R/plot.R
In GeneSurvey/TCGAGeneReport: Access to Gene Report Data
Defines functions
plot_fromGene_internal
plot_GeneSymbol_Mutations
plot_GeneSymbol_RnaSeq2
plot_GeneSymbol_RnaSeq
plot_GeneSymbol_SNP6
plot_Probe_Meth450
plot_Probe_Meth27
plot_CombinedHsaMimat_miRNASeq
plot_GeneSymbol_Meth450
plot_GeneSymbol_Meth27
Documented in
plot_CombinedHsaMimat_miRNASeq
plot_GeneSymbol_Meth27
plot_GeneSymbol_Meth450
plot_GeneSymbol_Mutations
plot_GeneSymbol_RnaSeq
plot_GeneSymbol_RnaSeq2
plot_GeneSymbol_SNP6
plot_Probe_Meth27
plot_Probe_Meth450
#TCGAGeneReport Copyright 2014, 2015, 2016 University of Texas MD Anderson Cancer Center
#
#This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.
#
#This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
#
#You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
#################################################################
#################################################################
# internal
#################################################################
#################################################################
plot_fromGene_internal <- function(theGene, theOutputDir, theZipFile,
theMapGeneToProbesFunction, theReadProbeFunction, theReadGeneFunction,
theDataType, theDataTypeLabel, theVerboseFlag, theUseDeltaFlag=FALSE,
theReplicateFlag=FALSE)
{
dir.create(theOutputDir, recursive = TRUE, showWarnings=FALSE)
returnFilename <- c()
myBarcodeDiseases <- NULL
myBarcodeSampleType <- NULL
myTag <- ""
myPathCombined <- NULL
myGeneEqPre <- NULL
# read gene data
if (FALSE==theUseDeltaFlag)
{
verboseMessage("plot_fromGene_internal FALSE==theUseDeltaFlag", theVerboseFlag=theVerboseFlag)
myTag <- ""
myBarcodeDiseases <- getMetadataPop_BarcodeDisease(theZipFile, theVerboseFlag=theVerboseFlag)
myBarcodeSampleType <- getMetadataPop_BarcodeSamplecode(theZipFile, theVerboseFlag=theVerboseFlag)
}
else
{
verboseMessage("plot_fromGene_internal TRUE==theUseDeltaFlag", theVerboseFlag=theVerboseFlag)
myTag <- "Delta"
myBarcodeDiseases <- getMetadataPop_PatientDisease(theZipFile, theVerboseFlag=theVerboseFlag)
myBarcodeSampleType <- getMetadataPop_PatientDisease(theZipFile, theVerboseFlag=theVerboseFlag)
}
probeList <- as.vector(unlist(theMapGeneToProbesFunction(theGene, theZipFile, theVerboseFlag=theVerboseFlag)))
locations <- as.vector(unlist(lapply(probeList, function(theProbe, theZipFile, theVerboseFlag=theVerboseFlag)
{
probeData <- as.vector(unlist(theReadProbeFunction(theProbe, theZipFile=theZipFile, theVerboseFlag=theVerboseFlag)))
# this is only one value, but you cannot unlist a list/vector of classes, I think
probeData[[1]]@mProbeLocation
},theZipFile=theZipFile, theVerboseFlag=theVerboseFlag)))
probeList <- probeList[order(locations)]
maxLocationSize <- max(as.vector(unlist(lapply(locations, nchar))))
probeDataList <- lapply(probeList, function(theProbe, thePath, theVerboseFlag)
{
theReadGeneFunction(theProbe, theZipFile, theVerboseFlag=theVerboseFlag, theUseDeltaFlag=theUseDeltaFlag)
}, thePath=myPathCombined, theVerboseFlag=theVerboseFlag)
# first write individual probe plots
for (index in 1:length(probeDataList))
{
myGeneData <- probeDataList[[index]]
probe <- probeList[index]
myProbeData <- as.vector(unlist(theReadProbeFunction(probe, theZipFile=theZipFile, theVerboseFlag=theVerboseFlag)))
# this is only one value, but you cannot unlist a list/vector of classes, I think
myLocation <- myProbeData[[1]]@mProbeLocation
if(!is.na(as.numeric(myLocation)))
{
myLocation <- sprintf(paste("%0", maxLocationSize, "d", sep=""), as.numeric(myLocation))
}
# this is only one value, but you cannot unlist a list/vector of classes, I think
geneEqPre <- paste(padChromosomeName(myProbeData[[1]]@mChromosome), "-", myLocation, "-", sep="")
returnFilename <- c(returnFilename,
plotGenericOutput(paste(theGene, probe, sep="-"),
theOutputDir, myGeneData, myBarcodeDiseases,
myBarcodeSampleType, theDataType, theDataTypeLabel,
theVerboseFlag=theVerboseFlag,
theTag=myTag, theGeneEqPre=geneEqPre,
theReplicateFlag=theReplicateFlag))
}
# now do combined probe plots
# first write individual probe plots
#for (index in 1:length(probeDataList))
#{
# myGeneData <- probeDataList[[index]]
# probe <- probeList[index]
# message(paste("probe=",probe," ",paste(myGeneData[1:3],collapse=", ", sep=""), sep=""))
#}
numberOfRows <- length(probeDataList[[1]])
sampleList <- colnames(probeDataList[[1]])
