# This file was copied from the flowUtils package on 5/6/2019.
# This represents the work of Josef Spidlen and the other flowUtils
# authors who are also accordingly credited in the authors list for CytoML.
#
# Details:
# https://github.com/jspidlen/flowUtils/
# GitHub version: 1.35.8
# Bioconductor version: 1.49.0
setGeneric(
"identifyNode",
def=function(object, flowEnv, ...) standardGeneric("identifyNode"),
useAsDefault=function(object, flowEnv, ...)
{
stop(paste("Not a supported node in Gating-ML format:", paste(object, collapse = ", "), sep = " "))
}
)
setMethod(
"identifyNode",
"http...www.isac.net.org.std.Gating.ML.v2.0.datatypes_custom_info",
function(object, flowEnv, ...) { }
)
setMethod(
"identifyNode",
"http...www.isac.net.org.std.Gating.ML.v2.0.gating_PolygonGate",
function(object, flowEnv, ...)
{
if (flowEnv[['.flowUtilsRead.GatingML.PassNo']] == 2)
{
gateId = (xmlGetAttr(object, "id", genid(flowEnv)))
parentId = (xmlGetAttr(object, "parent_id", "NULL"))
dimensionList= xmlElementsByTagName(object, "dimension")
len = length(dimensionList)
transformationList <- getTransformationListGml2(dimensionList, flowEnv)
vertexList = xmlElementsByTagName(object, "vertex")
len = length(vertexList)
vertexLimits = matrix(nrow=len, ncol=length(dimensionList))
for (i in seq(len)) vertexLimits[i,] = getParameters(vertexList[[i]])
filt = polygonGate(filterId=gateId, .gate=vertexLimits, transformationList)
if(parentId == "NULL")
{
flowEnv[[as.character(gateId)]] = filt
}
else
{
temp = new("filterReference", name=parentId, env=flowEnv, filterId="NULL")
flowEnv[[as.character(gateId)]] = new("subsetFilter", filters=list(filt, temp), filterId=gateId)
}
}
}
)
setMethod(
"identifyNode",
"http...www.isac.net.org.std.Gating.ML.v2.0.gating_RectangleGate",
function(object, flowEnv, ...)
{
if (flowEnv[['.flowUtilsRead.GatingML.PassNo']] == 2)
{
gateId = (xmlGetAttr(object, "id", genid(flowEnv)))
parentId = (xmlGetAttr(object, "parent_id", "NULL"))
dimensionList = xmlElementsByTagName(object, "dimension")
len = length(dimensionList)
gateLimits = matrix(nrow=2, ncol=len)
for (i in seq(len))
{
gateLimits[,i] = getParameters(dimensionList[[i]])
}
transformationList <- getTransformationListGml2(dimensionList, flowEnv)
filt = rectangleGate(filterId=gateId, .gate=gateLimits, transformationList)
if (parentId == "NULL")
{
flowEnv[[as.character(gateId)]] = filt
}
else
{
temp = new("filterReference", name=parentId, env=flowEnv, filterId="NULL")
flowEnv[[as.character(gateId)]] = new("subsetFilter", filters=list(filt, temp), filterId=gateId)
}
}
}
)
setMethod(
"identifyNode",
"http...www.isac.net.org.std.Gating.ML.v2.0.gating_EllipsoidGate",
function(object, flowEnv, ...)
{
if (flowEnv[['.flowUtilsRead.GatingML.PassNo']] == 2)
{
gateId = (xmlGetAttr(object, "id", genid(flowEnv)))
parentId = (xmlGetAttr(object, "parent_id", "NULL"))
dimensionList = xmlElementsByTagName(object, "dimension")
len = length(dimensionList)
transformationList <- getTransformationListGml2(dimensionList, flowEnv)
meanList = xmlElementsByTagName(object, "mean")
meanLimits = getParameters(meanList[[1]])
covarianceList = xmlChildren(xmlElementsByTagName(object, "covarianceMatrix")[[1]])
len=length(covarianceList)
covMat = matrix(nrow=len, ncol=length(dimensionList))
for (i in seq(len))
{
covMat[i,] = getParameters(covarianceList[[i]])
}
distance = sqrt(getParameters(xmlElementsByTagName(object, "distanceSquare")[[1]]))
filt = ellipsoidGate(filterId=gateId, .gate=covMat, mean=meanLimits, distance=distance, transformationList)
if(parentId == "NULL")
{
flowEnv[[as.character(gateId)]] = filt
}
else
{
temp = new("filterReference", name=parentId, env=flowEnv, filterId="NULL")
flowEnv[[as.character(gateId)]] = new("subsetFilter", filters=list(filt, temp), filterId=gateId)
}
}
}
)
# J. Spidlen, Oct 23, 2013:
# It seems that flowCore's Quad gate will not work for this easily since we want to
# have custom identifiers of these quads and want to be able to reference these
# as parent populations or Boolean gate arguments. Also, it doesn't seem to be
# possible to use the quadGate on top of compensated or scaled parameters (since
# the constructor is taking parameter names and not transformations). So we are
# simply creating n-dimensional rectangle gates for all the Quads from here.
setMethod(
"identifyNode",
"http...www.isac.net.org.std.Gating.ML.v2.0.gating_QuadrantGate",
function(object, flowEnv, ...)
