write.gatingML: Function to write a Gating-ML XML file based on gating and...
In jspidlen/flowUtils: Utilities for flow cytometry
Description
Usage
Arguments
Details
Author(s)
References
See Also
Examples
View source: R/writeGatingML.R
Description
This function saves gating and transformation objects stored in an R environment to
a Gating-ML 2.0 XML file. The objects expected and supported in the R environment are
those that can normally be created by the read.gatingML function when a Gating-ML 2.0
XML file is read.
Usage
1
write.gatingML(flowEnv, file = NULL)
Arguments
flowEnv
The R environment that is being searched for gating objects and transformations
file
The name of the output Gating-ML XML file. The standard output will be used if file
is NULL.
Details
The Gating-ML specification has been developed as an interchange format for the description of
gates relevant to a flow cytometry experiment. Presently, flowUtils can read Gating-ML versions
1.5 and 2.0 of the specification (see read.gatingML). Gating-ML version 2.0 only
is being used when saving Gating-ML.
Author(s)
Spidlen, J.
References
Spidlen J, ISAC DSTF, Brinkman RR. 2014.
Gating-ML 2.0. International Society for Advancement of
Cytometry (ISAC) standard for representing gating
descriptions in flow cytometry.
http://flowcyt.sf.net/gating/20141009.pdf
http://flowcyt.sf.net/gating/20141009.full.zip
See Also
Examples
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library("flowCore")
#################################################################
# Read a Gating-ML file and write the objects back in Gating-ML #
#################################################################
flowEnv <- new.env()
gateFile <- system.file("extdata/Gml2/Gating-MLFiles",
"gates1.xml", package="gatingMLData")
read.gatingML(gateFile, flowEnv)
ls(flowEnv)
write.gatingML(flowEnv)
################################################
# Create a quad gate and write it to Gating-ML #
################################################
flowEnv=new.env()
myQuad <- quadGate(filterId = "myQuad", "FSC-A" = 15000,
"SSC-A" = 16000)
flowEnv[['myQuad']] <- myQuad
write.gatingML(flowEnv)
##############################################
# If we wanted the output to a file instead: #
##############################################
gatingOutputFile <- tempfile(fileext=".gating-ml2.xml")
write.gatingML(flowEnv, gatingOutputFile)
##################################################
# Again a quad gate, but now adding compensation #
##################################################
flowEnv=new.env()
myCompQuad <- quadGate(filterId = "myCompQuad", "PE-A" = 100,
"PerCP-Cy5-5-A" = 200)
compPars = list(
compensatedParameter(parameters="PE-A", spillRefId="SpillFromFCS",
transformationId=paste("PE-A", "_compensated_according_to_FCS",
sep=""), searchEnv=flowEnv),
compensatedParameter(parameters="PerCP-Cy5-5-A", spillRefId="SpillFromFCS",
transformationId=paste("PerCP-Cy5-5-A", "_compensated_according_to_FCS",
sep=""), searchEnv=flowEnv)
)
myCompQuad@parameters = new("parameters", compPars)
flowEnv[['myCompQuad']] <- myCompQuad
write.gatingML(flowEnv)
##############################################################
# Again a quad gate, but now adding a scaling transformation #
##############################################################
flowEnv=new.env()
myTrQuad <- quadGate(filterId = "myTrQuad", "APC-A" = 0.5, "APC-Cy7-A" = 0.5)
trArcSinH1 = asinhtGml2(parameters = "APC-A",
T = 1000, M = 4.5, A = 0, transformationId="trArcSinH1")
trLogicle1 = logicletGml2(parameters = "APC-Cy7-A",
T = 1000, W = 0.5, M = 4.5, A = 0, transformationId="trLogicle1")
flowEnv[['trArcSinH1']] <- trArcSinH1
flowEnv[['trLogicle1']] <- trLogicle1
trPars = list(
transformReference("trArcSinH1", flowEnv),
transformReference("trLogicle1", flowEnv)
)
myTrQuad@parameters = new("parameters", trPars)
flowEnv[['myTrQuad']] <- myTrQuad
write.gatingML(flowEnv)
#######################################################################
# Now, we will be adding both scaling transformation and compensation #
# Also demonstrating what happens if 'bad' characters are part of the #
# name #
#######################################################################
flowEnv=new.env()
myTrCompQuad <- quadGate(filterId = "myTr!Comp Quad", "APC-A" = 0.5,
