plotBatchVariance: Plot the percent of the variation that is explained by batch...

In mmkhan19/singleCellTK: Interactive Analysis of Single Cell RNA-Seq Data

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")
}

mmkhan19/singleCellTK documentation built on March 22, 2022, 7:43 a.m.