plotDist: Distance heatmap

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

Description

Plot a heatmap of sample distance or feature distance calculated from the raw data in a BiclusterExperiment-class object. Default is Euclidean distance between samples.

Usage

plotDist(bce, type, ordering = c("input", "distance", "cluster"),
  distType = c("euclidean", "pearson"), ...)

## S4 method for signature 'BiclusterExperiment'
plotDist(bce, type = c("sample",
  "feature"), ordering = c("input", "distance", "cluster"),
  distType = c("euclidean", "pearson"), phenoLabels = c(),
  biclustLabels = c(), strategy = "", rowColNames = FALSE)

Arguments

bce	A BiclusterExperiment object
type	"sample" or "feature"
ordering	The default ordering = "input" preserves the order of samples or features from bce@assayData. "distance" reorders based on the distance calculated from distType. "cluster" reorders based on bicluster membership.
distType	The formula to use for distance
...	Optional parameters phenoLabels, biclustLabels, strategy, and rowColNames, 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.
strategy	The name or index of an object in bce@strategies from which to obtain bicluster annotations, or a BiclusterStrategy-class object.
rowColNames	Should feature/sample names be printed

Value

a pheatmap-class object

Examples

bce <- BiclusterExperiment(cancer_benchmark[[1]]$data)
plotDist(bce, type = "sample", ordering = "distance", rowColNames = TRUE)
plotDist(bce, type = "feature", distType = "pearson", ordering = "distance")

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