probeDataList <- as.vector(unlist(probeDataList))
probeData <- matrixWithIssues(probeDataList, nrow=numberOfRows)
colnames(probeData) <- probeList
rownames(probeData) <- sampleList
# probeData[sample,probe]
returnFilename <- c(returnFilename,
plotHeatmapOutput(theGene, theOutputDir, probeData, myBarcodeDiseases, myBarcodeSampleType,
theDataType, theDataTypeLabel, theZipFile,
theVerboseFlag, theReadProbeFunction, myTag))
returnFilename
}
#################################################################
#################################################################
# exported
#################################################################
#################################################################
####
#### uses gene equivalent from data file
####
plot_GeneSymbol_Mutations <- function(theGeneEq, theOutputDir,
theZipFile="/rsrch1/bcb/batcheffects/GENE_REPORT/GeneSurvey.zip",
theVerboseFlag=FALSE, theUseDeltaFlag=FALSE, theReplicateFlag=FALSE)
{
stopifnot(is.character(theGeneEq))
stopifnot(1==length(theGeneEq))
stopifnot(isValidDirectoryPath(theOutputDir))
stopifnot(file.exists(theZipFile))
stopifnot((TRUE==theVerboseFlag)||(FALSE==theVerboseFlag))
stopifnot((TRUE==theUseDeltaFlag)||(FALSE==theUseDeltaFlag))
stopifnot((TRUE==theReplicateFlag)||(FALSE==theReplicateFlag))
# read gene data
myGeneData <- NULL
myBarcodeDiseases <- NULL
myBarcodeSampleType <- NULL
myTag <- ""
myGeneData <- getData_GeneSymbol_Mutations(theGeneEq, theZipFile, theVerboseFlag=theVerboseFlag, theUseDeltaFlag=theUseDeltaFlag)
if(TRUE==theUseDeltaFlag)
{
myTag <- "Delta"
myBarcodeDiseases <- getMetadataPop_PatientDisease(theZipFile, theVerboseFlag=theVerboseFlag)
myBarcodeSampleType <- myBarcodeDiseases
myBarcodeSampleType[myBarcodeSampleType] <- "Delta"
}
else
{
myBarcodeDiseases <- getMetadataPop_BarcodeDisease(theZipFile, theVerboseFlag=theVerboseFlag)
myBarcodeSampleType <- getMetadataPop_BarcodeSamplecode(theZipFile, theVerboseFlag=theVerboseFlag)
}
plotGenericOutput(theGeneEq, theOutputDir, myGeneData, myBarcodeDiseases,
myBarcodeSampleType, "Mutations", "Count", theVerboseFlag=theVerboseFlag,
theTag=myTag, theGeneEqPre="", theReplicateFlag=theReplicateFlag)
}
plot_GeneSymbol_RnaSeq2 <- function(theGeneEq, theOutputDir,
theZipFile="/rsrch1/bcb/batcheffects/GENE_REPORT/GeneSurvey.zip",
theVerboseFlag=FALSE, theUseDeltaFlag=FALSE, theReplicateFlag=FALSE)
{
stopifnot(is.character(theGeneEq))
stopifnot(1==length(theGeneEq))
stopifnot(isValidDirectoryPath(theOutputDir))
stopifnot(file.exists(theZipFile))
stopifnot((TRUE==theVerboseFlag)||(FALSE==theVerboseFlag))
stopifnot((TRUE==theUseDeltaFlag)||(FALSE==theUseDeltaFlag))
stopifnot((TRUE==theReplicateFlag)||(FALSE==theReplicateFlag))
# read gene data
myGeneData <- NULL
myBarcodeDiseases <- NULL
myBarcodeSampleType <- NULL
myTag <- ""
myGeneData <- getData_GeneSymbol_RnaSeq2(theGeneEq, theZipFile, theVerboseFlag=theVerboseFlag, theUseDeltaFlag=theUseDeltaFlag)
if(TRUE==theUseDeltaFlag)
{
myTag <- "Delta"
myBarcodeDiseases <- getMetadataPop_PatientDisease(theZipFile, theVerboseFlag=theVerboseFlag)
myBarcodeSampleType <- myBarcodeDiseases
myBarcodeSampleType[myBarcodeSampleType] <- "Delta"
}
else
{
myBarcodeDiseases <- getMetadataPop_BarcodeDisease(theZipFile, theVerboseFlag=theVerboseFlag)
myBarcodeSampleType <- getMetadataPop_BarcodeSamplecode(theZipFile, theVerboseFlag=theVerboseFlag)
}
plotGenericOutput(theGeneEq, theOutputDir, myGeneData, myBarcodeDiseases,
myBarcodeSampleType, "RNASeqV2", "Log Normalized Count", theVerboseFlag=theVerboseFlag,
theTag=myTag, theGeneEqPre="", theReplicateFlag=theReplicateFlag)
}
plot_GeneSymbol_RnaSeq <- function(theGeneEq, theOutputDir, theZipFile="/rsrch1/bcb/batcheffects/GENE_REPORT/GeneSurvey.zip",
theVerboseFlag=FALSE, theUseDeltaFlag=FALSE, theReplicateFlag=FALSE)
{
stopifnot(is.character(theGeneEq))
stopifnot(1==length(theGeneEq))
stopifnot(isValidDirectoryPath(theOutputDir))
stopifnot(file.exists(theZipFile))
stopifnot((TRUE==theVerboseFlag)||(FALSE==theVerboseFlag))
stopifnot((TRUE==theUseDeltaFlag)||(FALSE==theUseDeltaFlag))
stopifnot((TRUE==theReplicateFlag)||(FALSE==theReplicateFlag))
# read gene data
myGeneData <- NULL
myBarcodeDiseases <- NULL
myBarcodeSampleType <- NULL
myTag <- ""
myGeneData <- getData_GeneSymbol_RnaSeq(theGeneEq, theZipFile, theVerboseFlag=theVerboseFlag, theUseDeltaFlag=theUseDeltaFlag)
if(TRUE==theUseDeltaFlag)
{
myTag <- "Delta"
