heatdiagram: Stemmed Heat Diagram

Description

Creates a heat diagram showing the co-regulation of genes under one condition with a range of other conditions.

Usage

heatDiagram(results, coef, primary=1, names=NULL, treatments=colnames(coef), limit=NULL, orientation="landscape", low="green", high="red", cex=1, mar=NULL, ncolors=123, ...)
heatdiagram(stat, coef, primary=1, names=NULL, treatments=colnames(stat), critical.primary=4, critical.other=3, limit=NULL, orientation="landscape", low="green", high="red", cex=1, mar=NULL, ncolors=123, ...)

Arguments

results

TestResults matrix, containing elements -1, 0 or 1, from decideTests

stat

numeric matrix of test statistics. Rows correspond to genes and columns to treatments or contrasts between treatments.

coef

numeric matrix of the same size as stat. Holds the coefficients to be displayed in the plot.

primary

number or name of the column to be compared to the others. Genes are included in the diagram according to this column of stat and are sorted according to this column of coef. If primary is a name, then stat and coef must have the same column names.

names

optional character vector of gene names

treatments

optional character vector of treatment names

critical.primary

critical value above which the test statistics for the primary column are considered significant and included in the plot

critical.other

critical value above which the other test statistics are considered significant. Should usually be no larger than critical.primary although larger values are permitted.

limit

optional value for coef above which values will be plotted in extreme color. Defaults to max(abs(coef)).

orientation

"portrait" for upright plot or "landscape" for plot orientated to be wider than high. "portrait" is likely to be appropriate for inclusion in printed document while "landscape" may be appropriate for a presentation on a computer screen.

low

color associated with repressed gene regulation

high

color associated with induced gene regulation

ncolors

number of distinct colors used for each of up and down regulation

cex

factor to increase or decrease size of column and row text

mar

numeric vector of length four giving the size of the margin widths. Default is cex*c(5,6,1,1) for landscape and cex*c(1,1,4,3) for portrait.

...

any other arguments will be passed to the image function

Value

A matrix with named rows containing the coefficients used in the plot is also invisibly returned.

Details

Users are encouraged to use heatDiagram rather than heatdiagram as the later function may be removed in future versions of limma.

This function plots an image of gene expression profiles in which rows (or columns for portrait orientation) correspond to treatment conditions and columns (or rows) correspond to genes. Only genes which are significantly differentially expressed in the primary condition are included. Genes are sorted by differential expression under the primary condition.

Note: the plot produced by this function is unique to the limma package. It should not be confused with "heatmaps" often used to display results from cluster analyses.

Examples

Run this code

## Not run: 
# MA <- normalizeWithinArrays(RG)
# design <- cbind(c(1,1,1,0,0,0),c(0,0,0,1,1,1))
# fit <- lmFit(MA,design=design)
# contrasts.mouse <- cbind(Control=c(1,0),Mutant=c(0,1),Difference=c(-1,1))
# fit <- eBayes(contrasts.fit(fit,contrasts=contrasts.mouse))
# results <- decideTests(fit,method="global",p=0.1)
# heatDiagram(results,fit$coef,primary="Difference")
# ## End(Not run)