{
if (flowEnv[['.flowUtilsRead.GatingML.PassNo']] == 2)
{
gateId = (xmlGetAttr(object, "id", genid(flowEnv)))
parentId = (xmlGetAttr(object, "parent_id", "NULL"))
dividerList = xmlElementsByTagName(object, "divider")
dividers <- list()
transformations <- list()
compensations <- list()
for (i in seq(length(dividerList)))
{
fcsDimension = xmlElementsByTagName(dividerList[[i]], "fcs-dimension")
itIsRatio = FALSE
if (length(fcsDimension) == 0)
{
fcsDimension = xmlElementsByTagName(dividerList[[i]], "new-dimension")
name = xmlGetAttr(fcsDimension[[1]], "transformation-ref")
itIsRatio = TRUE
}
else
name = xmlGetAttr(fcsDimension[[1]], "name")
dividerValues <- list()
dividerId = (xmlGetAttr(dividerList[[i]], "id", genid(flowEnv)))
transformationRef = (xmlGetAttr(dividerList[[i]], "transformation-ref", "unitytransform"))
compensationRef = (xmlGetAttr(dividerList[[i]], "compensation-ref", "FCS"))
values = xmlElementsByTagName(dividerList[[i]], "value")
for (j in seq(length(values)))
{
dividerValues[[j]] = getElementValueAsNumeric(values[[j]])
}
dividerValues[[j + 1]] = as.character(name)
dividerValues[[j + 2]] = itIsRatio
dividers[[as.character(dividerId)]] = dividerValues
transformations[[as.character(dividerId)]] = transformationRef
compensations[[as.character(dividerId)]] = compensationRef
}
quadrantList = xmlElementsByTagName(object, "Quadrant")
for (i in seq(length(quadrantList)))
{
quadrant <- getParameters(quadrantList[[i]])
quadrantId = (xmlGetAttr(quadrantList[[i]], "id", genid(flowEnv)))
len = length(quadrant)
gateLimits = matrix(nrow=2, ncol=len)
for (i in seq(len))
{
gateLimits[,i] = getBounds(quadrant[[i]], names(quadrant)[[i]], dividers)
}
transformationList <- getTransformationListForQuadrantGate(quadrant, dividers, transformations, compensations, flowEnv)
filt = rectangleGate(filterId=quadrantId, .gate=gateLimits, transformationList)
if (parentId == "NULL")
{
flowEnv[[as.character(quadrantId)]] = filt
}
else
{
temp = new("filterReference", name=parentId, env=flowEnv, filterId="NULL")
flowEnv[[as.character(gateId)]] = new("subsetFilter", filters=list(filt, temp), filterId=gateId)
}
}
}
}
)
setMethod(
"identifyNode",
"http...www.isac.net.org.std.Gating.ML.v2.0.gating_BooleanGate",
function(object, flowEnv, ...)
{
if (flowEnv[['.flowUtilsRead.GatingML.PassNo']] == 2)
{
gateId = (xmlGetAttr(object, "id", genid(flowEnv)))
parentId = (xmlGetAttr(object, "parent_id", "NULL"))
childern = xmlChildren(object)
filt <- identifyNode(childern[[length(childern)]], flowEnv)
if (parentId == "NULL")
{
filt@filterId = as.character(gateId)
flowEnv[[as.character(gateId)]] = filt
}
else
{
temp = new("filterReference", name=parentId, env=flowEnv, filterId="NULL")
flowEnv[[as.character(gateId)]] = new("subsetFilter", filters=list(filt, temp), filterId=gateId)
}
}
}
)
setMethod(
"identifyNode",
"http...www.isac.net.org.std.Gating.ML.v2.0.gating_gateReference",
function(object, flowEnv, ...)
{
gateRefId = getParameters(object)
useAsComplement = xmlGetAttr(object, "use-as-complement")
gRef <- new("filterReference", name=gateRefId, env=flowEnv, filterId=gateRefId)
if ((!is.null(useAsComplement)) && (useAsComplement == "true" || useAsComplement == "1"))
{
complFiltId = paste("Not", gateRefId, sep="_")
complFilter <- new("complementFilter", filterId=complFiltId, filters=list(gRef))
flowEnv[[complFiltId]] = complFilter
new("filterReference", name=complFiltId, env=flowEnv, filterId=complFiltId)
}
else
gRef
}
)
setMethod(
"identifyNode",
"http...www.isac.net.org.std.Gating.ML.v2.0.gating_and",
function(object, flowEnv, ...)
