plotCytoK {cytoKernel} | R Documentation |
CytoK
and CytoKDEData
function.This function plots a heatmap of the expression matrix with features (e.g., cluster-marker combinations) on the rows and samples (group factors) as the columns.
plotCytoK(object, group_factor, topK, featureVars = NULL)
object |
a CytoK object from |
group_factor |
a group level binary categorical
response associated with each sample or column in the
|
topK |
top K differentially expressed features. |
featureVars |
(Optional) Vector of the columns which identify features. If a 'SummarizedExperiment' is used for 'data', row variables will be used. |
A heatmap will be created showing the samples on the columns and features on the rows.
data <- cbind(matrix(rnorm(1200,mean=2, sd=1.5), nrow=200, ncol=6), matrix(rnorm(1200,mean=5, sd=1.9), nrow=200, ncol=6)) data_CytoK <- CytoK(object=data, group_factor = rep(c(0,1), each=6), lowerRho=2, upperRho=12,gridRho=4,alpha = 0.05, featureVars = NULL) data("cytoHDBMW") data_CytoK_HD <- CytoK(object=cytoHDBMW, group_factor = rep(c(0, 1), c(4, 4)), lowerRho=2, upperRho=12,gridRho=4,alpha = 0.05, featureVars = NULL) plotCytoK(data_CytoK_HD, group_factor = rep(c(0, 1), c(4, 4)),topK=10, featureVars = NULL)