|
| 398 |
+ addChildren(root, kids = newNodes) |
|
| 399 |
+} |
|
| 400 |
+ |
|
| 401 |
+#' @importFrom jsonlite toJSON |
|
| 402 |
+#' @importFrom XML xmlNode |
|
| 403 |
+GateSetNode <- function(gate_id, pop_name, gate_id_path, nodePaths, guid_mapping){
|
|
| 404 |
+ |
|
| 405 |
+ attrs = c("gating:id" = paste("GateSet", gate_id, sep = "_"))
|
|
| 406 |
+ |
|
| 407 |
+ definition <- toJSON(list(gates = gate_id_path, negGates = vector())) |
|
| 408 |
+ |
|
| 409 |
+ #duplicate the refs if it is the root |
|
| 410 |
+ ref_gate_id_path <- gate_id_path |
|
| 411 |
+ if(length(ref_gate_id_path) == 1) |
|
| 412 |
+ ref_gate_id_path <- c(ref_gate_id_path, ref_gate_id_path) |
|
| 413 |
+ xmlNode("gating:BooleanGate", attrs = attrs
|
|
| 414 |
+ , xmlNode("data-type:custom_info"
|
|
| 415 |
+ , xmlNode("cytobank"
|
|
| 416 |
+ , xmlNode("name", pop_name)
|
|
| 417 |
+ , xmlNode("gate_set_id", gate_id)
|
|
| 418 |
+ , xmlNode("definition", I(definition))#set AsIs to avoid xml escaping
|
|
| 419 |
+ ) |
|
| 420 |
+ ) |
|
| 421 |
+ |
|
| 422 |
+ , xmlNode("gating:and"
|
|
| 423 |
+ #create two dummy reference |
|
| 424 |
+ , .children = lapply(ref_gate_id_path, function(gate_id){
|
|
| 425 |
+ |
|
| 426 |
+ guid <- guid_mapping[[gate_id]] |
|
| 427 |
+ attrs = c("gating:ref" = guid)
|
|
| 428 |
+ xmlNode("gating:gateReference", attrs = attrs)
|
|
| 429 |
+ }) |
|
| 430 |
+ ) |
|
| 431 |
+ ) |
|
| 432 |
+} |
|
| 433 |
+ |
|
| 434 |
+#' add customInfo nodes to each gate node and add BooleanAndGates |
|
| 435 |
+#' @importFrom XML xmlAttrs getNodeSet addChildren xmlAttrs<- |
|
| 436 |
+addCustomInfo <- function(root, gs, flowEnv, cytobank.default.scale = TRUE, showHidden){
|
|
| 437 |
+ nodePaths <- getNodes(gs, showHidden = showHidden)[-1] |
|
| 438 |
+ pd <- pData(gs) |
|
| 439 |
+ fcs_names <- pd[["name"]] |
|
| 440 |
+ fcs_guids <- rownames(pd) |
|
| 441 |
+ translist <- getTransformations(gs[[1]], only.function = FALSE) |
|
| 442 |
+ transNames <- names(translist) |
|
| 443 |
+ rng <- range(getData(gs[[1]], use.exprs = FALSE)) |
|
| 444 |
+ for(id in 1:length(root)){
|
|
| 445 |
+ |
|
| 446 |
+ curNode <- root[[id]] |
|
| 447 |
+ guid <- as.vector(xmlAttrs(curNode, "gating:id")) |
|
| 448 |
+ if(!is.null(guid)&&grepl("gate_", guid)){
|
|
| 449 |
+ #parse pop and fcs info from guid |
|
| 450 |
+ fields <- strsplit(guid, "_")[[1]] |
|
| 451 |
+ gate_id <- as.integer(fields[[2]]) |
|
| 452 |
+ fcs_id <- as.integer(fields[[3]]) |
|
| 453 |
+ |
|
| 454 |
+ nodePath <- nodePaths[gate_id] |
|
| 455 |
+ pop_name<- basename(nodePath) |
|
| 456 |
+ fcs_name <- fcs_names[fcs_id] |
|
| 457 |
+ fcs_guid <- fcs_guids[fcs_id] |
|
| 458 |
+ # browser() |
|
| 459 |
+ |
|
| 460 |
+ gate <- flowEnv[[guid]] |
|
| 461 |
+ gate_type <- class(gate) |
|
| 462 |
+ if(gate_type == "rectangleGate"){
|
|
| 463 |
+ if(length(parameters(gate)) == 1) |
|
| 464 |
+ gate_type <- "RangeGate" |
|
| 465 |
+ else |
|
| 466 |
+ gate_type <- "RectangleGate" |
|
| 467 |
+ }else if(gate_type == "polygonGate") |
|
| 468 |
+ gate_type <- "PolygonGate" |
|
| 469 |
+ else if(gate_type == "ellipsoidGate") |
|
| 470 |
+ gate_type <- "EllipseGate" |
|
| 471 |
+ else |
|
| 472 |
+ stop("unsupported gate: ", gate_type)
|
|
| 473 |
+ # browser() |
|
| 474 |
+ # message(guid) |
|
| 475 |
+ #parse scale info from gate parameter |
|
| 476 |
+ scale <- lapply(gate@parameters@.Data, function(param){
|
|
| 477 |
+ # browser() |
|
| 478 |
+ if(class(param) == "compensatedParameter"){
|
|
| 479 |
+ if(cytobank.default.scale){
|
|
| 480 |
+ thisRng <- c(1, 262144.0) |
|
| 481 |
+ }else{
|
|
| 482 |
+ chnl <- as.vector(parameters(param)) |
|
| 483 |
+ thisRng <- rng[, chnl] |
|
| 484 |
+ } |
|
| 485 |
+ |
|
| 486 |
+ flag <- 1 |
|
| 487 |
+ argument <- "1" |
|
| 488 |
+ }else if(is(param, "singleParameterTransform")){
|
|
| 489 |
+ |
|
| 490 |
+ chnl <- as.vector(parameters(param@parameters)) |
|
| 491 |
+ chnl <- sub("(^Comp_)(.*)", "\\2", chnl) #strip the prefix before matching
|
|
| 492 |
+ ind <- grepl(chnl, names(rng)) |
|
| 493 |
+ nMatched <- sum(ind) |
|
| 494 |
+ if(nMatched == 1){
|
|
| 495 |
+ if(cytobank.default.scale){
|
|
| 496 |
+ thisRng <- c(-200, 262144.0) |
|
| 497 |
+ }else |
|
| 498 |
+ thisRng <- rng[, ind] |
|
| 499 |
+ }else |
|
| 500 |
+ stop(chnl , " not found in range info") |
|
