pipe.PlotGene: Plot Gene Expression as Wiggle Track Pileups

In robertdouglasmorrison/DuffyNGS: Duffy Lab NGS Analysis Pipeline for RNA-seq, DNA-seq, ChIP-seq, and RIP-seq

Plot Gene Expression as Wiggle Track Pileups

Description

Plot gene expression for one or more genes from one or more samples, and optionally save them as PNG images.

Usage

pipe.PlotGene(sampleIDs, genes, annotationFile = "Annotation.txt", 
	optionsFile = "Options.txt", results.path = NULL, targetID = NULL, colorColumn = "Color",
	PLOT.FUN = NULL, plotFormat = c( "", "png", "pdf"), plot.path = "Gene_Plots", 
	keepShortGeneName = NULL, pileup.col=c(4,2,1), png.width=1000, png.height=700, 
	pdf.width=10, pdf.height=7, ...)

Arguments

sampleIDs	A vector or one or more SampleIDs.
genes	A vector of one or more genes, from any species in the current target.
annotationFile	The file of sample annotations.
optionsFile	The file of program options.
results.path	The folder of pipeline results, to find existing wiggle track objects for each SampleID.
targetID	optionally specify the current target organism(s). Affects the display of genome uniqueness and detectability on default read pileup plots.
PLOT.FUN	Optional function to call for generating the gene expression plot. By default, calls the standard read pileups functions, either plotWIGgene or plotMultiWIGgene depending on the number of SampleIDs.
plotFormat	Controls the plotting behaviour. Default is to write to the current graphics device. Optionally it can create PNG or PDF files on disk, using the name of the gene as the filename.
plot.path	Folder to write PNG or PDF image files to.
keepShortGeneName	When not NULL, an integer value passed to shortGeneName to trim the image filename down to a shortened version of the full GeneID name.
pileup.col	a vector of 3 colors, for drawing of forward strand, reverse strand, and "combo strand" colors, respectively. (Combo strand only applies to ChIP-seq plots)
...	Other arguments to be passed to the plot function, including 'type', 'useLog', 'tailWidth', etc.

Details

This function gives a simpler interface wrapper to the lower level gene expression plot functions, handling all details about SpeciesIDs, WIG objects, etc.

Value

If plotFormat is not empty, then PNG or PDF files are written to disk. Otherwise creates a gene expression plot image in the current graphics device.

Note

The default behavoir of showing full read pileup images for many samples at one time consumes lots of memory and time. When the number of samples gets large, consider providing a simpler plot function based on some other display metric such as RPKM expression values. Secondly, the pileup images are not ideal for quantitative comparisons.

See Also

pipe.PlotSNP for aligned read plot images that examine the base call distributions around possible SNP locations at single nucleotide resolution.

robertdouglasmorrison/DuffyNGS documentation built on March 24, 2024, 4:16 p.m.