plotBatchVariance {singleCellTK} | R Documentation

## Plot the percent of the variation that is explained by batch and condition in the data

### Description

Visualize the percent variation in the data that is explained by batch and condition if it is given.

### Usage

    plotBatchVariance(inSCE, useAssay = "logcounts", batch,
      condition = NULL)

### Arguments

`inSCE` | Input SCtkExperiment object. Required
`useAssay` | Indicate which assay to use for PCA. Default is "logcounts"
`batch` | The column in the annotation data that corresponds to batch. Required
`condition` | The column in the annotation data that corresponds to condition. Optional

### Value

A boxplot of variation explained by batch, condition, and batch+condition (if applicable).

### Examples

    if(requireNamespace("bladderbatch", quietly = TRUE)) {
      library(bladderbatch)
      data(bladderdata)
      dat <- as(as(bladderEset, "SummarizedExperiment"), "SCtkExperiment")
      plotBatchVariance(dat, useAssay="exprs", batch="batch", condition = "cancer")
    }

[Package singleCellTK version 1.2.3 Index]