| 501 |
+ if(is(param, "asinhtGml2")){
|
|
| 502 |
+ flag <- 4 |
|
| 503 |
+ argument <- as.character(round(param@T/sinh(1))) |
|
| 504 |
+ }else if(is(param, "logicletGml2")){
|
|
| 505 |
+ flag <- 4 |
|
| 506 |
+ argument <- as.character(round(param@T/sinh(1))) |
|
| 507 |
+ }else |
|
| 508 |
+ stop("unsupported transform: ", class(param))
|
|
| 509 |
+ if(!cytobank.default.scale){
|
|
| 510 |
+ #inverse range into raw scale |
|
| 511 |
+ ind <- sapply(transNames, function(transName)grepl(chnl, transName), USE.NAMES = FALSE) |
|
| 512 |
+ nMatched <- sum(ind) |
|
| 513 |
+ if(nMatched == 1){
|
|
| 514 |
+ trans.obj <- translist[[which(ind)]] |
|
| 515 |
+ trans.fun <- trans.obj[["inverse"]] |
|
| 516 |
+ thisRng <- round(trans.fun(thisRng))#cytobank experiment scale expect 0 digits after decimal |
|
| 517 |
+ }else |
|
| 518 |
+ stop("can't find the transformation function in GatingSet to inverse the range for :", chnl)
|
|
| 519 |
+ } |
|
| 520 |
+ |
|
| 521 |
+ }else |
|
| 522 |
+ stop("unsupported transform: ", class(param))
|
|
| 523 |
+ |
|
| 524 |
+ thisRng <- round(thisRng, 2) |
|
| 525 |
+ list(flag = flag, argument = argument, min = thisRng[1], max = thisRng[2], bins = 256, size = 256) |
|
| 526 |
+ }) |
|
| 527 |
+ if(length(scale) == 1){
|
|
| 528 |
+ scale <- unlist(scale, recursive = FALSE) |
|
| 529 |
+ }else{
|
|
| 530 |
+ names(scale) <- c("x", "y")
|
|
| 531 |
+ } |
|
| 532 |
+ definition <- list(scale = scale) |
|
| 533 |
+ definition <- toJSON(definition, auto_unbox = TRUE) |
|
| 534 |
+ #insert custom info |
|
| 535 |
+ customNode <- customInfoNodeForGate(id, gate_id, pop_name, fcs_id, fcs_name, gate_type, definition) |
|
| 536 |
+ newNode <- addChildren(curNode, kids = list(customNode), at = 0) |
|
| 537 |
+ #modify id |
|
| 538 |
+ guid.new <- paste("Gate", id, base64encode_cytobank(pop_name), sep = "_")
|
|
| 539 |
+ xmlAttrs(newNode, suppressNamespaceWarning = TRUE, append = FALSE) <- c("gating:id" = guid.new)
|
|
| 540 |
+ #update the tree |
|
| 541 |
+ root[[id]] <- newNode |
|
| 542 |
+ |
|
| 543 |
+ #record the mapping between gate_id and guid.new for the refs of GateSets |
|
| 544 |
+ if(fcs_id == 1) |
|
| 545 |
+ flowEnv[["guid_mapping"]][[gate_id]] <- guid.new |
|
| 546 |
+ } |
|
| 547 |
+ } |
|
| 548 |
+ root |
|
| 549 |
+ |
|
| 550 |
+} |
|
| 551 |
+ |
|
| 552 |
+#' @importFrom XML newXMLNode |
|
| 553 |
+customInfoNodeForGate <- function(id, gate_id, pop_name, fcs_id, fcs_name, type, definition) |
|
| 554 |
+{
|
|
| 555 |
+ if(fcs_id == 1){
|
|
| 556 |
+ fcs_id <- fcs_name <- "" |
|
| 557 |
+ } |
|
| 558 |
+ |
|
| 559 |
+ #avoid using newXMLNode since it is not segfault-free. |
|
| 560 |
+ xmlNode("data-type:custom_info"
|
|
| 561 |
+ , xmlNode("cytobank"
|
|
| 562 |
+ , xmlNode("name", pop_name)
|
|
| 563 |
+ , xmlNode("id", id)
|
|
| 564 |
+ , xmlNode("gate_id", gate_id)
|
|
| 565 |
+ , xmlNode("type", type)
|
|
| 566 |
+ , xmlNode("version", 1)
|
|
| 567 |
+ , xmlNode("fcs_file_id", fcs_id)
|
|
| 568 |
+ , xmlNode("fcs_file_filename", fcs_name)
|
|
| 569 |
+ , xmlNode("definition", I(definition))
|
|
| 570 |
+ ) |
|
| 571 |
+ ) |
|
| 572 |
+} |
|
| 573 |
+ |
|
| 574 |
+addExperimentInfo <- function(root, experiment_number = ""){
|
|
| 575 |
+ |
|
| 576 |
+ customNode <- root[["custom_info"]] |
|
| 577 |
+ customNode <- addChildren(customNode, xmlNode("flowWorkspace-version", packageVersion("flowWorkspace")))
|
|
| 578 |
+ |
|
| 579 |
+ newNode <- xmlNode("cytobank"
|
|
| 580 |
+ , xmlNode("experiment_number", experiment_number)
|
|
| 581 |
+ ) |
|
| 582 |
+ customNode <- addChildren(customNode, newNode, at = 0) |
|
| 583 |
+ |
|
| 584 |
+ root[["custom_info"]] <- customNode |
|
| 585 |
+ root |
|
| 586 |
+} |
|
| 587 |
+ |
|
| 588 |
+inverse <- function(gate, boundary){
|
|
| 589 |
+ UseMethod("inverse")
|
|
| 590 |
+} |
|
| 591 |
+ |
|
| 592 |
+inverse.polygonGate <- function(gate, ...){
|
|
| 593 |
+ gate@boundaries <- inverse.polygon(gate@boundaries, ...) |
|
| 594 |
+ gate |
|
| 595 |
+} |
|
| 596 |
+inverse.ellipsoidGate <- function(gate, ...){
|
|
| 597 |
+ inverse(as(gate, "polygonGate"), ...) |
|
| 598 |
+} |
|
| 599 |
+inverse.rectangleGate <- function(gate, ...){
|
|
| 600 |
+ param <- as.vector(parameters(gate)) |
|
| 601 |
+ if(length(param) == 1){
|
|
| 602 |
+ stop("to be implemented!")