myBarcodeDiseases <- getMetadataPop_PatientDisease(theZipFile, theVerboseFlag=theVerboseFlag)
myBarcodeSampleType <- myBarcodeDiseases
myBarcodeSampleType[myBarcodeSampleType] <- "Delta"
}
else
{
myBarcodeDiseases <- getMetadataPop_BarcodeDisease(theZipFile, theVerboseFlag=theVerboseFlag)
myBarcodeSampleType <- getMetadataPop_BarcodeSamplecode(theZipFile, theVerboseFlag=theVerboseFlag)
}
plotGenericOutput(theGeneEq, theOutputDir, myGeneData, myBarcodeDiseases,
myBarcodeSampleType, "RNASeq", "Log Normalized Count", theVerboseFlag=theVerboseFlag,
theTag=myTag, theGeneEqPre="", theReplicateFlag=theReplicateFlag)
}
plot_GeneSymbol_SNP6 <- function(theGeneEq, theOutputDir, theZipFile="/rsrch1/bcb/batcheffects/GENE_REPORT/GeneSurvey.zip",
theVerboseFlag=FALSE, theUseDeltaFlag=FALSE, theReplicateFlag=FALSE)
{
stopifnot(is.character(theGeneEq))
stopifnot(1==length(theGeneEq))
stopifnot(isValidDirectoryPath(theOutputDir))
stopifnot(file.exists(theZipFile))
stopifnot((TRUE==theVerboseFlag)||(FALSE==theVerboseFlag))
stopifnot((TRUE==theUseDeltaFlag)||(FALSE==theUseDeltaFlag))
stopifnot((TRUE==theReplicateFlag)||(FALSE==theReplicateFlag))
# read gene data
myGeneData <- NULL
myBarcodeDiseases <- NULL
myBarcodeSampleType <- NULL
myTag <- ""
myGeneData <- getData_GeneSymbol_SNP6(theGeneEq, theZipFile, theVerboseFlag=theVerboseFlag, theUseDeltaFlag=theUseDeltaFlag)
if(TRUE==theUseDeltaFlag)
{
myTag <- "Delta"
myBarcodeDiseases <- getMetadataPop_PatientDisease(theZipFile, theVerboseFlag=theVerboseFlag)
myBarcodeSampleType <- myBarcodeDiseases
myBarcodeSampleType[myBarcodeSampleType] <- "Delta"
}
else
{
myBarcodeDiseases <- getMetadataPop_BarcodeDisease(theZipFile, theVerboseFlag=theVerboseFlag)
myBarcodeSampleType <- getMetadataPop_BarcodeSamplecode(theZipFile, theVerboseFlag=theVerboseFlag)
}
plotGenericOutput(theGeneEq, theOutputDir, myGeneData, myBarcodeDiseases,
myBarcodeSampleType, "SNP6", "Log Normalized Copy Number", theVerboseFlag=theVerboseFlag,
theTag=myTag, theGeneEqPre="", theReplicateFlag=theReplicateFlag)
}
plot_Probe_Meth450 <- function(theGeneEq, theOutputDir, theZipFile="/rsrch1/bcb/batcheffects/GENE_REPORT/GeneSurvey.zip",
theVerboseFlag=FALSE, theUseDeltaFlag=FALSE, theReplicateFlag=FALSE)
{
stopifnot(is.character(theGeneEq))
stopifnot(1==length(theGeneEq))
stopifnot(isValidDirectoryPath(theOutputDir))
stopifnot(file.exists(theZipFile))
stopifnot((TRUE==theVerboseFlag)||(FALSE==theVerboseFlag))
stopifnot((TRUE==theUseDeltaFlag)||(FALSE==theUseDeltaFlag))
stopifnot((TRUE==theReplicateFlag)||(FALSE==theReplicateFlag))
# read gene data
myProbe <- getMetadata_Probe_Meth450(theGeneEq, theZipFile)
myGeneData <- NULL
myBarcodeDiseases <- NULL
myBarcodeSampleType <- NULL
myTag <- ""
myGeneData <- getData_Probe_Meth450(theGeneEq, theZipFile, theVerboseFlag=theVerboseFlag, theUseDeltaFlag=theUseDeltaFlag)
if(TRUE==theUseDeltaFlag)
{
myTag <- "Delta"
myBarcodeDiseases <- getMetadataPop_PatientDisease(theZipFile, theVerboseFlag=theVerboseFlag)
myBarcodeSampleType <- myBarcodeDiseases
myBarcodeSampleType[myBarcodeSampleType] <- "Delta"
}
else
{
myBarcodeDiseases <- getMetadataPop_BarcodeDisease(theZipFile, theVerboseFlag=theVerboseFlag)
myBarcodeSampleType <- getMetadataPop_BarcodeSamplecode(theZipFile, theVerboseFlag=theVerboseFlag)
}
geneEqPre <- paste(padChromosomeName(myProbe[[1]]@mChromosome), "-", myProbe[[1]]@mProbeLocation, "-", sep="")
plotGenericOutput(theGeneEq, theOutputDir, myGeneData, myBarcodeDiseases,
myBarcodeSampleType, "Meth450", "Beta Value", theVerboseFlag=theVerboseFlag,
theTag=myTag, theGeneEqPre=geneEqPre, theReplicateFlag=theReplicateFlag)
}
plot_Probe_Meth27 <- function(theGeneEq, theOutputDir, theZipFile="/rsrch1/bcb/batcheffects/GENE_REPORT/GeneSurvey.zip",
theVerboseFlag=FALSE, theUseDeltaFlag=FALSE, theReplicateFlag=FALSE)
{
stopifnot(is.character(theGeneEq))
stopifnot(1==length(theGeneEq))
stopifnot(isValidDirectoryPath(theOutputDir))
stopifnot(file.exists(theZipFile))
stopifnot((TRUE==theVerboseFlag)||(FALSE==theVerboseFlag))
stopifnot((TRUE==theUseDeltaFlag)||(FALSE==theUseDeltaFlag))
stopifnot((TRUE==theReplicateFlag)||(FALSE==theReplicateFlag))
# read gene data
myProbe <- getMetadata_Probe_Meth27(theGeneEq, theZipFile)
stopifnot(FALSE==is.null(myProbe[[1]]))
myGeneData <- NULL
myBarcodeDiseases <- NULL
myBarcodeSampleType <- NULL
myTag <- ""
myGeneData <- getData_Probe_Meth27(theGeneEq, theZipFile, theVerboseFlag=theVerboseFlag, theUseDeltaFlag=theUseDeltaFlag)
