R: A function to generate heatmap panels sorted by integrated...

plotHeatmap {iCluster} | R Documentation

## A function to generate heatmap panels sorted by integrated cluster assignment.

### Description

A function to generate heatmap panels sorted by integrated cluster assignment.

### Usage

    plotHeatmap(fit, datasets, sample.order=NULL, feature.order=NULL,
    width=5, scale=NULL, col.scheme=NULL, sparse=NULL, threshold=NULL,
    chr=NULL, plot.chr=NULL, cap=NULL)

### Arguments

`fit` | A iCluster object
`datasets` | A list object of data matrices
`feature.order` | A vector of logical values each specificy whether the genomic features in the corresponding data matrix should be reordered by similarity. Default is FALSE.
`sparse` | A vector of logical values each specificy whether to plot the top cluster-discriminant features. Default is FALSE.
`threshold` | When sparse is TRUE, a vector of threshold values to include the genomic features for which the absolute value of the associated coefficient estimates fall in the top quantile. threshold=c(0.25,0.25) takes the top quartile most discriminant features in data type 1 and data type 2 for plot.
`plot.chr` | A vector of logical values each specificy whether to annotate chromosome number on the left of the panel. Typically used for copy number data type. Default is FALSE.
`chr` | A vector of chromosome number.
`col.scheme` | Color scheme. Can use bluered(n) in gplots R package.
`sample.order` | User supplied cluster assignment.
`width` | Width of the figure in inches
`cap` | Image color option
`scale` | A vector of logical values each specify whether data should be scaled. Default is FALSE.

### Value

no value returned.

### Author(s)

Ronglai Shen shenr@mskcc.org

### References

Ronglai Shen, Adam Olshen, Marc Ladanyi. (2009). Integrative clustering of multiple genomic data types using a joint latent variable model with application to breast and lung cancer subtype analysis. Bioinformatics 25, 2906-2912.

Ronglai Shen, Qianxing Mo, Nikolaus Schultz, Venkatraman E. Seshan, Adam B. Olshen, Jason Huse, Marc Ladanyi, Chris Sander. (2012). Integrative Subtype Discovery in Glioblastoma Using iCluster. PLoS ONE 7, e35236

### See Also

`iCluster`,`iCluster2`

### Examples

    #library(iCluster)
    #data(gbm)
    #data(coord)
    #chr=chr[,1]
    #fit=iCluster2(datasets=gbm, k=3, lambda=list(0.44,0.33,0.28))
    #plotHeatmap(fit=fit, datasets=datasets, feature.order=c(FALSE,TRUE,TRUE),
    #sparse=c(FALSE,TRUE,TRUE),plot.chr=c(TRUE,FALSE,FALSE), chr=chr)

[Package iCluster version 2.1.0 Index]