|
|
| 603 |
+ }else |
|
| 604 |
+ inverse(as(gate, "polygonGate"), ...) |
|
| 605 |
+} |
|
| 606 |
+ |
|
| 607 |
+inverse.polygon <- function(mat, boundary){
|
|
| 608 |
+ |
|
| 609 |
+ |
|
| 610 |
+ dims <- colnames(mat) |
|
| 611 |
+ stopifnot(all(dims %in% colnames(boundary))) |
|
| 612 |
+ |
|
| 613 |
+ #enlarge the boundary to ensure the negated polygon includes all events outside of original polygon |
|
| 614 |
+ boundary["min", ] <- boundary["min", ] - 1e4 |
|
| 615 |
+ boundary["max", ] <- boundary["max", ] + 1e4 |
|
| 616 |
+ |
|
| 617 |
+ x <- dims[1] |
|
| 618 |
+ y <- dims[2] |
|
| 619 |
+ |
|
| 620 |
+ #find the top most point as starting point |
|
| 621 |
+ ind <- which.max(mat[, y]) |
|
| 622 |
+ #reorder mat starting from top most |
|
| 623 |
+ nRow <- nrow(mat) |
|
| 624 |
+ orig.seq <- seq_len(nRow) |
|
| 625 |
+ seq1 <- ind:nRow |
|
| 626 |
+ seq2 <- setdiff(orig.seq, seq1) |
|
| 627 |
+ new.seq <- c(seq1, seq2) |
|
| 628 |
+ new.seq |
|
| 629 |
+ mat.new <- mat[new.seq, ] |
|
| 630 |
+ |
|
| 631 |
+ |
|
| 632 |
+ mat.inv <- mat.new[1, ] |
|
| 633 |
+ #extend to upper bound |
|
| 634 |
+ pt1 <- c(mat.new[1, x], boundary["max", y]) |
|
| 635 |
+ mat.inv <- rbind(mat.inv, pt1, deparse.level = 0) |
|
| 636 |
+ #left top |
|
| 637 |
+ mat.inv <- rbind(mat.inv, c(boundary["min", x], boundary["max",y])) |
|
| 638 |
+ #left bottom |
|
| 639 |
+ mat.inv <- rbind(mat.inv, c(boundary["min", x], boundary["min",y])) |
|
| 640 |
+ #right bottom |
|
| 641 |
+ mat.inv <- rbind(mat.inv, c(boundary["max", x], boundary["min",y])) |
|
| 642 |
+ #right top |
|
| 643 |
+ mat.inv <- rbind(mat.inv, c(boundary["max", x], boundary["max",y])) |
|
| 644 |
+ #back to first extended point |
|
| 645 |
+ mat.inv <- rbind(mat.inv, pt1, deparse.level = 0) |
|
| 646 |
+ #connect to the remain mat.new in reverse order |
|
| 647 |
+ mat.inv <- rbind(mat.inv, mat.new[rev(seq_len(nRow)[-1]), ]) |
|
| 648 |
+ |
|
| 649 |
+# plot(mat.inv, type = "n") |
|
| 650 |
+# polygon(mat.new, col = "red") |
|
| 651 |
+# polygon(mat.inv, col = "blue") |
|
| 652 |
+ mat.inv |
|
| 653 |
+} |
| 0 | 654 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,368 @@ |
| 1 |
+#' get nodes from {graphGML} object
|
|
| 2 |
+#' |
|
| 3 |
+#' @param x \code{graphGML}
|
|
| 4 |
+#' @param y \code{character} node index. When \code{missing}, return all the nodes
|
|
| 5 |
+#' @param order \code{character} specifying the order of nodes. options are "default", "bfs", "dfs", "tsort"
|
|
| 6 |
+#' @param only.names \code{logical} specifiying whether user wants to get the entire \code{nodeData} or just the name of the population node
|
|
| 7 |
+#' @return It returns the node names and population names by default. Or return the entire nodeData associated with each node. |
|
| 8 |
+#' @importFrom flowWorkspace getNodes |
|
| 9 |
+#' @importFrom graph nodeData |
|
| 10 |
+#' @export |
|
| 11 |
+#' @examples |
|
| 12 |
+#' \dontrun{
|
|
| 13 |
+#' xmlfile <- system.file("extdata/cytotrol_tcell_cytobank.xml", package = "CytoML")
|
|
| 14 |
+#' g <- read.gatingML.cytobank(xmlfile) |
|
| 15 |
+#' getNodes(g) |
|
| 16 |
+#' getNodes(g, only.names = FALSE) |
|
| 17 |
+#' } |
|
| 18 |
+setMethod("getNodes", signature = c("graphGML"),
|
|
| 19 |
+ definition = function(x, y |
|
| 20 |
+ , order = c("default", "bfs", "dfs", "tsort")
|
|
| 21 |
+ , only.names = TRUE) {
|
|
| 22 |
+ |
|
| 23 |
+ if (missing(y)){
|
|
| 24 |
+ res <- nodeData(x) |
|
| 25 |
+ order <- match.arg(order) |
|
| 26 |
+ if(order != "default"){
|
|
| 27 |
+ nodeIds <- eval(substitute(f1(x),list(f1=as.symbol(order)))) |
|
| 28 |
+ if(order == "dfs") |
|
| 29 |
+ nodeIds <- nodeIds$discovered |
|
| 30 |
+ res <- res[nodeIds] |
|
| 31 |
+ } |
|
| 32 |
+ }else |
|
| 33 |
+ {
|
|
| 34 |
+ res <- nodeData(x, y) |
|
| 35 |
+ |
|
| 36 |
+ } |
|
| 37 |
+ if(only.names){
|
|
| 38 |
+ res <- sapply(res,`[[`,"popName") |
|
| 39 |
+ } |
|
| 40 |
+ if(length(res) == 1 && class(res) == "list") |
|
| 41 |
+ res <- res[[1]] |
|
| 42 |
+ res |
|
| 43 |
+}) |
|
| 44 |
+ |
|
| 45 |
+#' get full path of the parent |
|
| 46 |
+#' @param x \code{graphGML}
|
|
| 47 |
+#' @param y \code{character} node index. When \code{missing}, return all the nodes
|
|
| 48 |
+.getPath <- function(x, y){
|
|
| 49 |
+ #get full path |
|
| 50 |
+ nodeIds <- y |
|
| 51 |
+ thisNodeID <- y |
|
| 52 |
+ while(length(thisNodeID) > 0){
|
|
| 53 |
+ thisNodeID <- getParent(x, thisNodeID) |
|
| 54 |
+ nodeIds <- c(thisNodeID,nodeIds) |
|
| 55 |
+ } |
|
| 56 |
+ |
|
| 57 |
+ pops <- lapply(nodeIds, function(i)nodeData(x,i)[[1]][["popName"]]) |
|
| 58 |
+ path <- paste(pops, collapse = "/") |
|
| 59 |
+ paste0("/", path)
|
|
| 60 |
+} |
|
| 61 |
+ |
|
| 62 |
+#' get children nodes |
|
| 63 |
+#' |
|
| 64 |
+#' @param obj \code{graphGML}
|
|
| 65 |
+#' @param y \code{character} parent node path
