plot: Expression plot

In jonalim/mfBiclust: Pipelines for Bi-Clustering Using Matrix Factorization

Description

Create a heatmap from assay data in a BiclusterExperiment object. A BiclusterStrategy and bicluster must be named if ordering = "cluster" or annotateCluster = TRUE.

Usage

plot(x, y, ...)

## S4 method for signature 'BiclusterExperiment,ANY'
plot(x, logBase = 0,
  phenoLabels = c(), biclustLabels = c(), ordering = c("input",
  "distance", "cluster"), strategy = "", rowNames = FALSE,
  colNames = FALSE)

Arguments

x	A link{BiclusterExperiment-class} object
y	Not used in the BiclusterStrategy method
...	Additional arguments, described below:
logBase	If TRUE, every assay value is transformed by the natural log
phenoLabels	Display phenotype labels along the samples?
biclustLabels	Display bicluster labels along the samples and features?
ordering	If "input", samples and features are not reordered. If "distance", sampels and features are reordered based on Euclidean distance. If "cluster", samples and features are reordered based on bicluster membership.
strategy	The BiclusterStrategy to read biclusters from, if bicluster- based information is to be plotted.
rowNames	TRUE to show feature names
colNames	TRUE to show sample names

Value

a pheatmap-class object

Examples

bce <- BiclusterExperiment(cancer_benchmark[[1]]$data,
                           phenoData = cancer_benchmark[[1]]$labels)
phenoData(bce)
plot(bce, phenoLabels = "phenotype")

jonalim/mfBiclust documentation built on May 4, 2019, 4:13 a.m.