if(TRUE==theUseDeltaFlag)
{
myTag <- "Delta"
myBarcodeDiseases <- getMetadataPop_PatientDisease(theZipFile, theVerboseFlag=theVerboseFlag)
myBarcodeSampleType <- myBarcodeDiseases
myBarcodeSampleType[myBarcodeSampleType] <- "Delta"
}
else
{
myBarcodeDiseases <- getMetadataPop_BarcodeDisease(theZipFile, theVerboseFlag=theVerboseFlag)
myBarcodeSampleType <- getMetadataPop_BarcodeSamplecode(theZipFile, theVerboseFlag=theVerboseFlag)
}
geneEqPre <- paste(padChromosomeName(myProbe[[1]]@mChromosome), "-", myProbe[[1]]@mProbeLocation, "-", sep="")
plotGenericOutput(theGeneEq, theOutputDir, myGeneData, myBarcodeDiseases,
myBarcodeSampleType, "Meth27", "Beta Value", theVerboseFlag=theVerboseFlag,
theTag=myTag, theGeneEqPre=geneEqPre, theReplicateFlag=theReplicateFlag)
}
plot_CombinedHsaMimat_miRNASeq <- function(theGeneEq, theOutputDir, theZipFile="/rsrch1/bcb/batcheffects/GENE_REPORT/GeneSurvey.zip",
theVerboseFlag=FALSE, theUseDeltaFlag=FALSE, theReplicateFlag=FALSE)
{
stopifnot(is.character(theGeneEq))
stopifnot(1==length(theGeneEq))
stopifnot(isValidDirectoryPath(theOutputDir))
stopifnot(file.exists(theZipFile))
stopifnot((TRUE==theVerboseFlag)||(FALSE==theVerboseFlag))
stopifnot((TRUE==theUseDeltaFlag)||(FALSE==theUseDeltaFlag))
stopifnot((TRUE==theReplicateFlag)||(FALSE==theReplicateFlag))
# read gene data
myGeneData <- NULL
myBarcodeDiseases <- NULL
myBarcodeSampleType <- NULL
myTag <- ""
myGeneData <- getData_CombinedHsaMimat_miRNASeq(theGeneEq, theZipFile, theVerboseFlag=theVerboseFlag, theUseDeltaFlag=theUseDeltaFlag)
if(TRUE==theUseDeltaFlag)
{
myTag <- "Delta"
myBarcodeDiseases <- getMetadataPop_PatientDisease(theZipFile, theVerboseFlag=theVerboseFlag)
myBarcodeSampleType <- myBarcodeDiseases
myBarcodeSampleType[myBarcodeSampleType] <- "Delta"
}
else
{
myBarcodeDiseases <- getMetadataPop_BarcodeDisease(theZipFile, theVerboseFlag=theVerboseFlag)
myBarcodeSampleType <- getMetadataPop_BarcodeSamplecode(theZipFile, theVerboseFlag=theVerboseFlag)
}
plotGenericOutput(theGeneEq, theOutputDir, myGeneData, myBarcodeDiseases,
myBarcodeSampleType, "miRNASeq", "isoform", theVerboseFlag=theVerboseFlag,
theTag=myTag, theGeneEqPre="", theReplicateFlag=theReplicateFlag)
}
####
#### uses mapping functions
####
plot_GeneSymbol_Meth450 <- function(theGene, theOutputDir, theZipFile="/rsrch1/bcb/batcheffects/GENE_REPORT/GeneSurvey.zip",
theVerboseFlag=FALSE, theUseDeltaFlag=FALSE, theReplicateFlag=FALSE)
{
stopifnot(is.character(theGene))
stopifnot(1==length(theGene))
stopifnot(isValidDirectoryPath(theOutputDir))
stopifnot(file.exists(theZipFile))
stopifnot((TRUE==theVerboseFlag)||(FALSE==theVerboseFlag))
stopifnot((TRUE==theUseDeltaFlag)||(FALSE==theUseDeltaFlag))
stopifnot((TRUE==theReplicateFlag)||(FALSE==theReplicateFlag))
plot_fromGene_internal(theGene, theOutputDir, theZipFile,
theMapGeneToProbesFunction=getNames_ProbeFromGeneSymbol_Meth450,
theReadProbeFunction=getMetadata_Probe_Meth450,
theReadGeneFunction=getData_Probe_Meth450,
theDataType="Meth450",
theDataTypeLabel="Beta Value",
theVerboseFlag=theVerboseFlag,
theUseDeltaFlag=theUseDeltaFlag,
theReplicateFlag=theReplicateFlag)
}
plot_GeneSymbol_Meth27 <- function(theGene, theOutputDir, theZipFile="/rsrch1/bcb/batcheffects/GENE_REPORT/GeneSurvey.zip",
theVerboseFlag=FALSE, theUseDeltaFlag=FALSE, theReplicateFlag=FALSE)
{
stopifnot(is.character(theGene))
stopifnot(1==length(theGene))
stopifnot(isValidDirectoryPath(theOutputDir))
stopifnot(file.exists(theZipFile))
stopifnot((TRUE==theVerboseFlag)||(FALSE==theVerboseFlag))
stopifnot((TRUE==theUseDeltaFlag)||(FALSE==theUseDeltaFlag))
stopifnot((TRUE==theReplicateFlag)||(FALSE==theReplicateFlag))
plot_fromGene_internal(theGene, theOutputDir, theZipFile,
theMapGeneToProbesFunction=getNames_ProbeFromGeneSymbol_Meth27,
theReadProbeFunction=getMetadata_Probe_Meth27,
theReadGeneFunction=getData_Probe_Meth27,
theDataType="Meth27",
theDataTypeLabel="Beta Value",
theVerboseFlag=theVerboseFlag,
theUseDeltaFlag=theUseDeltaFlag,
theReplicateFlag=theReplicateFlag)
}
#################################################################
#################################################################
#################################################################
#################################################################
GeneSurvey/TCGAGeneReport documentation built on May 6, 2019, 6:27 p.m.
