plotFeatureBoxplot: Plot boxplot of feature values by cluster

In clusterExperiment: Compare Clusterings for Single-Cell Sequencing

Description

Plot a boxplot of the (transformed) values for a particular gene, separated by cluster

Usage

## S4 method for signature 'ClusterExperiment,character'
plotFeatureBoxplot(object, feature, whichCluster = "primary", ...)

## S4 method for signature 'ClusterExperiment,numeric'
plotFeatureBoxplot(
  object,
  feature,
  whichCluster = "primary",
  plotUnassigned = FALSE,
  unassignedColor = NULL,
  missingColor = NULL,
  main = NULL,
  whichAssay = 1,
  ...
)

Arguments

object	a ClusterExperiment object
feature	identification of feature to plot, either row name or index
whichCluster	argument that can be a single numeric or character value indicating the single clustering to be used. Giving values that result in more than one clustering will result in an error. See details of getClusterIndex.
...	arguments passed to boxplot
plotUnassigned	whether to plot the unassigned samples as a cluster (either -1 or -2)
unassignedColor	If not NULL, should be character value giving the color for unassigned (-2) samples (overrides clusterLegend) default.
missingColor	If not NULL, should be character value giving the color for missing (-2) samples (overrides clusterLegend) default.
main	title of plot. If NULL, given default title.
whichAssay	numeric or character specifying which assay to use. See assay for details.

Value

A plot is created. The output of boxplot is returned (see boxplot), with additional elements colors and clusterIds that gives the colors and internal ids that match each boxplot (pulled from clusterLegend but in the order of plot)

See Also

boxplot

Examples

data(simData)
#Create a ClusterExperiment object
cl <- clusterMany(simData, nReducedDims=c(5, 10, 50), reducedDim="PCA",
   clusterFunction="pam", ks=2:4, findBestK=c(TRUE,FALSE),
   removeSil=c(TRUE,FALSE), makeMissingDiss=TRUE)
#give names to the clusters
cl<-renameClusters(cl, whichCluster=1, 
   value=letters[1:nClusters(cl)[1]])
plotFeatureBoxplot(cl,feature=1)

clusterExperiment documentation built on Feb. 11, 2021, 2 a.m.