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Last data update: 2014.03.03

R: csHeatmap

csHeatmap

R Documentation

csHeatmap

Description

Creates a ggplot plot object with a geom_tile layer of FPKM values per feature and sample.

Usage

## S4 method for signature 'CuffFeatureSet'
csHeatmap(object, rescaling='none', clustering='none', labCol=T, labRow=T, logMode=T, pseudocount=1.0, 
		border=FALSE, heatscale= c(low='lightyellow',mid='orange',high='darkred'), heatMidpoint=NULL, fullnames = T, replicates=FALSE,method='none', ...)
## S4 method for signature 'CuffFeatureSet'
csFoldChangeHeatmap(object, control_condition, replicate_num=NULL, clustering='none', labCol=T, labRow=T, logMode=F, pseudocount=1.0, 
		border=FALSE, heatscale=c(low='steelblue',mid='white',high='tomato'), heatMidpoint=0,fullnames=T,replicates=FALSE,method='none',heatRange=3, ...)

Arguments

`object`	An object of class 'CuffFeatureSet' or 'CuffGeneSet'
`control_condition`	A character argument indicating which condition should be used as the denominator for fold change. (e.g. "Day0", "Control", etc)
`replicate_num`	If replicates == TRUE, you must specify both a control condition and a replicate number to use as the denominator.
`rescaling`	Rescaling can either be 'row' or 'column' OR you can pass rescale a function that operates on a matrix to do your own rescaling. Default is 'none'.
`clustering`	Clustering can either be 'row','column','none', or 'both', in which case the appropriate indices are re-ordered based on the pairwise Jensen-Shannon distance of FPKM values.
`labCol`	A logical argument to display column labels.
`labRow`	A logical argument to display row labels.
`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)
`border`	A logical argument to draw border around plot.
`heatscale`	A list with min length=2, max length=3 that detail the low,mid,and high colors to build the color scale.
`heatMidpoint`	Value for midpoint of color scale.
`fullnames`	A logical value whether to use 'fullnames' (concatenated gene_short_name and gene_id) for rows in heatmap. Default [ TRUE ].
`replicates`	A logical value whether or not to plot individual replicates or aggregate condition values.
`method`	Function to be used for clustering. Default is JS-distance. You can pass your own function to this argument as long as the output is an instance of the 'dist' class and is applied to the rows of the input matrix.
`heatRange`	Numerical argument for upper bound on log fold change to be visualized.
`...`	Additional arguments to csHeatmap

Details

None

Value

A ggplot2 plot object with a geom_tile layer to display FPKM values by sample (x) and feature (y)

Note

None

Author(s)

Loyal A. Goff and Cole Trapnell

References

None.

Examples

	data(sampleData)
	csHeatmap(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.
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Type 'license()' or 'licence()' for distribution details.

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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/csHeatmap.Rd_%03d_medium.png", width=480, height=480)
> ### Name: csHeatmap
> ### Title: csHeatmap
> ### Aliases: csHeatmap csFoldChangeHeatmap csHeatmap,CuffFeatureSet-method
> ###   csFoldChangeHeatmap,CuffFeatureSet-method
> ### Keywords: heatmap
> 
> ### ** Examples
> 
> 	data(sampleData)
> 	csHeatmap(sampleGeneSet)
Using tracking_id, sample_name as id variables
No id variables; using all as measure variables
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>