plot.DesignContrast: Plot a DesignContrast object with two heatmaps

In bedapub/ribiosExpression: Expression Analysis with RibiosExpression

Plot a DesignContrast object with two heatmaps

Description

The function plots a ComplexHeatmap containing two matrices, one of the design matrix and the other of the contrast matrix.

Usage

## S3 method for class 'DesignContrast'
plot(
  x,
  y = NULL,
  title = NULL,
  clusterDesign = FALSE,
  clusterSamples = FALSE,
  clusterContrasts = FALSE,
  designRange = NULL,
  contrastRange = NULL,
  designParams = NULL,
  contrastParams = NULL,
  ...
)

Arguments

x	A DesignContrast object
y	NULL, ignored
title	Title of the object, used in the title of the heatmaps
clusterDesign	Logical, cluster rows of the design matrix
clusterSamples	Logical, cluster columns of the design matrix
clusterContrasts	Logical, cluster rows of the contrast matrix (notice that the contrast matrix required by limma is the transposed contrast matrix)
designRange	NULL or a vector of length 2, giving range of the design matrix to be visualized. If NULL, the whole range is used.
contrastRange	NULL or a vector of length 2, giving range of the contrast matrix to be visualized. If NULL, a symmetric range of the largest absolute value and its negate is used.
designParams	Other parameters passed to Heatmap for the design matrix
contrastParams	Other parameters passed to Heatmap for the contrast matrix
...	Ignored

Value

Heatmap object

Examples

myFac <- gl(3,3, labels=c("baseline", "treat1", "treat2"))
myDesign <- model.matrix(~myFac)
colnames(myDesign) <- c("baseline", "treat1", "treat2")
myContrast <- limma::makeContrasts(contrasts=c("treat1", "treat2"), levels=myDesign)
res1 <- DesignContrast(myDesign, myContrast, groups=myFac)
res2 <- DesignContrast(myDesign, myContrast, groups=myFac, dispLevels=c("C", "T1", "T2"))
plot(res1, title="DesCon 1")
plot(res2, title="DesCon 1 (identical)")
plot(res2, title="DesCon 1 (identical)", designRange=c(-2,2), 
    contrastRange=c(-2,1),
    designParams=list(row_names_gp=grid::gpar(fontsize=8)),
    contrastParams=list(column_names_gp=grid::gpar(fontsize=12, color="red")))

bedapub/ribiosExpression documentation built on Feb. 2, 2025, 3:21 p.m.