plotCytoK {cytoKernel} | R Documentation

## Heatmap of the differentially expressed data with features on the rows and samples (group factors) as the columns from `CytoK` and `CytoKDEData` function.

### Description

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.

### Usage

    plotCytoK(object, group_factor, topK, featureVars = NULL)

### Arguments

`object` | a CytoK object from `CytoK`
`group_factor` | a group level binary categorical response associated with each sample or column in the `object`. The order of the `group_factor` must match the order of the columns in `object`.
`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.

### Value

A heatmap will be created showing the samples on the columns and features on the rows.

### Examples

    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)

[Package cytoKernel version 1.0.0 Index]