@@ -1,7 +1,7 @@

 Package: CytoML

 Type: Package

 Title: A GatingML Interface for Cross Platform Cytometry Data Sharing

-Version: 1.9.5

+Version: 1.9.6

 Date: 2016-04-15

 Author: Mike Jiang

 Maintainer: Mike Jiang <wjiang2@fhcrc.org>

@@ -31,7 +31,8 @@ Imports:

     grDevices,

     methods,

     ggcyto (>= 1.11.4),

-    yaml

+    yaml,

+    lattice

 biocViews: ImmunoOncology, FlowCytometry, DataImport, DataRepresentation

 LinkingTo: Rcpp, BH(>= 1.62.0-1), RProtoBufLib(>= 1.3.7), cytolib(>= 1.3.3), RcppParallel

 Suggests:

@@ -56,5 +57,6 @@ Collate:

     'graphGML_methods.R'

     'parseDivaWorkspace_old.R'

     'utils.R'

+    'zzz.R'

 SystemRequirements: xml2, GNU make, C++11    

 Encoding: UTF-8

@@ -11,6 +11,8 @@ S3method(getTransformations,cytobankExperiment)

 S3method(getTransformations,graphGML)

 S3method(openWorkspace,character)

 S3method(print,cytobankExperiment)

+export(CytoML.par.get)

+export(CytoML.par.set)

 export(GatingSet2cytobank)

 export(GatingSet2flowJo)

 export(closeWorkspace)

@@ -157,7 +157,7 @@ DerivedParameterNode <- function(sn, parent, childnodes, vec, cluster_name, env.

   csvfile <- paste(sn, pname, "EPA.csv", sep = ".")

   csvpath <- file.path(outputdir, csvfile)

   write.csv(vec, csvpath, row.names = FALSE)

-  message("DerivedParameter: ", csvpath)

+  message("DerivedParameter: ", normalizePath(csvpath))

   xmlNode("DerivedParameter"

           , attrs = c(name = pname

                     , type = "importCsv"

@@ -6,15 +6,17 @@

 #' @rdname cytobank2GatingSet

 #' @examples

 #' \dontrun{

-#' xmlfile <- system.file("extdata/cytotrol_tcell_cytobank.xml", package = "CytoML")

-#' fcsFiles <- list.files(pattern = "CytoTrol", 

-#'       system.file("extdata", package = "flowWorkspaceData"), full = TRUE)

-#' gs <- cytobank2GatingSet(xmlfile, fcsFiles)

-#' #plotGate(gs[[1]])

+#' acsfile <- system.file("extdata/cytobank_experiment.acs", package = "CytoML")

+#' ce <- cytobankExperiment(acsfile)

+#' xmlfile <- ce$gatingML

+#' fcsFiles <- list.files(ce$fcsdir, full.names = TRUE)

+#' gs <<- cytobank2GatingSet(xmlfile, fcsFiles)

+#' library(ggcyto)

+#' autoplot(gs[[1]])

 #' }

 #' @importFrom flowWorkspace GatingSet transform

 #' @importFrom ncdfFlow read.ncdfFlowSet

-cytobank2GatingSet.default <- function(x, FCS){

+cytobank2GatingSet.default <- function(x, FCS, ...){

   g <- read.gatingML.cytobank(x)

   fs <- read.ncdfFlowSet(FCS)

   gs <- GatingSet(fs)

@@ -42,12 +44,11 @@ cytobank2GatingSet.default <- function(x, FCS){

 #' @export compare.counts

 #' @examples

 #'

-#' xmlfile <- system.file("extdata/cytotrol_tcell_cytobank.xml", package = "CytoML")

-#' fcsFiles <- list.files(pattern = "CytoTrol", 

-#'         system.file("extdata", package = "flowWorkspaceData"), full = TRUE)

-#' gs <- cytobank2GatingSet(xmlfile, fcsFiles)

+#' acsfile <- system.file("extdata/cytobank_experiment.acs", package = "CytoML")

