@@ -56,5 +56,6 @@ 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)

@@ -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")

@@ -286,6 +291,7 @@ 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

@@ -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

+}

@@ -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)

 }

+}

@@ -8,6 +8,8 @@

 }

 \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

 }

+}