csDistHeat: csDistHeat

In gofflab/cummeRbund-BioC-Bridge: Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.

Description

Creates a ggplot plot object with a geom_tile layer of JS Distance values between samples or genes.

Usage

## S4 method for signature 'CuffFeatureSet'
csDistHeat(object, replicates=F, samples.not.genes=T,
  logMode=T, pseudocount=1.0,
  heatscale=c(low='lightyellow',mid='orange',high='darkred'),
  heatMidpoint=NULL, ...)

Arguments

object	An object of class 'CuffFeatureSet' or 'CuffGeneSet'
replicates	A logical argument whether or not to use individual replicate FPKM values as opposed to condition FPKM estimates. (default: FALSE)
samples.not.genes	Compute distances between samples rather than genes. If False, compute distances between genes.
logMode	A logical argument to log10-transform FPKM values prior to plotting.
pseudocount	Value to be added to FPKM for appropriate log transformation and clustering. (Avoids zero-based errors)
heatscale	A list with min length=2, max length=3 that describe the the color scale.
heatMidpoint	Value for midpoint of color scale.
...	Additional arguments to csHeatmap

Details

None

Value

A ggplot2 plot object with a geom_tile layer to display distance between samples or genes.

Note

None

Author(s)

Loyal A. Goff, Cole Trapnell, and David Kelley

References

None

Examples

	data(sampleData)
	csDistHeat(sampleGeneSet) 

gofflab/cummeRbund-BioC-Bridge documentation built on May 17, 2019, 7:30 a.m.