+#' ce <- cytobankExperiment(acsfile)

+#' gs <- cytobank2GatingSet(ce)

 #' ## verify the stats are correct

-#' statsfile <- system.file("extdata/cytotrol_tcell_cytobank_counts.csv", package = "CytoML")

+#' statsfile <- ce$attachments[1]

 #' dt_merged <- compare.counts(gs, statsfile, id.vars = "population", skip = "FCS Filename")

 #' all.equal(dt_merged[, count.x], dt_merged[, count.y], tol = 5e-4)

 #'

@@ -42,9 +42,11 @@ cytobankExperiment <- function(acs, exdir = tempfile()){

                         )

                    , class = "cytobankExperiment")

 }

+#' @rdname cytobank2GatingSet

 #' @export

 cytobank2GatingSet <- function(x, ...)UseMethod("cytobank2GatingSet")

 #' @importFrom flowWorkspace markernames<-

+#' @param ... other arguments

 #' @export

 #' @method cytobank2GatingSet cytobankExperiment

 #' @rdname cytobank2GatingSet

@@ -73,9 +75,10 @@ setOldClass("cytobankExperiment")

 #' @param x cytobankExperiment object

 #' @rdname cytobankExperiment

+#' @param ... not used

 #' @export

 #' @method print cytobankExperiment

-print.cytobankExperiment <- function(x){

+print.cytobankExperiment <- function(x, ...){

   exp <- x[["experiment"]]

   cat("cytobank Experiment: ", exp[["name"]],"\n");

   cat("gatingML File: ",x[["gatingML"]], "\n");

@@ -90,6 +93,7 @@ print.cytobankExperiment <- function(x){

 #' @rdname cytobankExperiment

 #' @method getCompensationMatrices cytobankExperiment

 #' @export

+#' @aliases getCompensationMatrices

 #' @export getCompensationMatrices

 getCompensationMatrices.cytobankExperiment <- function(x){

   comps <- x[["experiment"]][["compensations"]]

@@ -122,6 +126,7 @@ setMethod("markernames",

           })

 #' @rdname cytobankExperiment

+#' @param do.NULL,prefix not used

 #' @export

 setMethod("colnames",

           signature=signature(x="cytobankExperiment"),

@@ -148,7 +153,8 @@ get_panel_per_file <- function(ce){

 #' @export

 #' @method getTransformations cytobankExperiment

 #' @export getTransformations

-getTransformations.cytobankExperiment <- function(x){

+#' @aliases getTransformations

+getTransformations.cytobankExperiment <- function(x, ...){

   chnls <- colnames(x)

   low.chnls <- tolower(chnls)

   scales <- x$experiment$scales

@@ -127,7 +127,7 @@ setMethod("closeWorkspace","flowJoWorkspace",function(workspace){

 #' @return the macthed workspace type

 #' @noRd 

 .getWorkspaceType <- function(wsversion){

-  curSupport <- unlist(flowWorkspace.par.get("flowJo_versions"))

+  curSupport <- unlist(CytoML.par.get("flowJo_versions"))

   ver_ind <- match(wsversion, curSupport)

   if(is.na(ver_ind))

     stop("Unsupported version: ", wsversion)

@@ -244,7 +244,7 @@ setMethod("parseWorkspace",signature("flowJoWorkspace"),function(obj, ...){

   	wsversion <- obj@version

     wsType <- .getWorkspaceType(wsversion)

-    wsNodePath <- flowWorkspace.par.get("nodePath")[[wsType]]

+    wsNodePath <- CytoML.par.get("nodePath")[[wsType]]

     #sample info  

     allSamples <- .getSamples(x, wsType, sampNloc = sampNloc)

@@ -692,7 +692,7 @@ getFileNames <- function(ws){

   }

 }

 .getFileNames <- function(x, wsType){

-  wsNodePath <- flowWorkspace.par.get("nodePath")[[wsType]]