|
|
| 66 |
+#' @export |
|
| 67 |
+#' @examples |
|
| 68 |
+#' \dontrun{
|
|
| 69 |
+#' xmlfile <- system.file("extdata/cytotrol_tcell_cytobank.xml", package = "CytoML")
|
|
| 70 |
+#' g <- read.gatingML.cytobank(xmlfile) |
|
| 71 |
+#' getChildren(g, "GateSet_722326") |
|
| 72 |
+#' getParent(g, "GateSet_722326") |
|
| 73 |
+#' } |
|
| 74 |
+#' @importClassesFrom methods character ANY data.frame environment list logical matrix missing numeric oldClass |
|
| 75 |
+#' @importFrom flowWorkspace getChildren |
|
| 76 |
+setMethod("getChildren", signature = c("graphGML", "character"),
|
|
| 77 |
+ definition = function(obj, y) {
|
|
| 78 |
+ edges(obj, y)[[1]] |
|
| 79 |
+}) |
|
| 80 |
+ |
|
| 81 |
+#' get parent nodes |
|
| 82 |
+#' |
|
| 83 |
+#' @param obj \code{graphGML}
|
|
| 84 |
+#' @param y \code{character} child node path
|
|
| 85 |
+#' |
|
| 86 |
+#' @export |
|
| 87 |
+#' @importFrom flowWorkspace getParent |
|
| 88 |
+setMethod("getParent", signature = c("graphGML", "character"),
|
|
| 89 |
+ definition = function(obj, y) {
|
|
| 90 |
+ |
|
| 91 |
+ inEdges(y, obj)[[1]] |
|
| 92 |
+ |
|
| 93 |
+}) |
|
| 94 |
+ |
|
| 95 |
+#' get gate from the node |
|
| 96 |
+#' |
|
| 97 |
+#' @param obj \code{graphGML}
|
|
| 98 |
+#' @param y \code{character} node path
|
|
| 99 |
+#' @export |
|
| 100 |
+#' @importFrom flowWorkspace getGate |
|
| 101 |
+setMethod("getGate", signature = c("graphGML", "character"),
|
|
| 102 |
+ definition = function(obj, y) {
|
|
| 103 |
+ |
|
| 104 |
+ nodeData(obj, y)[["gateInfo"]] |
|
| 105 |
+}) |
|
| 106 |
+ |
|
| 107 |
+ |
|
| 108 |
+#' show method for graphGML |
|
| 109 |
+#' |
|
| 110 |
+#' show method for graphGML |
|
| 111 |
+#' |
|
| 112 |
+#' @param object \code{graphGML}
|
|
| 113 |
+#' @export |
|
| 114 |
+#' @importFrom methods show |
|
| 115 |
+setMethod("show", signature = c("graphGML"),
|
|
| 116 |
+ definition = function(object) {
|
|
| 117 |
+ cat("--- Gating hieararchy parsed from GatingML: ")
|
|
| 118 |
+ |
|
| 119 |
+ cat("\n")
|
|
| 120 |
+ cat("\twith ", length(object@nodes), " populations defined\n")
|
|
| 121 |
+}) |
|
| 122 |
+ |
|
| 123 |
+ |
|
| 124 |
+#' plot the population tree stored in graphGML. |
|
| 125 |
+#' |
|
| 126 |
+#' The node with dotted order represents the population that has tailored gates (sample-specific gates) defined. |
|
| 127 |
+#' |
|
| 128 |
+#' @param x a graphNEL generated by constructTree function |
|
| 129 |
+#' @param y not used |
|
| 130 |
+#' @param label specifies what to be dispaled as node label. Can be either 'popName' (population name parsed from GateSets) or 'gateName'(the name of the actual gate associated with each node) |
|
| 131 |
+#' @export |
|
| 132 |
+#' @importFrom graph nodeData nodes<- nodeRenderInfo<- |
|
| 133 |
+#' @importFrom Rgraphviz renderGraph layoutGraph |
|
| 134 |
+#' @importFrom graphics plot |
|
| 135 |
+#' @examples |
|
| 136 |
+#' \dontrun{
|
|
| 137 |
+#' xmlfile <- system.file("extdata/cytotrol_tcell_cytobank.xml", package = "CytoML")
|
|
| 138 |
+#' g <- read.gatingML.cytobank(xmlfile) |
|
| 139 |
+#' plot(g) |
|
| 140 |
+#' |
|
| 141 |
+#' } |
|
| 142 |
+setMethod("plot", signature = c(x = "graphGML", y = "missing"), definition = function(x, y = "missing", label = c("popName", "gateName")){
|
|
| 143 |
+ label <- match.arg(label, c("popName", "gateName"))
|
|
| 144 |
+ if(label == "popName") |
|
| 145 |
+ nodeLabel <- sapply(nodeData(x), `[[`, "popName") |
|
| 146 |
+ else |
|
| 147 |
+ nodeLabel <- sapply(nodeData(x), function(i)i[["gateInfo"]][["gateName"]]) |
|
| 148 |
+ |
|
| 149 |
+ |
|
| 150 |
+ #annotate the node with tailor gate info |
|
| 151 |
+ nTailoredGate <- sapply(nodeData(x), function(i)length(i[["gateInfo"]][["tailored_gate"]])) |
|
| 152 |
+ |
|
| 153 |
+ nAttrs <- list() |
|
| 154 |
+ |
|
| 155 |
+ nAttrs$label <- nodeLabel |
|
| 156 |
+ |
|
| 157 |
+ nAttrs$lty <- sapply(nTailoredGate |
|
| 158 |
+ ,function(i) |
|
| 159 |
+ {
|
|
| 160 |
+ ifelse(i>0,"dotted","solid") |
|
| 161 |
+ }) |
|
| 162 |
+ |
|
| 163 |
+ nodeRenderInfo(x) <- nAttrs |
|
| 164 |
+ lay <- layoutGraph(x |
|
| 165 |
+ ,attrs=list(graph=list(rankdir="LR",page=c(8.5,11)) |
|
| 166 |
+ ,node=list(fixedsize=FALSE |
|
| 167 |
+ ,fontsize = 12 |
|
| 168 |
+ ,shape="ellipse" |
|
| 169 |
+ ) |
|
| 170 |
+ ) |
|
| 171 |
+ ) |
|
| 172 |
+ renderGraph(lay) |
|
| 173 |
+ |
|
| 174 |
+}) |
|
| 175 |
+ |
|
| 176 |
+ |
|
| 177 |
+#' Apply the gatingML graph to a GatingSet |
|
| 178 |
+#' |
|
| 179 |
+#' It applies the gates to the GatingSet based on the population tree described in graphGML. |
|
| 180 |
+#' |
|
| 181 |
+#' @param x graphGML |
|
| 182 |
+#' @param y GatingSet |
|
| 183 |
+#' @param ... other arguments |
|
| 184 |
+#' @return |
|
| 185 |
+#' Nothing. As the side effect, gates generated by gating methods are saved in \code{GatingSet}.
