factorHeatmap: Plot a heatmap showing bicluster membership of samples or...

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

Description

Reads data from BiclusterStrategy@factors to create a heatmap of bicluster membership across all samples or features.

Usage

factorHeatmap(bce, bcs, type, ordering = "input", ...)

## S4 method for signature 'BiclusterExperiment,character'
factorHeatmap(bce, bcs, type,
  ordering = "input", ...)

## S4 method for signature 'BiclusterExperiment,numeric'
factorHeatmap(bce, bcs, type,
  ordering = "input", ...)

## S4 method for signature 'BiclusterExperiment,BiclusterStrategy'
factorHeatmap(bce, bcs,
  type = c("feature", "sample"), ordering = c("input", "distance",
  "cluster"), phenoLabels = c(), biclustLabels = c(),
  colNames = FALSE)

Arguments

bce	A BiclusterExperiment object
bcs	The name or index of a BiclusterStrategy contained by bce, or the BiclusterStrategy object itself
type	either "feature" for feature-bicluster membership or "sample" for sample-bicluster membership
ordering	The default ordering = "input" preserves the order of samples or features from bce@assayData. "distance" reorders based on Euclidean distance calculated from bce@assayData. "cluster" reorders based on bicluster membership.
...	Optional arguments phenoLabels, biclustLabels, ordering, and colNames, described below:
phenoLabels	an optional character vector of labels to annotate. If type = "feature", phenoLabels should be column names of Biobase::phenoData(bce)
biclustLabels	an optional character vector of labels to annotate. Should be elements of bcNames(bcs). Both phenoLabels and biclustLabels may be specified.
colNames	if TRUE, labels the samples/features

Value

a pheatmap-class object

Methods (by class)

• bce = BiclusterExperiment,bcs = character: Plots a matrix factor from the BiclusterStrategy-class object named bcs in bce@strategies.

• bce = BiclusterExperiment,bcs = numeric: Plots a matrix factor from the BiclusterStrategy-class object at the index specified by bcs

• bce = BiclusterExperiment,bcs = BiclusterStrategy: Plots a matrix factor from bcs.

Examples

bce <- BiclusterExperiment(yeast_benchmark[[1]])
bce <- addStrat(bce, k = 2, method = "als-nmf")
bcs <- getStrat(bce, 1)
factorHeatmap(bce, bcs, type = "sample")

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