+  wsNodePath <- CytoML.par.get("nodePath")[[wsType]]

   unlist(xpathApply(x, file.path(wsNodePath[["sample"]], "Keywords/Keyword[@name='$FIL']")

                     , function(x)xmlGetAttr(x,"value")

                     )

@@ -736,7 +736,7 @@ setMethod("getKeywords",c("flowJoWorkspace","character"),function(obj,y, ...){

       x <- obj@doc

       wsversion <- obj@version

       wsType <- .getWorkspaceType(wsversion)

-      wsNodePath <- flowWorkspace.par.get("nodePath")[[wsType]]

+      wsNodePath <- CytoML.par.get("nodePath")[[wsType]]

       .getKeywordsBySampleName(obj@doc,y, wsNodePath[["sample"]], ...)

 })

 #' @rdname getKeywords

@@ -747,7 +747,7 @@ setMethod("getKeywords",c("flowJoWorkspace","numeric"),function(obj,y, ...){

       x <- obj@doc

       wsversion <- obj@version

       wsType <- .getWorkspaceType(wsversion)

-      wsNodePath <- flowWorkspace.par.get("nodePath")[[wsType]]

+      wsNodePath <- CytoML.par.get("nodePath")[[wsType]]

       .getKeywordsBySampleID(obj@doc,y, wsNodePath[["sampleID"]],...)

     })

@@ -840,7 +840,7 @@ getFJWSubsetIndices<-function(ws,key=NULL,value=NULL,group,requiregates=TRUE){

     x <- ws@doc

     wsversion <- ws@version

     wsType <- .getWorkspaceType(wsversion)

-    wsNodePath <- flowWorkspace.par.get("nodePath")[[wsType]]

+    wsNodePath <- CytoML.par.get("nodePath")[[wsType]]

 	s<- .getSamples(x, wsType);

 	#TODO Use the actual value of key to name the column

@@ -929,7 +929,7 @@ setMethod("getSampleGroups","flowJoWorkspace",function(x){

 #' @importFrom stats na.omit

 .getSampleGroups<-function(x, wsType){

-  wsNodePath <- flowWorkspace.par.get("nodePath")[[wsType]]

+  wsNodePath <- CytoML.par.get("nodePath")[[wsType]]

 	if(grepl("mac", wsType)){

 		do.call(rbind,xpathApply(x, wsNodePath[["group"]],function(x){

@@ -980,7 +980,7 @@ setMethod("getSampleGroups","flowJoWorkspace",function(x){

 .getSamples<-function(x, wsType, sampNloc="keyword"){

-    wsNodePath <- flowWorkspace.par.get("nodePath")[[wsType]]

+    wsNodePath <- CytoML.par.get("nodePath")[[wsType]]

 	lastwarn<-options("warn")[[1]]

 	options("warn"=-1)

 	top <- xmlRoot(x)

@@ -12,10 +12,12 @@ NULL

 #' @importFrom graph nodeData

 #' @export

 #' @examples

+#' \dontrun{

 #' xmlfile <- system.file("extdata/cytotrol_tcell_cytobank.xml", package = "CytoML")

 #' g <- read.gatingML.cytobank(xmlfile)

 #' getNodes(g)

 #' getNodes(g, only.names = FALSE)

+#' }

 setMethod("getNodes", signature = c("graphGML"),

           definition = function(x, y

                                   , order = c("default", "bfs", "dfs", "tsort")

@@ -68,10 +70,12 @@ setMethod("getNodes", signature = c("graphGML"),

 #' @export

 #' @return a graphNEL node

 #' @examples

+#' \dontrun{

 #' xmlfile <- system.file("extdata/cytotrol_tcell_cytobank.xml", package = "CytoML")

 #' g <- read.gatingML.cytobank(xmlfile)

 #' getChildren(g, "GateSet_722326")

 #' getParent(g, "GateSet_722326")

+#' }

 #' @importClassesFrom methods character ANY data.frame environment list logical matrix missing numeric oldClass