|
|
| 186 |
+#' @export |
|
| 187 |
+#' @aliases |
|
| 188 |
+#' gating,graphGML,GatingSet-method |
|
| 189 |
+#' @rdname gating-methods |
|
| 190 |
+#' @importFrom openCyto gating |
|
| 191 |
+setMethod("gating", signature = c("graphGML", "GatingSet"), function(x, y, ...){
|
|
| 192 |
+ gating.graphGML(x, y, ...) |
|
| 193 |
+}) |
|
| 194 |
+ |
|
| 195 |
+#' @importFrom flowWorkspace getTransformations add recompute sampleNames |
|
| 196 |
+#' @importFrom RBGL tsort |
|
| 197 |
+gating.graphGML <- function(gt, gs, ...) {
|
|
| 198 |
+ |
|
| 199 |
+ trans <- getTransformations(gt) |
|
| 200 |
+ |
|
| 201 |
+ gt_nodes <- tsort(gt) |
|
| 202 |
+ for (nodeID in gt_nodes) {
|
|
| 203 |
+ |
|
| 204 |
+ # get parent node to gate |
|
| 205 |
+ gt_node <- getNodes(gt, nodeID, only.names = F) |
|
| 206 |
+ popName <- gt_node[["popName"]] |
|
| 207 |
+ |
|
| 208 |
+ |
|
| 209 |
+ parentID <- getParent(gt, nodeID) |
|
| 210 |
+ |
|
| 211 |
+ if(length(parentID) == 0) |
|
| 212 |
+ parent <- "root" |
|
| 213 |
+ else{
|
|
| 214 |
+ parent <- .getPath(gt, parentID) |
|
| 215 |
+ } |
|
| 216 |
+ |
|
| 217 |
+ |
|
| 218 |
+ gs_nodes <- basename(getChildren(gs[[1]], parent)) |
|
| 219 |
+ |
|
| 220 |
+ if (length(gs_nodes) == 0) |
|
| 221 |
+ isGated <- FALSE |
|
| 222 |
+ else |
|
| 223 |
+ isGated <- any(popName %in% gs_nodes) |
|
| 224 |
+ |
|
| 225 |
+ #TODO: rename the node name with path in order to match against gs |
|
| 226 |
+# parentInd <- match(parent, getNodes(gs[[1]], showHidden = TRUE)) |
|
| 227 |
+# if (is.na(parentInd)) |
|
| 228 |
+# stop("parent node '", parent, "' not gated yet!")
|
|
| 229 |
+ if(isGated){
|
|
| 230 |
+ message("Skip gating! Population '", paste(popName, collapse = ","), "' already exists.")
|
|
| 231 |
+ next |
|
| 232 |
+ } |
|
| 233 |
+ message(popName) |
|
| 234 |
+ gateInfo <- gt_node[["gateInfo"]] |
|
| 235 |
+ this_gate <- gateInfo[["gate"]] |
|
| 236 |
+ |
|
| 237 |
+# if(popName == "PD-1(Histo)") |
|
| 238 |
+# browser() |
|
| 239 |
+ |
|
| 240 |
+ # transform bounds if applicable |
|
| 241 |
+ bound <- gateInfo[["bound"]] |
|
| 242 |
+ if(!is.null(trans)) |
|
| 243 |
+ {
|
|
| 244 |
+ for(rn in rownames(bound)){
|
|
| 245 |
+ thisTrans <- trans[[rn]] |
|
| 246 |
+ if(!is.null(thisTrans)) |
|
| 247 |
+ bound[rn, ] <- thisTrans[["transform"]](unlist(bound[rn, ])) |
|
| 248 |
+ } |
|
| 249 |
+ } |
|
| 250 |
+ |
|
| 251 |
+ |
|
| 252 |
+ this_gate <- extend(this_gate,bound = bound) |
|
| 253 |
+ |
|
| 254 |
+ sn <- sampleNames(gs) |
|
| 255 |
+ this_gate <- sapply(sn, function(i)this_gate) |
|
| 256 |
+ |
|
| 257 |
+ #update gates that are tailored for specific samples |
|
| 258 |
+ tailor_gate <- gateInfo[["tailored_gate"]] |
|
| 259 |
+ tg_sn <- names(tailor_gate) |
|
| 260 |
+ tg_sn <- tg_sn[tg_sn %in% sn] #filter tailor gates in case sample set provided are not complete |
|
| 261 |
+ if(length(tg_sn) >0){
|
|
| 262 |
+ this_tgs <- lapply(tailor_gate[tg_sn], extend,bound = bound) |
|
| 263 |
+ this_gate[tg_sn] <- this_tgs |
|
| 264 |
+ } |
|
| 265 |
+ |
|
| 266 |
+ |
|
| 267 |
+ |
|
| 268 |
+ |
|
| 269 |
+ add(gs, this_gate, parent = parent, name = popName) |
|
| 270 |
+ |
|
| 271 |
+ } |
|
| 272 |
+ recompute(gs) |
|
| 273 |
+} |
|
| 274 |
+ |
|
| 275 |
+#' Extract compensation from graphGML object. |
|
| 276 |
+#' @param x graphGML |
|
| 277 |
+#' @return compensation object or "FCS" when compensation comes from FCS keywords |
|
| 278 |
+#' @export |
|
| 279 |
+#' @importFrom flowWorkspace getCompensationMatrices |
|
| 280 |
+setMethod("getCompensationMatrices", signature = "graphGML", definition = function(x){
|
|
| 281 |
+ x@graphData[["compensation"]] |
|
| 282 |
+ |
|
| 283 |
+}) |
|
| 284 |
+ |
|
| 285 |
+#' Extract transformations from graphGML object. |
|
| 286 |
+#' @param x graphGML |
|
| 287 |
+#' @return transformerList object |
|
| 288 |
+#' @importFrom flowCore eval parameters colnames |
|
| 289 |
+#' @importFrom flowWorkspace transformerList asinh_Gml2 flow_trans |
|
| 290 |
+#' @export |
|
| 291 |
+setMethod("getTransformations", signature = c(x = "graphGML"), function(x){
|
|
| 292 |
+ trans <- x@graphData[["transformations"]] |
|
| 293 |
+ if(!is.null(trans)){
|
|
| 294 |
+ chnls <- names(trans) |
|
| 295 |
+ trans <- sapply(trans, function(thisTrans){
|
|
| 296 |
+ |
|
| 297 |
+ #convert from transform object to function since transform has empty function in .Data slot |
|
| 298 |
+ #which is not suitable for transformList constructor |
|
| 299 |
+ trans.fun <- eval(thisTrans) |
|
| 300 |
+ trans.type <- class(thisTrans) |
|
| 301 |
+ if(extends(trans.type, "asinhtGml2")){
|
|
| 302 |
+ inv.func <- asinh_Gml2(thisTrans@T, thisTrans@M, thisTrans@A, inverse = TRUE) |
|
| 303 |
+ |
|
| 304 |
+ }else |
|
| 305 |
+ stop("Don't know how to inverse transformation: ", trans.type)
|
|
| 306 |
+ |
|
| 307 |
+ trans.obj <- flow_trans(trans.type, trans.fun, inv.func) |
|
| 308 |
+ |
|
| 309 |
+ } |
|
| 310 |
+ , USE.NAMES = FALSE, simplify = FALSE) |
|
| 311 |
+ |
|
| 312 |
+ trans <- transformerList(chnls, trans) |
|
| 313 |
+ } |
|
| 314 |
+ trans |
|
| 315 |
+}) |
|
| 316 |
+ |
|
| 317 |
+#' compensate a GatingSet based on the compensation information stored in graphGML object |
|
| 318 |
+#' |
|
| 319 |
+#' |
|
| 320 |
+#' @param x GatingSet |
|
| 321 |
+#' @param spillover graphGML |
|
| 322 |
+#' @param ... unused. |
|
| 323 |
+#' @return compensated GatingSet |
