plotHeatmapOutput: plotHeatmapOutput

In MD-Anderson-Bioinformatics/GeneSurvey: MD Anderson Gene Survey

Description

Plot heatmap for methylation probes.

Usage

plotHeatmapOutput(theGene, theOutputDir, theProbeData, theBarcodeDiseases,
theBarcodeSampleType, theDataType, theDataTypeLabel, theZipFile,
theVerboseFlag, theReadProbeFunction, theTag = "")

Arguments

theGene	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
theProbeData	This is a matrix with probes as columns (colnames) and rows (rownames) as barcodes (or patient ids). For this function there can (and probably should) be multiple columns and multiple rows. This is the transposed output from getData_Probe_Meth450.
theBarcodeDiseases	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.
theBarcodeSampleType	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.
theZipFile	No default. For DQS Servers, use "/geneSurveyData/GeneSurvey.zip".
theVerboseFlag	Default: FALSE. TRUE means write all output, which can be very verbose.
theReadProbeFunction	Function to get data about a probe – getData_Probe_Meth450 or getData_Probe_Meth27
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.

Examples

#See examples in tests directory in the install.

MD-Anderson-Bioinformatics/GeneSurvey documentation built on May 7, 2019, 2:04 p.m.