 #' @importFrom flowWorkspace getChildren

 setMethod("getChildren", signature = c("graphGML", "character"),

@@ -136,10 +140,11 @@ setMethod("show", signature = c("graphGML"),

 #' @importFrom graph nodeData nodes<- nodeRenderInfo<-

 #' @importFrom Rgraphviz renderGraph layoutGraph

 #' @examples

+#' \dontrun{

 #' xmlfile <- system.file("extdata/cytotrol_tcell_cytobank.xml", package = "CytoML")

 #' g <- read.gatingML.cytobank(xmlfile)

 #' plot(g)

-#'

+#'}

 setMethod("plot", signature = c(x = "graphGML", y = "missing"), definition = function(x, y = "missing", label = c("popName", "gateName")){

   label <- match.arg(label, c("popName", "gateName"))

   if(label == "popName")

@@ -286,13 +291,14 @@ getCompensationMatrices.graphGML <- function(x){

 #' Extract transformations from graphGML object.

 #' @param x graphGML

+#' @param ... not used

 #' @return transformerList object

 #' @importFrom flowCore eval parameters colnames

 #' @importFrom flowWorkspace transformerList asinh_Gml2 flow_trans asinhtGml2_trans logicleGml2_trans logtGml2_trans

 #' @importFrom methods extends

 #' @export

 #' @method getTransformations graphGML

-getTransformations.graphGML <- function(x){

+getTransformations.graphGML <- function(x, ...){

   trans <- x@graphData[["transformations"]]

   if(!is.null(trans)){

     chnls <- names(trans)

@@ -25,9 +25,11 @@ setClass("graphGML", contains = "graphNEL")

 #' The gate and population name are stored in nodeData of each node.

 #' Compensation and transformations are stored in graphData.

 #' @examples

+#' \dontrun{

 #' xml <- system.file("extdata/cytotrol_tcell_cytobank.xml", package = "CytoML")

 #' g <- read.gatingML.cytobank(xml) #parse the population tree

 #' #plot(g) #visualize it

+#' }

 read.gatingML.cytobank <- function(file, ...){

   #parse all the elements:gate, GateSets, comp, trans

new file mode 100644

@@ -0,0 +1,107 @@

+## Store state info in this internal global environment

+CytoML.state <- new.env(hash = FALSE)

+CytoML.state[["par"]] <- list()

+

+#' workspace version is parsed from xml node '/Workspace/version' in flowJo workspace

+#' and matched with this list to dispatch to the one of the three workspace parsers 

+CytoML.par.init <- function(){

+  

+  fj_ver <- list(win = c("1.61", "1.6")

+                , macII = c("2.0")

+                , macIII = c("3.0")

+                , vX = c("1.8", "20.0")

+                )

+                          

+   mac_II_path <- list(group = "/Workspace/Groups/GroupNode"# abs path

+                    , sampleRef = ".//SampleRefs/SampleRef"#relative GroupNode

+                    , sample = "/Workspace/SampleList/Sample"#abs path

+                    , sampleNode = "./SampleNode"#relative to sample

+                    , popNode = "./Population"#relative to sampleNode

+                    , attrName = "name"

+                    , compMatName = "name"

+                    , compMatChName = "name"

+                    , compMatVal = "value"

+                    )

+  mac_II_path[["sampleID"]] <- mac_II_path[["sample"]]

+                    

+  #mac version 3.0 (flowJo version 9.7.2-9.7.4)

+  mac_III_path <- mac_II_path

+  mac_III_path[["sample"]] <- sub("SampleList", "Samples", mac_III_path[["sample"]]) 

+  mac_III_path[["attrName"]] <- "nodeName"

+  mac_III_path[["compMatName"]] <- "matrixName"

+  mac_III_path[["compMatChName"]] <- "fluorName"

+  mac_III_path[["compMatVal"]] <- "spillValue"

+  mac_III_path[["sampleID"]] <- mac_III_path[["sample"]]