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Defines functions plot_fromGene_internal plot_GeneSymbol_Mutations plot_GeneSymbol_RnaSeq2 plot_GeneSymbol_RnaSeq plot_GeneSymbol_SNP6 plot_Probe_Meth450 plot_Probe_Meth27 plot_CombinedHsaMimat_miRNASeq plot_GeneSymbol_Meth450 plot_GeneSymbol_Meth27
Documented in plot_CombinedHsaMimat_miRNASeq plot_GeneSymbol_Meth27 plot_GeneSymbol_Meth450 plot_GeneSymbol_Mutations plot_GeneSymbol_RnaSeq plot_GeneSymbol_RnaSeq2 plot_GeneSymbol_SNP6 plot_Probe_Meth27 plot_Probe_Meth450
#TCGAGeneReport Copyright 2014, 2015, 2016 University of Texas MD Anderson Cancer Center
#
#This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.
#
#This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
#
#You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
#################################################################
#################################################################
# internal
#################################################################
#################################################################
plot_fromGene_internal <- function(theGene, theOutputDir, theZipFile,
theMapGeneToProbesFunction, theReadProbeFunction, theReadGeneFunction,
theDataType, theDataTypeLabel, theVerboseFlag, theUseDeltaFlag=FALSE,
theReplicateFlag=FALSE)
{
dir.create(theOutputDir, recursive = TRUE, showWarnings=FALSE)
returnFilename <- c()
myBarcodeDiseases <- NULL
myBarcodeSampleType <- NULL
myTag <- ""
myPathCombined <- NULL
myGeneEqPre <- NULL
# read gene data
if (FALSE==theUseDeltaFlag)
{
verboseMessage("plot_fromGene_internal FALSE==theUseDeltaFlag", theVerboseFlag=theVerboseFlag)
myTag <- ""
myBarcodeDiseases <- getMetadataPop_BarcodeDisease(theZipFile, theVerboseFlag=theVerboseFlag)
myBarcodeSampleType <- getMetadataPop_BarcodeSamplecode(theZipFile, theVerboseFlag=theVerboseFlag)
}
else
{
verboseMessage("plot_fromGene_internal TRUE==theUseDeltaFlag", theVerboseFlag=theVerboseFlag)
myTag <- "Delta"
myBarcodeDiseases <- getMetadataPop_PatientDisease(theZipFile, theVerboseFlag=theVerboseFlag)
myBarcodeSampleType <- getMetadataPop_PatientDisease(theZipFile, theVerboseFlag=theVerboseFlag)
}
probeList <- as.vector(unlist(theMapGeneToProbesFunction(theGene, theZipFile, theVerboseFlag=theVerboseFlag)))
locations <- as.vector(unlist(lapply(probeList, function(theProbe, theZipFile, theVerboseFlag=theVerboseFlag)
{
probeData <- as.vector(unlist(theReadProbeFunction(theProbe, theZipFile=theZipFile, theVerboseFlag=theVerboseFlag)))
# this is only one value, but you cannot unlist a list/vector of classes, I think
probeData[[1]]@mProbeLocation
},theZipFile=theZipFile, theVerboseFlag=theVerboseFlag)))
probeList <- probeList[order(locations)]
maxLocationSize <- max(as.vector(unlist(lapply(locations, nchar))))
probeDataList <- lapply(probeList, function(theProbe, thePath, theVerboseFlag)
{
theReadGeneFunction(theProbe, theZipFile, theVerboseFlag=theVerboseFlag, theUseDeltaFlag=theUseDeltaFlag)
}, thePath=myPathCombined, theVerboseFlag=theVerboseFlag)
# first write individual probe plots
for (index in 1:length(probeDataList))
{
myGeneData <- probeDataList[[index]]
probe <- probeList[index]
myProbeData <- as.vector(unlist(theReadProbeFunction(probe, theZipFile=theZipFile, theVerboseFlag=theVerboseFlag)))
# this is only one value, but you cannot unlist a list/vector of classes, I think
myLocation <- myProbeData[[1]]@mProbeLocation
if(!is.na(as.numeric(myLocation)))
{
myLocation <- sprintf(paste("%0", maxLocationSize, "d", sep=""), as.numeric(myLocation))
}
# this is only one value, but you cannot unlist a list/vector of classes, I think
geneEqPre <- paste(padChromosomeName(myProbeData[[1]]@mChromosome), "-", myLocation, "-", sep="")
returnFilename <- c(returnFilename,
plotGenericOutput(paste(theGene, probe, sep="-"),
theOutputDir, myGeneData, myBarcodeDiseases,
myBarcodeSampleType, theDataType, theDataTypeLabel,
theVerboseFlag=theVerboseFlag,
theTag=myTag, theGeneEqPre=geneEqPre,
theReplicateFlag=theReplicateFlag))
}
# now do combined probe plots
# first write individual probe plots
#for (index in 1:length(probeDataList))
#{
# myGeneData <- probeDataList[[index]]
# probe <- probeList[index]
# message(paste("probe=",probe," ",paste(myGeneData[1:3],collapse=", ", sep=""), sep=""))
#}
numberOfRows <- length(probeDataList[[1]])
sampleList <- colnames(probeDataList[[1]])
probeDataList <- as.vector(unlist(probeDataList))