{
gateList = xmlChildren(object)
len = length(gateList)
parameters = list()
while (len > 0)
{
parameters[[len]] = identifyNode(gateList[[len]], flowEnv)
len = len-1
}
new("intersectFilter", filterId="", filters=parameters)
}
)
setMethod(
"identifyNode",
"http...www.isac.net.org.std.Gating.ML.v2.0.gating_or",
function(object, flowEnv, ...)
{
gateList = xmlChildren(object)
len = length(gateList)
parameters = list()
while (len > 0)
{
parameters[[len]] = identifyNode(gateList[[len]], flowEnv)
len = len-1
}
new("unionFilter", filterId="", filters=parameters)
}
)
setMethod(
"identifyNode",
"http...www.isac.net.org.std.Gating.ML.v2.0.gating_not",
function(object, flowEnv, ...)
{
gateList = xmlChildren(object)
len = length(gateList)
parameters = list()
if (len == 1)
{
parameters[[len]] = identifyNode(gateList[[len]], flowEnv)
}
else
{
stop("Not element should have only one operand")
}
new("complementFilter", filterId="", filters=parameters)
}
)
setMethod(
"identifyNode",
"http...www.isac.net.org.std.Gating.ML.v1.5.gating_and",
function(object, flowEnv, ...)
{
gateList = xmlChildren(object)
len = length(gateList)
parameters = list()
while (len > 0)
{
parameters[[len]] = identifyNode(gateList[[len]], flowEnv)
len = len-1
}
new("intersectFilter", filterId="", filters=parameters)
}
)
setMethod(
"identifyNode",
"http...www.isac.net.org.std.Gating.ML.v1.5.gating_or",
function(object, flowEnv, ...)
{
gateList = xmlChildren(object)
len = length(gateList)
parameters = list()
while (len > 0)
{
parameters[[len]] = identifyNode(gateList[[len]], flowEnv)
len = len-1
}
new("unionFilter", filterId="", filters=parameters)
}
)
setMethod(
"identifyNode",
"http...www.isac.net.org.std.Gating.ML.v1.5.gating_not",
function(object, flowEnv, ...)
{
gateList = xmlChildren(object)
len = length(gateList)
parameters = list()
if (len == 1)
{
parameters[[len]] = identifyNode(gateList[[len]], flowEnv)
}
else
{
stop("Not element should have only one operand")
}
new("complementFilter", filterId="", filters=parameters)
}
)
setMethod(
"identifyNode",
"http...www.isac.net.org.std.Gating.ML.v1.5.gating_gateReference",
function(object, flowEnv, ...)
{
gateRefId = getParameters(object)
new("filterReference", name=gateRefId, env=flowEnv, filterId=gateRefId)
}
)
setMethod(
"identifyNode",
"http...www.isac.net.org.std.Gating.ML.v1.5.gating_BooleanGate",
function(object, flowEnv, ...)
{
gateId = (xmlGetAttr(object, "id", genid(flowEnv)))
parentId = (xmlGetAttr(object, "parent_id", "NULL"))
filt <- identifyNode(xmlChildren(object)[[1]], flowEnv)
if (parentId == "NULL")
{
filt@filterId = as.character(gateId)
flowEnv[[as.character(gateId)]] = filt
}
else
{
temp = new("filterReference", name=parentId, env=flowEnv, filterId="NULL")
flowEnv[[as.character(gateId)]] = new("subsetFilter", filters=list(filt, temp), filterId=gateId)
}
}
)
setMethod(
"identifyNode",
"http...www.isac.net.org.std.Gating.ML.v1.5.gating_RectangleGate",
function(object, flowEnv, ...)
{
gateId = (xmlGetAttr(object, "id", genid(flowEnv)))
parentId = (xmlGetAttr(object, "parent_id", "NULL"))
dimensionList = xmlElementsByTagName(object, "dimension")
len = length(dimensionList)
gateLimits = matrix(nrow=2, ncol=len)
for (i in seq(len))
{
gateLimits[,i] = getParameters(dimensionList[[i]])
}
transformationList <- getTransformationList(dimensionList, flowEnv)
filt=rectangleGate(filterId=gateId, .gate=gateLimits, transformationList)
if (parentId == "NULL")
{
flowEnv[[as.character(gateId)]] = filt
}
else
{
temp = new("filterReference", name=parentId, env=flowEnv, filterId="NULL")
flowEnv[[as.character(gateId)]] = new("subsetFilter", filters=list(filt, temp), filterId=gateId)
}
}
)
setMethod(
"identifyNode",
"http...www.isac.net.org.std.Gating.ML.v1.5.gating_PolygonGate",
function(object, flowEnv, ...)