+  ####windows version

+  #inherit most paths from mac                                      

+  win_path <- mac_II_path

+  win_path[["popNode"]] <- "./*/Population"

+  win_path[["gateDim"]] <- "*[local-name()='dimension']"#relative to gateNode

+  win_path[["gateParam"]] <- "*[local-name()='parameter']"#relative to dimNode

+  win_path[["sampleID"]] <- file.path(win_path[["sample"]],"DataSet")

+

+  ####version X

+  #inherit most paths from win

+  vX_path <- win_path

+  vX_path[["gateParam"]] <- "*[local-name()='fcs-dimension']";                                        

+  

+  CytoML.state[["par"]] <- list(flowJo_versions = fj_ver 

+                                      , nodePath = list(win = win_path

+                                                        , macII = mac_II_path

+                                                        , macIII = mac_III_path

+                                                        , vX = vX_path

+                                                        )

+                                                                 )

+  

+}

+

+## call the init function

+CytoML.par.init()                                                           

+

+#' CytoML.par.set sets a set of parameters in the CytoML package namespace.

+#' 

+#' @param value A named list of values to set for category name or a list of such lists if name is missing.

+#' @rdname CytoML.par.get

+#' @export

+CytoML.par.set <- function (name, value) 

+{

+    old <- CytoML.state[["par"]]

+    if(name%in%names(old)){

+      CytoML.state[["par"]][[name]] <- lattice:::updateList(old[[name]], value)  

+    }else

+      stop(name, " is not a valid CytoML parameters!")

+    

+  invisible()

+}

+

+#' Query and set session-wide parameter defaults.

+#' 

+#' CytoML.par.get gets a set of parameters in the CytoML package namespace.

+#' 

+#' It is currently used to add/remove the support for a specific flowJo versions (parsed from xml node '/Workspace/version' in flowJo workspace)

+#' 

+#' @param name The name of a parameter category to get or set.

+#'

+#' 

+#' @examples

+#'  #get the flowJo versions currently supported 

+#'  old <- CytoML.par.get("flowJo_versions")

+#' 

+#'  #add the new version

+#'  old[["win"]] <- c(old[["win"]], "1.7")    

+#'  CytoML.par.set("flowJo_versions", old)

+#'  

+#'  CytoML.par.get("flowJo_versions")

+#' 

+#' @export 

+#' @rdname CytoML.par.get

+CytoML.par.get <- function (name = NULL) 

+{

+  lPars <- CytoML.state[["par"]]

+  if (is.null(name)) 

+    lPars

+  else if (name %in% names(lPars)) 

+    lPars[[name]]

+  else NULL

+}

+

new file mode 100644

@@ -0,0 +1,33 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/zzz.R

+\name{CytoML.par.set}

+\alias{CytoML.par.set}

+\alias{CytoML.par.get}

+\title{CytoML.par.set sets a set of parameters in the CytoML package namespace.}

+\usage{

+CytoML.par.set(name, value)

+

+CytoML.par.get(name = NULL)

+}

+\arguments{

+\item{name}{The name of a parameter category to get or set.}

+

+\item{value}{A named list of values to set for category name or a list of such lists if name is missing.}

+}

+\description{

+CytoML.par.get gets a set of parameters in the CytoML package namespace.

+}

+\details{

+It is currently used to add/remove the support for a specific flowJo versions (parsed from xml node '/Workspace/version' in flowJo workspace)

+}

+\examples{

+ #get the flowJo versions currently supported 

+ old <- CytoML.par.get("flowJo_versions")

+

+ #add the new version

+ old[["win"]] <- c(old[["win"]], "1.7")    

+ CytoML.par.set("flowJo_versions", old)

+ 

+ CytoML.par.get("flowJo_versions")

+

+}

new file mode 100644

@@ -0,0 +1,13 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/zzz.R

+\name{CytoML.par.init}

+\alias{CytoML.par.init}

+\title{workspace version is parsed from xml node '/Workspace/version' in flowJo workspace

+and matched with this list to dispatch to the one of the three workspace parsers}

+\usage{

+CytoML.par.init()

+}

+\description{

+workspace version is parsed from xml node '/Workspace/version' in flowJo workspace

+and matched with this list to dispatch to the one of the three workspace parsers

+}

@@ -4,8 +4,7 @@

 \alias{compare.counts}

 \title{compare the counts to cytobank's exported csv so that the parsing result can be verified.}

 \usage{

-\method{compare}{counts}(gs, file, id.vars = c("FCS Filename",

-  "population"), ...)

