csDistHeat {cummeRbund} | R Documentation |
Creates a ggplot plot object with a geom_tile layer of JS Distance values between samples or genes.
## 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, ...)
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 |
None
A ggplot2 plot object with a geom_tile layer to display distance between samples or genes.
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Loyal A. Goff, Cole Trapnell, and David Kelley
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data(sampleData) csDistHeat(sampleGeneSet)