csDistHeat {cummeRbund} | R Documentation

## csDistHeat

### 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)

[Package cummeRbund version 2.29.0 Index]