+compare.counts(gs, file, id.vars = c("FCS Filename", "population"), ...)

 }

 \arguments{

 \item{gs}{parsed GatingSet}

@@ -24,12 +23,11 @@ compare the counts to cytobank's exported csv so that the parsing result can be

 }

 \examples{

-xmlfile <- system.file("extdata/cytotrol_tcell_cytobank.xml", package = "CytoML")

-fcsFiles <- list.files(pattern = "CytoTrol", 

-        system.file("extdata", package = "flowWorkspaceData"), full = TRUE)

-gs <- cytobank2GatingSet(xmlfile, fcsFiles)

+acsfile <- system.file("extdata/cytobank_experiment.acs", package = "CytoML")

+ce <- cytobankExperiment(acsfile)

+gs <- cytobank2GatingSet(ce)

 ## verify the stats are correct

-statsfile <- system.file("extdata/cytotrol_tcell_cytobank_counts.csv", package = "CytoML")

+statsfile <- ce$attachments[1]

 dt_merged <- compare.counts(gs, statsfile, id.vars = "population", skip = "FCS Filename")

 all.equal(dt_merged[, count.x], dt_merged[, count.y], tol = 5e-4)

@@ -2,10 +2,13 @@

 % Please edit documentation in R/cytobank2GatingSet.R, R/cytobankExperiment.R

 \name{cytobank2GatingSet.default}

 \alias{cytobank2GatingSet.default}

+\alias{cytobank2GatingSet}

 \alias{cytobank2GatingSet.cytobankExperiment}

 \title{A wrapper that parse the gatingML and FCS files (or cytobankExperiment object) into GatingSet}

 \usage{

-\method{cytobank2GatingSet}{default}(x, FCS)

+\method{cytobank2GatingSet}{default}(x, FCS, ...)

+

+cytobank2GatingSet(x, ...)

 \method{cytobank2GatingSet}{cytobankExperiment}(x, ...)

 }

@@ -13,6 +16,8 @@

 \item{x}{the cytobankExperiment object or the full path of gatingML file}

 \item{FCS}{FCS files to be loaded}

+

+\item{...}{other arguments}

 }

 \value{

 a GatingSet

@@ -22,10 +27,12 @@ A wrapper that parse the gatingML and FCS files (or cytobankExperiment object) i

 }

 \examples{

 \dontrun{

-xmlfile <- system.file("extdata/cytotrol_tcell_cytobank.xml", package = "CytoML")

-fcsFiles <- list.files(pattern = "CytoTrol", 

-      system.file("extdata", package = "flowWorkspaceData"), full = TRUE)

-gs <- cytobank2GatingSet(xmlfile, fcsFiles)

-#plotGate(gs[[1]])

+acsfile <- system.file("extdata/cytobank_experiment.acs", package = "CytoML")

+ce <- cytobankExperiment(acsfile)

+xmlfile <- ce$gatingML

+fcsFiles <- list.files(ce$fcsdir, full.names = TRUE)

+gs <<- cytobank2GatingSet(xmlfile, fcsFiles)

+library(ggcyto)

+autoplot(gs[[1]])

 }

 }

@@ -5,16 +5,18 @@

 \alias{cytobankExperiment}

 \alias{print.cytobankExperiment}

 \alias{getCompensationMatrices.cytobankExperiment}

+\alias{getCompensationMatrices}

 \alias{markernames,cytobankExperiment-method}

 \alias{colnames,cytobankExperiment-method}

 \alias{getTransformations.cytobankExperiment}

+\alias{getTransformations}

 \alias{sampleNames,cytobankExperiment-method}

 \alias{pData,cytobankExperiment-method}

 \title{Construct cytobankExperiment object from ACS file}

 \usage{

 cytobankExperiment(acs, exdir = tempfile())

-\method{print}{cytobankExperiment}(x)

+\method{print}{cytobankExperiment}(x, ...)