|
| 324 |
+#' @importFrom flowCore compensate |
|
| 325 |
+#' @export |
|
| 326 |
+#' @importFrom flowCore compensate |
|
| 327 |
+setMethod("compensate", signature = c("GatingSet", "graphGML"), function(x, spillover, ...){
|
|
| 328 |
+ |
|
| 329 |
+ comp <- getCompensationMatrices(spillover) |
|
| 330 |
+ if(is(comp, "compensation")){
|
|
| 331 |
+ # prefix <- TRUE |
|
| 332 |
+ skip <- FALSE |
|
| 333 |
+ }else if(comp == "FCS"){
|
|
| 334 |
+ # prefix <- FALSE |
|
| 335 |
+ fs <- getData(x) |
|
| 336 |
+ fr <- fs[[1, use.exprs = FALSE]] |
|
| 337 |
+ #can't use spillover method directly because it will error out when none is found |
|
| 338 |
+ mat <- keyword(fr, c("spillover", "SPILL"))
|
|
| 339 |
+ mat <- compact(mat) |
|
| 340 |
+ if(length(mat) == 0){
|
|
| 341 |
+ skip <- TRUE |
|
| 342 |
+ warning("Compensation is skipped!Because gates refer to 'FCS' for compensation but no spillover is found in FCS.")
|
|
| 343 |
+ }else{
|
|
| 344 |
+ skip <- FALSE |
|
| 345 |
+ mat <- mat[[1]] |
|
| 346 |
+ comp <- compensation(mat) |
|
| 347 |
+ } |
|
| 348 |
+ } |
|
| 349 |
+ if(skip) |
|
| 350 |
+ return(x) |
|
| 351 |
+ else{
|
|
| 352 |
+ x <- compensate(x, comp) |
|
| 353 |
+ |
|
| 354 |
+# if(prefix){
|
|
| 355 |
+# |
|
| 356 |
+# comp_param <- colnames(comp@spillover) |
|
| 357 |
+# #strip prefix |
|
| 358 |
+# comp_param <- sapply(comp_param, function(i)sub("(^Comp_)(.*)", "\\2", i), USE.NAMES = FALSE)
|
|
| 359 |
+# #match to chnls |
|
| 360 |
+# chnls <- colnames(x) |
|
| 361 |
+# ind <- match(comp_param, chnls) |
|
| 362 |
+# chnls[ind] <- paste0("Comp_", chnls[ind])
|
|
| 363 |
+# colnames(x) <- chnls |
|
| 364 |
+# } |
|
| 365 |
+ return(x) |
|
| 366 |
+ } |
|
| 367 |
+ |
|
| 368 |
+}) |
| 0 | 369 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,769 @@ |
| 1 |
+#' A graph object returned by 'read.gatingML.cytobank' function. |
|
| 2 |
+#' |
|
| 3 |
+#' Each node corresponds to a population(or GateSet) defined in gatingML file. The actual gate object (both global and tailored gates) is |
|
| 4 |
+#' associated with each node as nodeData. Compensation and transformations are stored in graphData slot. |
|
| 5 |
+#' |
|
| 6 |
+#' The class simply extends the graphNEL class and exists for the purpose of method dispatching. |
|
| 7 |
+#' |
|
| 8 |
+#' @importClassesFrom graph graphNEL graphBase graph |
|
| 9 |
+#' @importClassesFrom Biobase AssayData |
|
| 10 |
+#' @export |
|
| 11 |
+setClass("graphGML", contains = "graphNEL")
|
|
| 12 |
+ |
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| 13 |
+#' Parser for gatingML exported by Cytobank |
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| 14 |
+#' |
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| 15 |
+#' The Default parser (flowUtils::read.gatingML) does not parse the population tree as well as |
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| 16 |
+#' the custom information from cytobank. (e.g. gate name, fcs filename). |
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| 17 |
+#' |
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| 18 |
+#' @param file Gating-ML XML file |
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| 19 |
+#' @param ... additional arguments passed to the handlers of 'xmlTreeParse' |
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| 20 |
+#' @export |
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| 21 |
+#' @importFrom flowUtils read.gatingML |
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| 22 |
+#' @importFrom flowCore parameters parameters<- |
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| 23 |
+#' @return a graphGML that represents the population tree. |
|
| 24 |
+#' The gate and population name are stored in nodeData of each node. |
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| 25 |
+#' Compensation and transformations are stored in graphData. |
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| 26 |
+#' @examples |
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| 27 |
+#' \dontrun{
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|
| 28 |
+#' xml <- system.file("extdata/cytotrol_tcell_cytobank.xml", package = "CytoML")
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| 29 |
+#' g <- read.gatingML.cytobank(xml) #parse the population tree |
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| 30 |
+#' plot(g) #visualize it |
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| 31 |
+#' } |
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| 32 |
+read.gatingML.cytobank <- function(file, ...){
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| 33 |
+ |
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| 34 |
+ #parse all the elements:gate, GateSets, comp, trans |
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| 35 |
+ flowEnv <- new.env() |
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| 36 |
+ read.gatingML(file, flowEnv) |
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| 37 |
+ |
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| 38 |
+ #parse gate info (id vs fcs and pop name) |
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| 39 |
+ gateInfo <- parse.gateInfo(file) |
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| 40 |
+ if(nrow(gateInfo) == 0) |
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| 41 |
+ stop("No gates defined in gatingML file!")
