plotBarplot: Barplot of 1 or 2 clusterings

In epurdom/clusterCells: Compare Clusterings for Single-Cell Sequencing

Barplot of 1 or 2 clusterings

Description

Make a barplot of sample's assignments to clusters for single clustering, or cross comparison for two clusterings.

Usage

## S4 method for signature 'ClusterExperiment'
plotBarplot(object, whichClusters = "primary", labels = c("names", "ids"), ...)

## S4 method for signature 'vector'
plotBarplot(object, ...)

## S4 method for signature 'matrix'
plotBarplot(
  object,
  xNames = NULL,
  legNames = NULL,
  legend = ifelse(ncol(object) == 2, TRUE, FALSE),
  xlab = NULL,
  legend.title = NULL,
  unassignedColor = "white",
  missingColor = "grey",
  colPalette = NULL,
  ...
)

Arguments

object	A matrix of with each column corresponding to a clustering and each row a sample or a ClusterExperiment object.
whichClusters	argument that can be either numeric or character vector indicating the clusterings to be used. See details of getClusterIndex.
labels	if object is a ClusterExperiment object, then labels defines whether the clusters will be identified by their names values in clusterLegend (labels="names", the default) or by their clusterIds value in clusterLegend (labels="ids").
...	for plotBarplot arguments passed either to the method of plotBarplot for matrices or ultimately to barplot.
xNames	names for the clusters on x-axis (i.e. clustering given 1st). By default uses names of the 1st column of clusters matrix. See details.
legNames	names for the clusters dividing up the 1st clusters (will appear in legend). By default uses names of the 2nd cluster of clusters matrix. If only one clustering, xNames and legNames refer to the same clustering. See details.
legend	whether to plot the legend
xlab	label for x-axis. By default or if equal NULL the column name of the 1st cluster of clusters matrix
legend.title	label for legend. By default or if equal NULL the column name of the 2st cluster of clusters matrix
unassignedColor	If “-1” in clusters, will be given this color (meant for samples not assigned to cluster).
missingColor	If “-2” in clusters, will be given this color (meant for samples that were missing from the clustering, mainly when comparing clusterings run on different sets of samples)
colPalette	a vector of colors used for the different clusters. See details.

Details

The first column of the cluster matrix will be on the x-axis and the second column (if present) will separate the groups of the first column.

All arguments of the matrix version can be passed to the ClusterExperiment version. As noted above, however, some arguments have different interpretations.

If whichClusters = "workflow", then the most recent two clusters of the workflow will be chosen where recent is based on the following order (most recent first): final, mergeClusters, makeConsensus, clusterMany.

xNames, legNames and colPalette should all be named vectors, with the names referring to the clusters they should match to (for ClusterExperiment objects, it is determined by the argument labels as to whether the names should match the cluster names or the clusterIds). colPalette and legNames must be same length of the number of clusters found in the second clustering, or if only a single clustering, the same length as the number of clusters in that clustering.

Value

A plot is produced, nothing is returned

Author(s)

Elizabeth Purdom

Examples

## Not run: 
#clustering using pam: try using different dimensions of pca and different k
data(simData)

cl <- clusterMany(simData, nReducedDims=c(5, 10, 50), reduceMethod="PCA",
clusterFunction="pam", ks=2:4, findBestK=c(TRUE,FALSE),
removeSil=c(TRUE,FALSE), makeMissingDiss=TRUE)

plotBarplot(cl)
plotBarplot(cl,whichClusters=1:2)

## End(Not run)

epurdom/clusterCells documentation built on Oct. 12, 2022, 4:44 a.m.