csDistHeat: csDistHeat

In cummeRbund: 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) 

cummeRbund documentation built on Nov. 8, 2020, 7:53 p.m.