 \method{getCompensationMatrices}{cytobankExperiment}(x)

@@ -23,7 +25,7 @@ cytobankExperiment(acs, exdir = tempfile())

 \S4method{colnames}{cytobankExperiment}(x, do.NULL = "missing",

   prefix = "missing")

-\method{getTransformations}{cytobankExperiment}(x)

+\method{getTransformations}{cytobankExperiment}(x, ...)

 \S4method{sampleNames}{cytobankExperiment}(object)

@@ -36,7 +38,11 @@ cytobankExperiment(acs, exdir = tempfile())

 \item{x}{cytobankExperiment object}

+\item{...}{not used}

+

 \item{object}{cytobankExperiment object}

+

+\item{do.NULL, prefix}{not used}

 }

 \value{

 cytobankExperiment object

@@ -19,8 +19,10 @@ a graphNEL node

 get children nodes

 }

 \examples{

+\dontrun{

 xmlfile <- system.file("extdata/cytotrol_tcell_cytobank.xml", package = "CytoML")

 g <- read.gatingML.cytobank(xmlfile)

 getChildren(g, "GateSet_722326")

 getParent(g, "GateSet_722326")

 }

+}

@@ -24,8 +24,10 @@ It returns the node names and population names by default. Or return the entire

 get nodes from {graphGML} object

 }

 \examples{

+\dontrun{

 xmlfile <- system.file("extdata/cytotrol_tcell_cytobank.xml", package = "CytoML")

 g <- read.gatingML.cytobank(xmlfile)

 getNodes(g)

 getNodes(g, only.names = FALSE)

 }

+}

@@ -4,10 +4,12 @@

 \alias{getTransformations.graphGML}

 \title{Extract transformations from graphGML object.}

 \usage{

-\method{getTransformations}{graphGML}(x)

+\method{getTransformations}{graphGML}(x, ...)

 }

 \arguments{

 \item{x}{graphGML}

+

+\item{...}{not used}

 }

 \value{

 transformerList object

@@ -22,8 +22,9 @@ nothing

 The node with dotted order represents the population that has tailored gates (sample-specific gates) defined.

 }

 \examples{

+\dontrun{

 xmlfile <- system.file("extdata/cytotrol_tcell_cytobank.xml", package = "CytoML")

 g <- read.gatingML.cytobank(xmlfile)

 plot(g)

-

+}

 }

@@ -21,7 +21,9 @@ The Default parser (flowUtils::read.gatingML) does not  parse the population tre

 the custom information from cytobank. (e.g. gate name, fcs filename).

 }

 \examples{

+\dontrun{

 xml <- system.file("extdata/cytotrol_tcell_cytobank.xml", package = "CytoML")

 g <- read.gatingML.cytobank(xml) #parse the population tree

 #plot(g) #visualize it

 }

+}

@@ -7,7 +7,7 @@ This makefile requires GNU Make.

 endif

 CXX_STD = CXX11

-PKG_CPPFLAGS =-DROUT -I../inst/include/ @PKG_CPPFLAGS@ -Wno-deprecated-declarations

+PKG_CPPFLAGS =-DROUT -I../inst/include/ @PKG_CPPFLAGS@

 PKG_LIBS =`${R_HOME}/bin/Rscript -e "RProtoBufLib:::LdFlags();cat(' ');RcppParallel::RcppParallelLibs()"` @PKG_LIBS@ 

 USERDIR = ${R_PACKAGE_DIR}/lib${R_ARCH}