plotFeatureBoxplot {clusterExperiment} | R Documentation |
Plot a boxplot of the (transformed) values for a particular gene, separated by cluster
## 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, ...)
object |
a ClusterExperiment object |
feature |
identification of feature to plot, either row name or index |
whichCluster |
which clusters to show on the plot |
... |
arguments passed to |
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 |
missingColor |
If not NULL, should be character value giving the color
for missing (-2) samples (overrides |
main |
title of plot. If NULL, given default title. |
whichAssay |
numeric or character specifying which assay to use. See
|
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)
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)) #give names to the clusters cl<-renameClusters(cl, whichCluster=1, value=letters[1:nClusters(cl)[1]]) plotFeatureBoxplot(cl,feature=1)