"APC-Cy7-A" = 0.5)
trArcSinH2 = asinhtGml2(parameters = "APC-A",
T = 1000, M = 4, A = 0, transformationId="trArcSinH2")
trLogicle2 = logicletGml2(parameters = "APC-Cy7-A",
T = 1000, W = 0.3, M = 4.5, A = 0, transformationId="trLogicle2")
trArcSinH2@parameters = compensatedParameter(parameters="APC-A",
spillRefId="SpillFromFCS", transformationId=paste("FL3-H",
"_compensated_according_to_FCS", sep=""), searchEnv=flowEnv)
trLogicle2@parameters = compensatedParameter(parameters="APC-Cy7-A",
spillRefId="SpillFromFCS", transformationId=paste("FL4-H",
"_compensated_according_to_FCS", sep=""), searchEnv=flowEnv)
trPars = list(trArcSinH2,trLogicle2)
myTrCompQuad@parameters = new("parameters", trPars)
flowEnv[['myTr!Comp Quad']] <- myTrCompQuad
write.gatingML(flowEnv)
##############################################################
# Creating a rectangle gate on a ratio of two parameters and #
# saving the result to a Gating-ML file. #
##############################################################
flowEnv=new.env()
rat1 <- ratio("FSC-A", "SSC-A", transformationId = "rat1")
gate1 <- rectangleGate(filterId="gate1", "rat1"=c(0.8, 1.4))
gate1@parameters = new("parameters", list(rat1))
flowEnv[['gate1']] <- gate1
trArcSinH = asinhtGml2(parameters = "rat2",
T = 1000, M = 4.5, A = 0, transformationId="trArcSinH")
rat2 <- ratio("FSC-A", "APC-A", transformationId = "rat2")
trArcSinH@parameters = rat2
gate2 <- rectangleGate(filterId="gate2", "rat2"=c(0.6, 1.3))
gate2@parameters = new("parameters", list(trArcSinH))
flowEnv[['gate2']] <- gate2
write.gatingML(flowEnv)
##########################################################
# Example with an ellipse gate on compensated parameters #
##########################################################
flowEnv <- new.env()
covM <- matrix(c(62.5, 37.5, 37.5, 62.5), nrow = 2, byrow=TRUE)
colnames(covM) <- c("FL1-H", "FL2-H")
compPars <- list(
compensatedParameter(parameters="FL1-H", spillRefId="SpillFromFCS",
transformationId=paste("FL1-H", "_compensated_according_to_FCS", sep=""),
searchEnv=flowEnv),
compensatedParameter(parameters="FL2-H", spillRefId="SpillFromFCS",
transformationId=paste("FL2-H", "_compensated_according_to_FCS", sep=""),
searchEnv=flowEnv)
)
myEl <- ellipsoidGate(mean=c(12, 16), distance=1, .gate=covM, filterId="myEl")
myEl@parameters <- new("parameters", compPars)
flowEnv[['myEl']] <- myEl
write.gatingML(flowEnv)
##########################################################################
# Creating some Boolean gates and saving the result to a Gating-ML file. #
##########################################################################
flowEnv=new.env()
rg1 <- rectangleGate(filterId="rg1", list("FSC-A"=c(0200, 16000),
"SSC-A"=c(0, 34000)))
rg2 <- rectangleGate(filterId="rg2", list("PE-A"=c(100, 8000),
"APC-Cy7-A"=c(0, 59000)))
orGate <- new("unionFilter", filterId="orGate",
filters=list(rg1, rg2))
flowEnv[['orGate']] <- orGate
andGate <- new("intersectFilter", filterId="andGate",
filters=list(rg1, rg2))
flowEnv[['andGate']] <- andGate
notGate <- new("complementFilter", filterId="notGate",
filters=list(rg1))
flowEnv[['notGate']] <- notGate
parentGate <- new("subsetFilter", filterId="parentGate",
filters=list(rg1, rg2))
flowEnv[['parentGate']] <- parentGate
write.gatingML(flowEnv)
#################################################
# Or if we wanted to write to a file instead... #
#################################################
gatingOutputFile <- tempfile(fileext=".gating-ml2.xml")
write.gatingML(flowEnv, gatingOutputFile)
###########################################################################
# A few of the Gating-ML 1.5 transforms can be converted to Gating-ML 2.0 #
# and therefore be used with the write.gatingML function. #
###########################################################################
flowEnv=new.env()
trArcSinHGml1.5 = asinht(parameters = "APC-A", a = 1, b = 1,
transformationId="trArcSinHGml1.5")
gateAsinhGml1.5 <- rectangleGate(filterId="gateAsinhGml1.5",
"trArcSinHGml1.5"=c(0.3, 4.7))
gateAsinhGml1.5@parameters = new("parameters", list(trArcSinHGml1.5))
flowEnv[['gateAsinhGml1.5']] <- gateAsinhGml1.5
gatingOutputFile <- tempfile(fileext=".gating-ml2.xml")
write.gatingML(flowEnv, gatingOutputFile)
jspidlen/flowUtils documentation built on Nov. 4, 2019, 3:25 p.m.