{
gateId = (xmlGetAttr(object, "id", genid(flowEnv)))
parentId = (xmlGetAttr(object, "parent_id", "NULL"))
dimensionList = xmlElementsByTagName(object, "dimension")
len = length(dimensionList)
transformationList <- getTransformationList(dimensionList, flowEnv)
vertexList = xmlElementsByTagName(object, "vertex")
len = length(vertexList)
vertexLimits = matrix(nrow=len, ncol=length(dimensionList))
for (i in seq(len))
{
vertexLimits[i,] = getParameters(vertexList[[i]])
}
filt = polygonGate(filterId=gateId,.gate=vertexLimits,transformationList)
if (parentId == "NULL")
{
flowEnv[[as.character(gateId)]] = filt
}
else
{
temp = new("filterReference", name=parentId, env=flowEnv, filterId="NULL")
flowEnv[[as.character(gateId)]] = new("subsetFilter", filters=list(filt, temp), filterId=gateId)
}
}
)
setMethod(
"identifyNode",
"http...www.isac.net.org.std.Gating.ML.v1.5.gating_EllipsoidGate",
function(object, flowEnv, ...)
{
gateId = (xmlGetAttr(object, "id", genid(flowEnv)))
parentId = (xmlGetAttr(object, "parent_id", "NULL"))
dimensionList= xmlElementsByTagName(object, "dimension")
len = length(dimensionList)
transformationList <- getTransformationList(dimensionList, flowEnv)
meanList = xmlElementsByTagName(object, "mean")
meanLimits = getParameters(meanList[[1]])
covarianceList = xmlChildren(xmlElementsByTagName(object, "covarianceMatrix")[[1]])
len = length(covarianceList)
covMat = matrix(nrow=len, ncol=length(dimensionList))
for (i in seq(len))
{
covMat[i,] = getParameters(covarianceList[[i]])
}
distance = sqrt(getParameters(xmlElementsByTagName(object, "distanceSquare")[[1]]))
filt = ellipsoidGate(filterId=gateId, .gate=covMat, mean=meanLimits, distance=distance, transformationList)
if (parentId == "NULL")
{
flowEnv[[as.character(gateId)]] = filt
}
else
{
temp = new("filterReference", name=parentId, env=flowEnv, filterId="NULL")
flowEnv[[as.character(gateId)]] = new("subsetFilter", filters=list(filt, temp), filterId=gateId)
}
}
)
setMethod(
"identifyNode",
"http...www.isac.net.org.std.Gating.ML.v1.5.gating_PolytopeGate",
function(object, flowEnv, ...)
{
gateId = (xmlGetAttr(object, "id", genid(flowEnv)))
parentId = (xmlGetAttr(object, "parent_id", "NULL"))
dimensionList = xmlElementsByTagName(object, "dimension")
len = length(dimensionList)
transformationList <- getTransformationList(dimensionList, flowEnv)
halfList = xmlElementsByTagName(object, "halfspace")
len = length(halfList)
halfValues = matrix(nrow=len, ncol=length(dimensionList) + 1)
for (i in seq(len))
{
halfValues[i,] = sapply(xmlChildren(halfList[[i]]), getParameters)
}
a = matrix(halfValues[,1:length(dimensionList)], ncol=length(dimensionList))
b = (halfValues[,length(dimensionList)+1])
filt = polytopeGate(filterId=gateId, .gate=a, b=b, transformationList)
if (parentId == "NULL")
{
flowEnv[[as.character(gateId)]] = filt
}
else
{
temp = new("filterReference", name=parentId, env=flowEnv, filterId="NULL")
flowEnv[[as.character(gateId)]] = new("subsetFilter", filters=list(filt, temp), filterId=gateId)
}
}
)
setMethod(
"identifyNode",
"http...www.isac.net.org.std.Gating.ML.v1.5.gating_DecisionTreeGate",
function(object, flowEnv, ...)
{
gateId = (xmlGetAttr(object, "id", genid(flowEnv)))
parentId = (xmlGetAttr(object, "parent_id", "NULL"))
root = xmlChildren(object)[[1]]
test = decisionHelper(root)
filt = do.call(expressionFilter, list(expr=test))
if (parentId == "NULL")
{
flowEnv[[as.character(gateId)]] = filt
}
else
{
temp = new("filterReference", name=parentId, env=flowEnv, filterId="NULL")
flowEnv[[as.character(gateId)]] = new("subsetFilter", filters=list(filt, temp), filterId=gateId)
}
}
)
