Description Usage Arguments Value Examples
Plots stripcharts and replicate diagrams for the given arguments.
1 | plot_CombinedHsaMimat_miRNASeq(theGeneEq, theOutputDir, theZipFile="/rsrch1/bcb/batcheffects/GENE_REPORT/GeneSurvey.zip", theVerboseFlag = FALSE, theUseDeltaFlag = FALSE, theReplicateFlag=FALSE)
|
theGeneEq |
The combined HSA/MIMAT id to plot which corresponds to an id from the appropriate getNames_ function. |
theOutputDir |
Directory to which to write files. Directory will be created if needed/possible. |
theZipFile |
Default: For DQS Servers. If you are on a server where the GENE_REPORT directory is on a different path, you can pass in a value to override the default of "/rsrch1/bcb/batcheffects/GENE_REPORT/GeneSurvey.zip". |
theVerboseFlag |
Default: FALSE. TRUE means write all output, which can be very verbose. |
theUseDeltaFlag |
Default: FALSE. A flag indicating to use the differences in value between tumor and normal samples. |
theReplicateFlag |
Default: FALSE. A flag indicating to write the replicate plots. |
A list of files output.
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 | ##---- Should be DIRECTLY executable !! ----
##-- ==> Define data, use random,
##-- or do help(data=index) for the standard data sets.
## The function is currently defined as
function (theGeneEq, theOutputDir, theZipFile="/rsrch1/bcb/batcheffects/GENE_REPORT/GeneSurvey.zip",
theVerboseFlag = FALSE, theUseDeltaFlag = FALSE)
{
myGeneData <- NULL
myBarcodeDiseases <- NULL
myBarcodeSampleType <- NULL
myTag <- ""
if (TRUE == theUseDeltaFlag) {
myTag <- "Delta"
}
myGeneData <- getData_CombinedHsaMimat_miRNASeq(theGeneEq,
theZipFile, theVerboseFlag = theVerboseFlag, theUseDeltaFlag = theUseDeltaFlag)
myBarcodeDiseases <- getMetadataPop_BarcodeDisease(file.path(theZipFile,
"data"), theVerboseFlag = theVerboseFlag)
myBarcodeSampleType <- getMetadataPop_BarcodeSamplecode(file.path(theZipFile,
"data"), theVerboseFlag = theVerboseFlag)
plotGenericOutput(theGeneEq, theOutputDir, myGeneData, myBarcodeDiseases,
myBarcodeSampleType, "miRNASeq", "isoform", theVerboseFlag = theVerboseFlag,
theTag = myTag, theGeneEqPre = "")
}
|
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