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Description Usage Arguments Details Author(s) References See Also Examples
View source: R/writeGatingML.R
Description
This function saves gating and transformation objects stored in an R environment to a Gating-ML 2.0 XML file. The objects expected and supported in the R environment are those that can normally be created by the read.gatingML function when a Gating-ML 2.0 XML file is read.
Usage
1 | write.gatingML(flowEnv, file = NULL)
|
Arguments
flowEnv |
The R environment that is being searched for gating objects and transformations |
file |
The name of the output Gating-ML XML file. The standard output will be used if file is NULL. |
Details
The Gating-ML specification has been developed as an interchange format for the description of
gates relevant to a flow cytometry experiment. Presently, flowUtils can read Gating-ML versions
1.5 and 2.0 of the specification (see read.gatingML). Gating-ML version 2.0 only
is being used when saving Gating-ML.
Author(s)
Spidlen, J.
References
Spidlen J, ISAC DSTF, Brinkman RR. 2014.
Gating-ML 2.0. International Society for Advancement of
Cytometry (ISAC) standard for representing gating
descriptions in flow cytometry.
http://flowcyt.sf.net/gating/20141009.pdf
http://flowcyt.sf.net/gating/20141009.full.zip
See Also
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 | library("flowCore")
#################################################################
# Read a Gating-ML file and write the objects back in Gating-ML #
#################################################################
flowEnv <- new.env()
gateFile <- system.file("extdata/Gml2/Gating-MLFiles",
"gates1.xml", package="gatingMLData")
read.gatingML(gateFile, flowEnv)
ls(flowEnv)
write.gatingML(flowEnv)
################################################
# Create a quad gate and write it to Gating-ML #
################################################
flowEnv=new.env()
myQuad <- quadGate(filterId = "myQuad", "FSC-A" = 15000,
"SSC-A" = 16000)
flowEnv[['myQuad']] <- myQuad
write.gatingML(flowEnv)
##############################################
# If we wanted the output to a file instead: #
##############################################
gatingOutputFile <- tempfile(fileext=".gating-ml2.xml")
write.gatingML(flowEnv, gatingOutputFile)
##################################################
# Again a quad gate, but now adding compensation #
##################################################
flowEnv=new.env()
myCompQuad <- quadGate(filterId = "myCompQuad", "PE-A" = 100,
"PerCP-Cy5-5-A" = 200)
compPars = list(
compensatedParameter(parameters="PE-A", spillRefId="SpillFromFCS",
transformationId=paste("PE-A", "_compensated_according_to_FCS",
sep=""), searchEnv=flowEnv),
compensatedParameter(parameters="PerCP-Cy5-5-A", spillRefId="SpillFromFCS",
transformationId=paste("PerCP-Cy5-5-A", "_compensated_according_to_FCS",
sep=""), searchEnv=flowEnv)
)
myCompQuad@parameters = new("parameters", compPars)
flowEnv[['myCompQuad']] <- myCompQuad
write.gatingML(flowEnv)
##############################################################
# Again a quad gate, but now adding a scaling transformation #
##############################################################
flowEnv=new.env()
myTrQuad <- quadGate(filterId = "myTrQuad", "APC-A" = 0.5, "APC-Cy7-A" = 0.5)
trArcSinH1 = asinhtGml2(parameters = "APC-A",
T = 1000, M = 4.5, A = 0, transformationId="trArcSinH1")
trLogicle1 = logicletGml2(parameters = "APC-Cy7-A",
T = 1000, W = 0.5, M = 4.5, A = 0, transformationId="trLogicle1")
flowEnv[['trArcSinH1']] <- trArcSinH1
flowEnv[['trLogicle1']] <- trLogicle1
trPars = list(
transformReference("trArcSinH1", flowEnv),
transformReference("trLogicle1", flowEnv)
)
myTrQuad@parameters = new("parameters", trPars)
flowEnv[['myTrQuad']] <- myTrQuad
write.gatingML(flowEnv)
#######################################################################
# Now, we will be adding both scaling transformation and compensation #
# Also demonstrating what happens if 'bad' characters are part of the #
# name #
#######################################################################
flowEnv=new.env()
myTrCompQuad <- quadGate(filterId = "myTr!Comp Quad", "APC-A" = 0.5,
"APC-Cy7-A" = 0.5)