probeData <- matrixWithIssues(probeDataList, nrow=numberOfRows)
colnames(probeData) <- probeList
rownames(probeData) <- sampleList
# probeData[sample,probe]
returnFilename <- c(returnFilename,
plotHeatmapOutput(theGene, theOutputDir, probeData, myBarcodeDiseases, myBarcodeSampleType,
theDataType, theDataTypeLabel, theZipFile,
theVerboseFlag, theReadProbeFunction, myTag))
returnFilename
}
#################################################################
#################################################################
# exported
#################################################################
#################################################################
####
#### uses gene equivalent from data file
####
plot_GeneSymbol_Mutations <- function(theGeneEq, theOutputDir,
theZipFile="/rsrch1/bcb/batcheffects/GENE_REPORT/GeneSurvey.zip",
theVerboseFlag=FALSE, theUseDeltaFlag=FALSE, theReplicateFlag=FALSE)
{
stopifnot(is.character(theGeneEq))
stopifnot(1==length(theGeneEq))
stopifnot(isValidDirectoryPath(theOutputDir))
stopifnot(file.exists(theZipFile))
stopifnot((TRUE==theVerboseFlag)||(FALSE==theVerboseFlag))
stopifnot((TRUE==theUseDeltaFlag)||(FALSE==theUseDeltaFlag))
stopifnot((TRUE==theReplicateFlag)||(FALSE==theReplicateFlag))
# read gene data
myGeneData <- NULL
myBarcodeDiseases <- NULL
myBarcodeSampleType <- NULL
myTag <- ""
myGeneData <- getData_GeneSymbol_Mutations(theGeneEq, theZipFile, theVerboseFlag=theVerboseFlag, theUseDeltaFlag=theUseDeltaFlag)
if(TRUE==theUseDeltaFlag)
{
myTag <- "Delta"
myBarcodeDiseases <- getMetadataPop_PatientDisease(theZipFile, theVerboseFlag=theVerboseFlag)
myBarcodeSampleType <- myBarcodeDiseases
myBarcodeSampleType[myBarcodeSampleType] <- "Delta"
}
else
{
myBarcodeDiseases <- getMetadataPop_BarcodeDisease(theZipFile, theVerboseFlag=theVerboseFlag)
myBarcodeSampleType <- getMetadataPop_BarcodeSamplecode(theZipFile, theVerboseFlag=theVerboseFlag)
}
plotGenericOutput(theGeneEq, theOutputDir, myGeneData, myBarcodeDiseases,
myBarcodeSampleType, "Mutations", "Count", theVerboseFlag=theVerboseFlag,
theTag=myTag, theGeneEqPre="", theReplicateFlag=theReplicateFlag)
}
plot_GeneSymbol_RnaSeq2 <- function(theGeneEq, theOutputDir,
theZipFile="/rsrch1/bcb/batcheffects/GENE_REPORT/GeneSurvey.zip",
theVerboseFlag=FALSE, theUseDeltaFlag=FALSE, theReplicateFlag=FALSE)
{
stopifnot(is.character(theGeneEq))
stopifnot(1==length(theGeneEq))
stopifnot(isValidDirectoryPath(theOutputDir))
stopifnot(file.exists(theZipFile))
stopifnot((TRUE==theVerboseFlag)||(FALSE==theVerboseFlag))
stopifnot((TRUE==theUseDeltaFlag)||(FALSE==theUseDeltaFlag))
stopifnot((TRUE==theReplicateFlag)||(FALSE==theReplicateFlag))
# read gene data
myGeneData <- NULL
myBarcodeDiseases <- NULL
myBarcodeSampleType <- NULL
myTag <- ""
myGeneData <- getData_GeneSymbol_RnaSeq2(theGeneEq, theZipFile, theVerboseFlag=theVerboseFlag, theUseDeltaFlag=theUseDeltaFlag)
if(TRUE==theUseDeltaFlag)
{
myTag <- "Delta"
myBarcodeDiseases <- getMetadataPop_PatientDisease(theZipFile, theVerboseFlag=theVerboseFlag)
myBarcodeSampleType <- myBarcodeDiseases
myBarcodeSampleType[myBarcodeSampleType] <- "Delta"
}
else
{
myBarcodeDiseases <- getMetadataPop_BarcodeDisease(theZipFile, theVerboseFlag=theVerboseFlag)
myBarcodeSampleType <- getMetadataPop_BarcodeSamplecode(theZipFile, theVerboseFlag=theVerboseFlag)
}
plotGenericOutput(theGeneEq, theOutputDir, myGeneData, myBarcodeDiseases,
myBarcodeSampleType, "RNASeqV2", "Log Normalized Count", theVerboseFlag=theVerboseFlag,
theTag=myTag, theGeneEqPre="", theReplicateFlag=theReplicateFlag)
}
plot_GeneSymbol_RnaSeq <- function(theGeneEq, theOutputDir, theZipFile="/rsrch1/bcb/batcheffects/GENE_REPORT/GeneSurvey.zip",
theVerboseFlag=FALSE, theUseDeltaFlag=FALSE, theReplicateFlag=FALSE)
{
stopifnot(is.character(theGeneEq))
stopifnot(1==length(theGeneEq))
stopifnot(isValidDirectoryPath(theOutputDir))
stopifnot(file.exists(theZipFile))
stopifnot((TRUE==theVerboseFlag)||(FALSE==theVerboseFlag))
stopifnot((TRUE==theUseDeltaFlag)||(FALSE==theUseDeltaFlag))
stopifnot((TRUE==theReplicateFlag)||(FALSE==theReplicateFlag))
# read gene data
myGeneData <- NULL
myBarcodeDiseases <- NULL
myBarcodeSampleType <- NULL
myTag <- ""
myGeneData <- getData_GeneSymbol_RnaSeq(theGeneEq, theZipFile, theVerboseFlag=theVerboseFlag, theUseDeltaFlag=theUseDeltaFlag)
if(TRUE==theUseDeltaFlag)
{
myTag <- "Delta"
