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

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) 

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(cummeRbund)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: RSQLite
Loading required package: DBI
Loading required package: ggplot2
Loading required package: reshape2
Loading required package: fastcluster

Attaching package: 'fastcluster'

The following object is masked from 'package:stats':

    hclust

Loading required package: rtracklayer
Loading required package: GenomicRanges
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Gviz
Loading required package: grid

Attaching package: 'cummeRbund'

The following object is masked from 'package:GenomicRanges':

    promoters

The following object is masked from 'package:IRanges':

    promoters

The following object is masked from 'package:BiocGenerics':

    conditions

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/cummeRbund/csDistHeat.Rd_%03d_medium.png", width=480, height=480)
> ### Name: csDistHeat
> ### Title: csDistHeat
> ### Aliases: csDistHeat csDistHeat,CuffFeatureSet-method
> ###   csDistHeat,CuffData-method
> ### Keywords: heatmap Jensen-Shannon distance
> 
> ### ** Examples
> 
> 	data(sampleData)
> 	csDistHeat(sampleGeneSet) 
Using tracking_id, sample_name as id variables
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>