trArcSinH2 = asinhtGml2(parameters = "APC-A",
T = 1000, M = 4, A = 0, transformationId="trArcSinH2")
trLogicle2 = logicletGml2(parameters = "APC-Cy7-A",
T = 1000, W = 0.3, M = 4.5, A = 0, transformationId="trLogicle2")
trArcSinH2@parameters = compensatedParameter(parameters="APC-A",
spillRefId="SpillFromFCS", transformationId=paste("FL3-H",
"_compensated_according_to_FCS", sep=""), searchEnv=flowEnv)
trLogicle2@parameters = compensatedParameter(parameters="APC-Cy7-A",
spillRefId="SpillFromFCS", transformationId=paste("FL4-H",
"_compensated_according_to_FCS", sep=""), searchEnv=flowEnv)
trPars = list(trArcSinH2,trLogicle2)
myTrCompQuad@parameters = new("parameters", trPars)
flowEnv[['myTr!Comp Quad']] <- myTrCompQuad
write.gatingML(flowEnv)
##############################################################
# Creating a rectangle gate on a ratio of two parameters and #
# saving the result to a Gating-ML file. #
##############################################################
flowEnv=new.env()
rat1 <- ratio("FSC-A", "SSC-A", transformationId = "rat1")
gate1 <- rectangleGate(filterId="gate1", "rat1"=c(0.8, 1.4))
gate1@parameters = new("parameters", list(rat1))
flowEnv[['gate1']] <- gate1
trArcSinH = asinhtGml2(parameters = "rat2",
T = 1000, M = 4.5, A = 0, transformationId="trArcSinH")
rat2 <- ratio("FSC-A", "APC-A", transformationId = "rat2")
trArcSinH@parameters = rat2
gate2 <- rectangleGate(filterId="gate2", "rat2"=c(0.6, 1.3))
gate2@parameters = new("parameters", list(trArcSinH))
flowEnv[['gate2']] <- gate2
write.gatingML(flowEnv)
##########################################################
# Example with an ellipse gate on compensated parameters #
##########################################################
flowEnv <- new.env()
covM <- matrix(c(62.5, 37.5, 37.5, 62.5), nrow = 2, byrow=TRUE)
colnames(covM) <- c("FL1-H", "FL2-H")
compPars <- list(
compensatedParameter(parameters="FL1-H", spillRefId="SpillFromFCS",
transformationId=paste("FL1-H", "_compensated_according_to_FCS", sep=""),
searchEnv=flowEnv),
compensatedParameter(parameters="FL2-H", spillRefId="SpillFromFCS",
transformationId=paste("FL2-H", "_compensated_according_to_FCS", sep=""),
searchEnv=flowEnv)
)
myEl <- ellipsoidGate(mean=c(12, 16), distance=1, .gate=covM, filterId="myEl")
myEl@parameters <- new("parameters", compPars)
flowEnv[['myEl']] <- myEl
write.gatingML(flowEnv)
##########################################################################
# Creating some Boolean gates and saving the result to a Gating-ML file. #
##########################################################################
flowEnv=new.env()
rg1 <- rectangleGate(filterId="rg1", list("FSC-A"=c(0200, 16000),
"SSC-A"=c(0, 34000)))
rg2 <- rectangleGate(filterId="rg2", list("PE-A"=c(100, 8000),
"APC-Cy7-A"=c(0, 59000)))
orGate <- new("unionFilter", filterId="orGate",
filters=list(rg1, rg2))
flowEnv[['orGate']] <- orGate
andGate <- new("intersectFilter", filterId="andGate",
filters=list(rg1, rg2))
flowEnv[['andGate']] <- andGate
notGate <- new("complementFilter", filterId="notGate",
filters=list(rg1))
flowEnv[['notGate']] <- notGate
parentGate <- new("subsetFilter", filterId="parentGate",
filters=list(rg1, rg2))
flowEnv[['parentGate']] <- parentGate
write.gatingML(flowEnv)
#################################################
# Or if we wanted to write to a file instead... #
#################################################
gatingOutputFile <- tempfile(fileext=".gating-ml2.xml")
write.gatingML(flowEnv, gatingOutputFile)
###########################################################################
# A few of the Gating-ML 1.5 transforms can be converted to Gating-ML 2.0 #
# and therefore be used with the write.gatingML function. #
###########################################################################
flowEnv=new.env()
trArcSinHGml1.5 = asinht(parameters = "APC-A", a = 1, b = 1,
transformationId="trArcSinHGml1.5")
gateAsinhGml1.5 <- rectangleGate(filterId="gateAsinhGml1.5",
"trArcSinHGml1.5"=c(0.3, 4.7))
gateAsinhGml1.5@parameters = new("parameters", list(trArcSinHGml1.5))
flowEnv[['gateAsinhGml1.5']] <- gateAsinhGml1.5
gatingOutputFile <- tempfile(fileext=".gating-ml2.xml")
write.gatingML(flowEnv, gatingOutputFile)
|
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