myBarcodeDiseases <- getMetadataPop_PatientDisease(theZipFile, theVerboseFlag=theVerboseFlag)
myBarcodeSampleType <- myBarcodeDiseases
myBarcodeSampleType[myBarcodeSampleType] <- "Delta"
}
else
{
myBarcodeDiseases <- getMetadataPop_BarcodeDisease(theZipFile, theVerboseFlag=theVerboseFlag)
myBarcodeSampleType <- getMetadataPop_BarcodeSamplecode(theZipFile, theVerboseFlag=theVerboseFlag)
}
plotGenericOutput(theGeneEq, theOutputDir, myGeneData, myBarcodeDiseases,
myBarcodeSampleType, "RNASeq", "Log Normalized Count", theVerboseFlag=theVerboseFlag,
theTag=myTag, theGeneEqPre="", theReplicateFlag=theReplicateFlag)
}
plot_GeneSymbol_SNP6 <- function(theGeneEq, theOutputDir, theZipFile="/rsrch1/bcb/batcheffects/GENE_REPORT/GeneSurvey.zip",
theVerboseFlag=FALSE, theUseDeltaFlag=FALSE, theReplicateFlag=FALSE)
{
stopifnot(is.character(theGeneEq))
stopifnot(1==length(theGeneEq))
stopifnot(isValidDirectoryPath(theOutputDir))
stopifnot(file.exists(theZipFile))
stopifnot((TRUE==theVerboseFlag)||(FALSE==theVerboseFlag))
stopifnot((TRUE==theUseDeltaFlag)||(FALSE==theUseDeltaFlag))
stopifnot((TRUE==theReplicateFlag)||(FALSE==theReplicateFlag))
# read gene data
myGeneData <- NULL
myBarcodeDiseases <- NULL
myBarcodeSampleType <- NULL
myTag <- ""
myGeneData <- getData_GeneSymbol_SNP6(theGeneEq, theZipFile, theVerboseFlag=theVerboseFlag, theUseDeltaFlag=theUseDeltaFlag)
if(TRUE==theUseDeltaFlag)
{
myTag <- "Delta"
myBarcodeDiseases <- getMetadataPop_PatientDisease(theZipFile, theVerboseFlag=theVerboseFlag)
myBarcodeSampleType <- myBarcodeDiseases
myBarcodeSampleType[myBarcodeSampleType] <- "Delta"
}
else
{
myBarcodeDiseases <- getMetadataPop_BarcodeDisease(theZipFile, theVerboseFlag=theVerboseFlag)
myBarcodeSampleType <- getMetadataPop_BarcodeSamplecode(theZipFile, theVerboseFlag=theVerboseFlag)
}
plotGenericOutput(theGeneEq, theOutputDir, myGeneData, myBarcodeDiseases,
myBarcodeSampleType, "SNP6", "Log Normalized Copy Number", theVerboseFlag=theVerboseFlag,
theTag=myTag, theGeneEqPre="", theReplicateFlag=theReplicateFlag)
}
plot_Probe_Meth450 <- function(theGeneEq, theOutputDir, theZipFile="/rsrch1/bcb/batcheffects/GENE_REPORT/GeneSurvey.zip",
theVerboseFlag=FALSE, theUseDeltaFlag=FALSE, theReplicateFlag=FALSE)
{
stopifnot(is.character(theGeneEq))
stopifnot(1==length(theGeneEq))
stopifnot(isValidDirectoryPath(theOutputDir))
stopifnot(file.exists(theZipFile))
stopifnot((TRUE==theVerboseFlag)||(FALSE==theVerboseFlag))
stopifnot((TRUE==theUseDeltaFlag)||(FALSE==theUseDeltaFlag))
stopifnot((TRUE==theReplicateFlag)||(FALSE==theReplicateFlag))
# read gene data
myProbe <- getMetadata_Probe_Meth450(theGeneEq, theZipFile)
myGeneData <- NULL
myBarcodeDiseases <- NULL
myBarcodeSampleType <- NULL
myTag <- ""
myGeneData <- getData_Probe_Meth450(theGeneEq, theZipFile, theVerboseFlag=theVerboseFlag, theUseDeltaFlag=theUseDeltaFlag)
if(TRUE==theUseDeltaFlag)
{
myTag <- "Delta"
myBarcodeDiseases <- getMetadataPop_PatientDisease(theZipFile, theVerboseFlag=theVerboseFlag)
myBarcodeSampleType <- myBarcodeDiseases
myBarcodeSampleType[myBarcodeSampleType] <- "Delta"
}
else
{
myBarcodeDiseases <- getMetadataPop_BarcodeDisease(theZipFile, theVerboseFlag=theVerboseFlag)
myBarcodeSampleType <- getMetadataPop_BarcodeSamplecode(theZipFile, theVerboseFlag=theVerboseFlag)
}
geneEqPre <- paste(padChromosomeName(myProbe[[1]]@mChromosome), "-", myProbe[[1]]@mProbeLocation, "-", sep="")
plotGenericOutput(theGeneEq, theOutputDir, myGeneData, myBarcodeDiseases,
myBarcodeSampleType, "Meth450", "Beta Value", theVerboseFlag=theVerboseFlag,
theTag=myTag, theGeneEqPre=geneEqPre, theReplicateFlag=theReplicateFlag)
}
plot_Probe_Meth27 <- function(theGeneEq, theOutputDir, theZipFile="/rsrch1/bcb/batcheffects/GENE_REPORT/GeneSurvey.zip",
theVerboseFlag=FALSE, theUseDeltaFlag=FALSE, theReplicateFlag=FALSE)
{
stopifnot(is.character(theGeneEq))
stopifnot(1==length(theGeneEq))
stopifnot(isValidDirectoryPath(theOutputDir))
stopifnot(file.exists(theZipFile))
stopifnot((TRUE==theVerboseFlag)||(FALSE==theVerboseFlag))
stopifnot((TRUE==theUseDeltaFlag)||(FALSE==theUseDeltaFlag))
stopifnot((TRUE==theReplicateFlag)||(FALSE==theReplicateFlag))
# read gene data
myProbe <- getMetadata_Probe_Meth27(theGeneEq, theZipFile)
stopifnot(FALSE==is.null(myProbe[[1]]))
myGeneData <- NULL
myBarcodeDiseases <- NULL
myBarcodeSampleType <- NULL
myTag <- ""
