Usage
plotHeatmap(fit,datasets,type=c("gaussian","binomial","poisson","multinomial"),
sample.order=NULL,row.order=NULL,sparse=NULL,threshold=rep(0.25,length(datasets)),
width=5,scale=rep("none",length(datasets)),col.scheme=rep(list(bluered(256)),
length(datasets)), chr=NULL, plot.chr=NULL, cap=NULL)
Arguments
datasets
A list object of data matrices.
type
Types of data in the datasets.
sample.order
User supplied cluster assignment.
row.order
A vector of logical values each specificy whether the genomic features in the corresponding data matrix should be reordered by similarity. Default is TRUE.
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.
width
Width of the figure in inches
scale
A vector of logical values each specify whether data should be scaled. Default is FALSE.
col.scheme
Color scheme. Can use bluered(n) in gplots R package.
chr
A vector of chromosome number.
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.