plotFeatureScatter {clusterExperiment} | R Documentation |
Plot a scatter plot of the (transformed) values for a set of gene expression values, colored by cluster
## S4 method for signature 'ClusterExperiment,character' plotFeatureScatter(object, features, ...) ## S4 method for signature 'ClusterExperiment,numeric' plotFeatureScatter( object, features, whichCluster = "primary", plotUnassigned = TRUE, unassignedColor = "grey", missingColor = "white", whichAssay = 1, legendLocation = NA, jitterFactor = NA, ... )
object |
a ClusterExperiment object |
features |
the indices of the features (either numeric or character matching rownames of object) to be plotted. |
... |
arguments passed to |
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 |
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 |
whichAssay |
numeric or character specifying which assay to use. See
|
legendLocation |
character value passed to |
jitterFactor |
numeric. If NA, no jittering is done. Otherwise, passed to
|
returns invisibly the results of pairs
or plot
command.
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]]) plotFeatureScatter(cl,feature=1:2,pch=19,legendLocation="topright")