plotThreshold: Threshold plot

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

Description

Plot cluster membership values and thresholding

Usage

plotThreshold(bce, bcs, type, bicluster, ...)

## S4 method for signature 'BiclusterExperiment,character'
plotThreshold(bce, bcs, type,
  bicluster, ...)

## S4 method for signature 'BiclusterExperiment,numeric'
plotThreshold(bce, bcs, type,
  bicluster, ...)

## S4 method for signature 'BiclusterExperiment,BiclusterStrategy'
plotThreshold(bce, bcs,
  type = c("feature", "sample"), bicluster = "Bicluster.1",
  thresholds = NULL, ordering = c("input", "distance", "cluster"),
  xlabs = FALSE)

Arguments

bce	A BiclusterExperiment
bcs	A BiclusterStrategy object, or the name or index of one of the BiclusterStrategy objects in bce@strategies
type	Specifies whether to show thresholding for features or samples
bicluster	The character name of a bicluster in bcs. See bcNames.
...	Optional arguments thresholds, ordering, and xlabs, described below.
thresholds	If not NULL, must be a numeric vector of theshold(s) to replace the algorithmically chosen thresholds contained in bcs.
ordering	Specifies the ordering of features or samples along the x-axis. If "input", the input ordering is used. If "distance", ordering is based on Euclidean distance calculated from bce@assayData. If "cluster", ordering is based on the bicluster membership of the samples or features.
xlabs	Should sample or feature labels be displayed?

Value

Invisibly returns NULL

Methods (by class)

• bce = BiclusterExperiment,bcs = character: Plots thresholding performed in the BiclusterStrategy-class object named bcs in bce@strategies.

• bce = BiclusterExperiment,bcs = numeric: Plots thresholding performed in the BiclusterStrategy-class object at the index specified by bcs

• bce = BiclusterExperiment,bcs = BiclusterStrategy: Plots thresholding performed in bcs.

Examples

bce <- BiclusterExperiment(yeast_benchmark[[1]])
bce <- addStrat(bce, k = 2, method = "als-nmf")
bcs <- getStrat(bce, 1)
bcNames(bcs)
plotThreshold(bce, bcs, type = "sample", bicluster = "Bicluster.1")

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