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|
| 42 |
+ |
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| 43 |
+ #restore the original gate parameter names |
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| 44 |
+ #because flowUtils add comp and tran names as prefix which is really not neccessary (even problematic) here. |
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| 45 |
+ for(objID in ls(flowEnv)){
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|
| 46 |
+ obj <- flowEnv[[objID]] |
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| 47 |
+ if(is(obj, "parameterFilter")){
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|
| 48 |
+ |
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| 49 |
+ # message(class(obj)) |
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| 50 |
+ |
|
| 51 |
+ sb <- gateInfo[id == objID, ] |
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| 52 |
+ if(nrow(sb)>0){
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|
| 53 |
+ orig_params <- sb[, params] |
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| 54 |
+ orig_params <- strsplit(split = ":", orig_params)[[1]] |
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| 55 |
+ params <- parameters(obj) |
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| 56 |
+ ind <- sapply(orig_params, function(orig_param)grep(paste0(orig_param, "$"), params)) |
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| 57 |
+ |
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| 58 |
+ orig_param <- orig_params[ind] |
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| 59 |
+ |
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| 60 |
+ #cytobank add Comp_ prefix when the custom compensation is specified and referred by gates |
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| 61 |
+ #We always strip it to ensure the bare channel names are used for gates (so that flow data does not need changes) |
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| 62 |
+ orig_param <- sub("(^Comp_)(.*)", "\\2", orig_param)
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|
| 63 |
+ |
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| 64 |
+ parameters(obj) <- orig_param |
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| 65 |
+ flowEnv[[objID]] <- obj |
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| 66 |
+ } |
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| 67 |
+ |
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| 68 |
+ } |
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| 69 |
+ |
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| 70 |
+ } |
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| 71 |
+ |
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| 72 |
+ |
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| 73 |
+ #construct tree from GateSets |
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| 74 |
+ g <- constructTree(flowEnv, gateInfo) |
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| 75 |
+ |
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| 76 |
+ #determine comps and trans to be used |
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| 77 |
+ |
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| 78 |
+ comp_refs <- gateInfo[, comp_ref] |
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| 79 |
+ comp_refs <- unique(comp_refs[comp_refs!=""]) |
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| 80 |
+ comp_refs <- comp_refs[comp_refs != "uncompensated"] |
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| 81 |
+ if(length(comp_refs) > 1) |
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| 82 |
+ stop("More than one compensation referred in gates!")
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|
| 83 |
+ else{
|
|
| 84 |
+ if(comp_refs == "FCS") |
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| 85 |
+ comps <- "FCS" |
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| 86 |
+ else{
|
|
| 87 |
+ comps <- flowEnv[[comp_refs]] |
|
| 88 |
+ #strip Comp_ prefix that was added by cytobank |
|
| 89 |
+# mat <- comps@spillover |
|
| 90 |
+# comp_param <- colnames(mat) |
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| 91 |
+# comp_param <- sapply(comp_param, function(i)sub("(^Comp_)(.*)", "\\2", i), USE.NAMES = FALSE)
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|
| 92 |
+# colnames(mat) <- comp_param |
|
| 93 |
+# comps <- compensation(mat) |
|
| 94 |
+ |
|
| 95 |
+ } |
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| 96 |
+ |
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| 97 |
+ } |
|
| 98 |
+ g@graphData[["compensation"]] <- comps |
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| 99 |
+ |
|
| 100 |
+ |
|
| 101 |
+ trans <- sapply(ls(flowEnv), function(i){
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|
| 102 |
+ |
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| 103 |
+ obj <- flowEnv[[i]] |
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| 104 |
+ #exclude the compensatedParameter since it also inherits transformation class |
|
| 105 |
+ if(is(obj, "transformation")&&!is(obj, "compensatedParameter")) |
|
| 106 |
+ obj |
|
| 107 |
+ }, USE.NAMES = FALSE) |
|
| 108 |
+ |
|
| 109 |
+ trans <- compact(trans) |
|
| 110 |
+ chnl <- sapply(trans, function(tran)unname(parameters(tran@parameters)), USE.NAMES = F) |
|
| 111 |
+ |
|
| 112 |
