plot.pvalue {plot.matrix}

plot.pvalue

Description

Visualizes a matrix of p-values with a colored or gray heatmap. As a rule of thumb the breaks are determined by c(0, 0.001, 0.01, 0.05, 0.1, 1) You may need to modify mar with the par command from its default c(5.1,4.1,4.1,2.1). See

• vignette('plot.matrix') for detailed examples, and

• plot.matrix for further parameters.

Usage

## S3 method for class 'pvalue'
plot(x, reorder = TRUE, gray = FALSE, grey = FALSE, ...)

Arguments

x

matrix: p-values within [0,1]

reorder

logical: if the rows (variables) of the loading matrix should be reordered (default: TRUE)

gray

logical: should be a gray scale color palette used or not (default: FALSE)

grey

logical: should be a gray scale color palette used or not (default: FALSE)

...

further parameter given to the plot.matrix command

Details

If either the parameter grey or gray is TRUE then a gray color palette is used.

Value

a plot

Examples

par(mar=c(5.1, 4.1, 4.1, 4.1))
# correlation matrix
data(air.pvalue)
plot(as.pvalue(air.pvalue))
plot(as.pvalue(air.pvalue), gray=TRUE)
plot(as.pvalue(air.pvalue[,1:3]), reorder=FALSE)