Plot the percent of the variation that is explained by batch and condition in the data
Source:R/plotBatchVariance.R
plotBatchVariance.RdVisualize the percent variation in the data that is explained by batch and condition if it is given.
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")
}
#> Warning: It is deprecated to specify `guide = FALSE` to remove a guide. Please use `guide = "none"` instead.