+ ind <- chnl != "any" |
|
| 113 |
+ |
|
| 114 |
+ chnl <- chnl[ind] |
|
| 115 |
+ trans <- trans[ind] |
|
| 116 |
+ names(trans) <- chnl |
|
| 117 |
+ if(length(trans) > 0) |
|
| 118 |
+ g@graphData[["transformations"]] <- trans |
|
| 119 |
+ |
|
| 120 |
+ as(g, "graphGML") |
|
| 121 |
+ |
|
| 122 |
+} |
|
| 123 |
+ |
|
| 124 |
+#' Parse the cytobank custom_info for each gate |
|
| 125 |
+#' |
|
| 126 |
+#' Fcs filename and gate name stored in 'custom_info' element are beyong the scope of |
|
| 127 |
+#' the gatingML standard and thus not covered by the default 'read.gatingML'. |
|
| 128 |
+#' |
|
| 129 |
+#' @param file xml file path |
|
| 130 |
+#' @param ... additional arguments passed to the handlers of 'xmlTreeParse' |
|
| 131 |
+#' @return a data.frame that contains three columns: id (gateId), name (gate name), fcs (fcs_file_filename). |
|
| 132 |
+#' @importFrom XML xmlRoot xmlName xmlGetAttr xmlValue xmlElementsByTagName xmlChildren |
|
| 133 |
+#' @import data.table |
|
| 134 |
+parse.gateInfo <- function(file, ...) |
|
| 135 |
+{
|
|
| 136 |
+ |
|
| 137 |
+ root <- xmlRoot(flowUtils:::smartTreeParse(file,...)) |
|
| 138 |
+ |
|
| 139 |
+ rbindlist( |
|
| 140 |
+ lapply(xmlChildren(root), function(node){
|
|
| 141 |
+ nodeName <- xmlName(node) |
|
| 142 |
+ |
|
| 143 |
+ if(grepl("*Gate", nodeName)){
|
|
| 144 |
+ |
|
| 145 |
+ |
|
| 146 |
+ id <- xmlGetAttr(node, "id") |
|
| 147 |
+ |
|
| 148 |
+ name <- getCustomNodeInfo(node, "name") |
|
| 149 |
+ fcs_file_filename <- getCustomNodeInfo(node, "fcs_file_filename") |
|
| 150 |
+ gate_id <- getCustomNodeInfo(node, "gate_id")#used to find tailored gate |
|
| 151 |
+ if(nodeName %in% c("BooleanGate"))
|
|
| 152 |
+ {
|
|
| 153 |
+ gate_def <- comp_ref <- trans_ref <- params <- "" |
|
| 154 |
+ }else |
|
| 155 |
+ {
|
|
| 156 |
+ |
|
| 157 |
+ gate_def <- getCustomNodeInfo(node, "definition") |
|
| 158 |
+ |
|
| 159 |
+ if(nodeName == "QuadrantGate"){
|
|
| 160 |
+ dimTag <- "divider" |
|
| 161 |
+ #update id with quardant definition |
|
| 162 |
+ quadrantList <- xmlElementsByTagName(node, "Quadrant") |
|
| 163 |
+ id <- unname(sapply(quadrantList, function(i)xmlGetAttr(i, "id"))) |
|
| 164 |
+ |
|
| 165 |
+ }else |
|
| 166 |
+ dimTag <- "dimension" |
|
| 167 |
+ |
|
| 168 |
+ dimNode <- xmlElementsByTagName(node, dimTag) |
|
| 169 |
+ comp_ref <- unique(sapply(dimNode, function(i)xmlGetAttr(i, "compensation-ref"))) |
|
| 170 |
+ trans_ref <- unique(unname(unlist(compact(sapply(dimNode, function(i)xmlGetAttr(i, "transformation-ref")))))) |
|
| 171 |
+ trans_ref <- ifelse(is.null(trans_ref), "", trans_ref) |
|
| 172 |
+ params <- paste(sapply(dimNode, function(i)xmlGetAttr(i[["fcs-dimension"]], "name")), collapse = ":") |
|
| 173 |
+ } |
|
| 174 |
+ # message(name) |
|
| 175 |
+ # browser() |
|
| 176 |
+ data.table(id = id, name = name, gate_id = gate_id, fcs = fcs_file_filename |
|
| 177 |
+ , comp_ref = comp_ref, trans_ref = trans_ref, params = params, gate_def = gate_def |
|
| 178 |
+ ) |
|
| 179 |
+ |
|
| 180 |
+ |
|
| 181 |
+ } |
|
| 182 |
+ |
|
| 183 |
+ }) |
|
| 184 |
+ ) |
|
| 185 |
+} |
|
| 186 |
+ |
|
| 187 |
+getCustomNodeInfo <- function(node, nodeName){
|
|
| 188 |
+ custom_node <- xmlElementsByTagName(node, nodeName, recursive = TRUE) |
|
| 189 |
+ if(length(custom_node) >0 ){
|
|
| 190 |
+ value <- xmlValue(custom_node[[1]]) |
|
| 191 |
+ if(length(value)==0) |
|
| 192 |
+ value <- "" |
|
| 193 |
+ } |
|
| 194 |
+ else |
|
| 195 |
+ value <- "" |
|
| 196 |
+ |
|
| 197 |
+ value |
|
| 198 |
+} |
|
| 199 |
+ |
|
| 200 |
+#' Given the leaf node, try to find out if a collection of nodes can be matched to a path in a graph(tree) by the bottom-up searching |
|
| 201 |
+#' @param g graphNEL |
|
| 202 |
+#' @param leaf the name of leaf(terminal) node |
|
| 203 |
+#' @param nodeSet a set of node names |
|
| 204 |
+#' @return TRUE if path is found, FALSE if not path is matched. |
|
| 205 |
+#' @importFrom graph inEdges |
|
| 206 |
+matchPath <- function(g, leaf, nodeSet){
|
|
| 207 |
+ |
|
| 208 |
+ if(leaf %in% nodeSet){
|
|
| 209 |
+ nodeSet <- nodeSet[-match(leaf, nodeSet)] #pop it out |
|
| 210 |
+ leaf <- inEdges(leaf, g)[[1]]#update it with parent node |
|
| 211 |
+ if(length(nodeSet) == 0){ #nodeSet emptied
|
|
| 212 |
+ if(length(leaf) == 0) #and path reach to the top |
|
| 213 |
+ return (TRUE) |
|
| 214 |
+ else |
|
| 215 |
+ return(FALSE) #path has not reached to the top |
|
| 216 |
+ }else |
|
| 217 |
+ {
|
|
| 218 |
+ if(length(leaf) == 0) #reach the top before nodeSet is emptied |
|
| 219 |
+ return(FALSE) |
|
| 220 |
+ else |
|
| 221 |
+ matchPath(g, leaf, nodeSet) #continue match the path against nodeSet |
|
| 222 |
+ } |
|
| 223 |
+ }else |
|
| 224 |
+ return(FALSE) |
|
| 225 |
+ |
|
| 226 |
+} |
|
| 227 |
+ |
|
| 228 |
+#' Reconstruct the population tree from the GateSets |
|
| 229 |
+#' @param flowEnv the enivornment contains the elements parsed by read.gatingML function |
|
| 230 |
+#' @param gateInfo the data.frame contains the gate name, fcs filename parsed by parse.gateInfo function |
|
| 231 |
+#' @return a graphNEL represent the population tree. The gate and population name are stored as nodeData in each node. |
|
| 232 |
+#' @importFrom graph graphNEL nodeDataDefaults<- nodeData<- addEdge edges removeNode |
|
| 233 |
+#' @importFrom jsonlite fromJSON |
|
| 234 |
+constructTree <- function(flowEnv, gateInfo){
|
|
| 235 |
+ |
|