Description Usage Arguments Details Value Examples
Creates a stripchart plot with optional replicate plot.
1 | plotGenericOutput(theGeneEq, theOutputDir, myGeneData, myBarcodeDiseases, myBarcodeSampleType, theDataType, theDataTypeLabel, theVerboseFlag, theTag, theGeneEqPre = "", theReplicateFlag = FALSE)
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theGeneEq |
A string used to form the title and file name for the images. This should be the gene equivalent being plotted. |
theOutputDir |
Directory in which to create the output |
myGeneData |
Data in the format from the getData function for a data type. This is a matrix with barcodes (or patiend ids) as columns (colnames) and rows (rownames) as genes. For this function there should only be one gene. |
myBarcodeDiseases |
Data in the format from the getMetadataPop_PatientDisease or getMetadataPop_BarcodeDisease function. This is a vector of string values (diseases) with the patient ids or barcodes as the names(). Regular data uses barcodes, delta data uses patient ids. |
myBarcodeSampleType |
Data in the format from the getMetadataPop_BarcodeSamplecode or getMetadataPop_PatientDisease. This is a vector of string values (diseases) with the patient ids or barcodes as the names(). Regular data uses barcodes, delta data uses patient ids. |
theDataType |
The data type is a string for the platform that is used in the title and file name. |
theDataTypeLabel |
A string label for the Y axis, describing the data type being plotted. |
theVerboseFlag |
TRUE means write all output, which can be very verbose. This has no default here. |
theTag |
An optional tag used to form the last part of the title and file name. This might be a good place to describe your data tweaks. Use "" to skip use. |
theGeneEqPre |
An optional tag used at the beginning of the totle and file name. Use "" to skip use. |
theReplicateFlag |
TRUE means to write a replicates plot. |
Creates a stripchart plot with optional replicate plot.
returns vector of file names created.
1 2 3 4 5 | # mydata <- getData_GeneSymbol_RnaSeq2("TP53", "/rsrch1/bcb/batcheffects/DEV/GeneSurvey/GENE_REPORT", FALSE, TRUE, FALSE)
# barDis <- getMetadataPop_BarcodeDisease("/rsrch1/bcb/batcheffects/DEV/GeneSurvey/GENE_REPORT/data")
# barSam <- getMetadataPop_BarcodeSamplecode("/rsrch1/bcb/batcheffects/DEV/GeneSurvey/GENE_REPORT/data")
# barTyp <- getMetadataPop_BarcodeSamplecode("/rsrch1/bcb/batcheffects/DEV/GeneSurvey/GENE_REPORT/data")
# plotGenericOutput("TP53", "/rsrch1/bcb/batcheffects/DEV/GeneSurvey/output/test", mydata, barDis, barTyp, "RnaSeq2", "Log Normalized Count", FALSE, "", "", FALSE)
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