myGeneData <- getData_Probe_Meth27(theGeneEq, theZipFile, theVerboseFlag=theVerboseFlag, theUseDeltaFlag=theUseDeltaFlag)
if(TRUE==theUseDeltaFlag)
{
myTag <- "Delta"
myBarcodeDiseases <- getMetadataPop_PatientDisease(theZipFile, theVerboseFlag=theVerboseFlag)
myBarcodeSampleType <- myBarcodeDiseases
myBarcodeSampleType[myBarcodeSampleType] <- "Delta"
}
else
{
myBarcodeDiseases <- getMetadataPop_BarcodeDisease(theZipFile, theVerboseFlag=theVerboseFlag)
myBarcodeSampleType <- getMetadataPop_BarcodeSamplecode(theZipFile, theVerboseFlag=theVerboseFlag)
}
geneEqPre <- paste(padChromosomeName(myProbe[[1]]@mChromosome), "-", myProbe[[1]]@mProbeLocation, "-", sep="")
plotGenericOutput(theGeneEq, theOutputDir, myGeneData, myBarcodeDiseases,
myBarcodeSampleType, "Meth27", "Beta Value", theVerboseFlag=theVerboseFlag,
theTag=myTag, theGeneEqPre=geneEqPre, theReplicateFlag=theReplicateFlag)
}
plot_CombinedHsaMimat_miRNASeq <- function(theGeneEq, theOutputDir, theZipFile="/rsrch1/bcb/batcheffects/GENE_REPORT/GeneSurvey.zip",
theVerboseFlag=FALSE, theUseDeltaFlag=FALSE, theReplicateFlag=FALSE)
{
stopifnot(is.character(theGeneEq))
stopifnot(1==length(theGeneEq))
stopifnot(isValidDirectoryPath(theOutputDir))
stopifnot(file.exists(theZipFile))
stopifnot((TRUE==theVerboseFlag)||(FALSE==theVerboseFlag))
stopifnot((TRUE==theUseDeltaFlag)||(FALSE==theUseDeltaFlag))
stopifnot((TRUE==theReplicateFlag)||(FALSE==theReplicateFlag))
# read gene data
myGeneData <- NULL
myBarcodeDiseases <- NULL
myBarcodeSampleType <- NULL
myTag <- ""
myGeneData <- getData_CombinedHsaMimat_miRNASeq(theGeneEq, theZipFile, theVerboseFlag=theVerboseFlag, theUseDeltaFlag=theUseDeltaFlag)
if(TRUE==theUseDeltaFlag)
{
myTag <- "Delta"
myBarcodeDiseases <- getMetadataPop_PatientDisease(theZipFile, theVerboseFlag=theVerboseFlag)
myBarcodeSampleType <- myBarcodeDiseases
myBarcodeSampleType[myBarcodeSampleType] <- "Delta"
}
else
{
myBarcodeDiseases <- getMetadataPop_BarcodeDisease(theZipFile, theVerboseFlag=theVerboseFlag)
myBarcodeSampleType <- getMetadataPop_BarcodeSamplecode(theZipFile, theVerboseFlag=theVerboseFlag)
}
plotGenericOutput(theGeneEq, theOutputDir, myGeneData, myBarcodeDiseases,
myBarcodeSampleType, "miRNASeq", "isoform", theVerboseFlag=theVerboseFlag,
theTag=myTag, theGeneEqPre="", theReplicateFlag=theReplicateFlag)
}
####
#### uses mapping functions
####
plot_GeneSymbol_Meth450 <- function(theGene, theOutputDir, theZipFile="/rsrch1/bcb/batcheffects/GENE_REPORT/GeneSurvey.zip",
theVerboseFlag=FALSE, theUseDeltaFlag=FALSE, theReplicateFlag=FALSE)
{
stopifnot(is.character(theGene))
stopifnot(1==length(theGene))
stopifnot(isValidDirectoryPath(theOutputDir))
stopifnot(file.exists(theZipFile))
stopifnot((TRUE==theVerboseFlag)||(FALSE==theVerboseFlag))
stopifnot((TRUE==theUseDeltaFlag)||(FALSE==theUseDeltaFlag))
stopifnot((TRUE==theReplicateFlag)||(FALSE==theReplicateFlag))
plot_fromGene_internal(theGene, theOutputDir, theZipFile,
theMapGeneToProbesFunction=getNames_ProbeFromGeneSymbol_Meth450,
theReadProbeFunction=getMetadata_Probe_Meth450,
theReadGeneFunction=getData_Probe_Meth450,
theDataType="Meth450",
theDataTypeLabel="Beta Value",
theVerboseFlag=theVerboseFlag,
theUseDeltaFlag=theUseDeltaFlag,
theReplicateFlag=theReplicateFlag)
}
plot_GeneSymbol_Meth27 <- function(theGene, theOutputDir, theZipFile="/rsrch1/bcb/batcheffects/GENE_REPORT/GeneSurvey.zip",
theVerboseFlag=FALSE, theUseDeltaFlag=FALSE, theReplicateFlag=FALSE)
{
stopifnot(is.character(theGene))
stopifnot(1==length(theGene))
stopifnot(isValidDirectoryPath(theOutputDir))
stopifnot(file.exists(theZipFile))
stopifnot((TRUE==theVerboseFlag)||(FALSE==theVerboseFlag))
stopifnot((TRUE==theUseDeltaFlag)||(FALSE==theUseDeltaFlag))
stopifnot((TRUE==theReplicateFlag)||(FALSE==theReplicateFlag))
plot_fromGene_internal(theGene, theOutputDir, theZipFile,
theMapGeneToProbesFunction=getNames_ProbeFromGeneSymbol_Meth27,
theReadProbeFunction=getMetadata_Probe_Meth27,
theReadGeneFunction=getData_Probe_Meth27,
theDataType="Meth27",
theDataTypeLabel="Beta Value",
theVerboseFlag=theVerboseFlag,
theUseDeltaFlag=theUseDeltaFlag,
theReplicateFlag=theReplicateFlag)
}
#################################################################
#################################################################
#################################################################
#################################################################
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