Plot pseudo vs. aligned counts

Usage

plotPseudoVsAlignedCounts(object, ...)

# S4 method for bcbioRNASeq
plotPseudoVsAlignedCounts(
  object,
  genes = NULL,
  title = "Pseudoaligned vs. aligned counts",
  ...
)

Arguments

object: Object.
genes: character. Gene identifiers.
title: character(1). Title.
...: Passthrough to AcidPlots::plotCountsCorrelationHeatmap() when genes = NULL or AcidPlots::plotCountsCorrelation() when genes are defined.

Value

ggplot.

Note

Updated 2023-10-05.

Currently supported for salmon or kallisto. The function will intentionally error for datasets containing aligned counts in the primary counts assay.

Author

Michael Steinbaugh

Examples

data(bcb)

## bcbioRNASeq ====
## Correlation heatmap.
plotPseudoVsAlignedCounts(bcb)
#> ! Censoring 29 genes containing an NA value.


## Individual genes.
## Checking the most expressed aligned genes here.
aligned <- SummarizedExperiment::assay(bcb, i = "aligned")
genes <- names(tail(sort(rowSums(aligned)), n = 2L))
plotPseudoVsAlignedCounts(bcb, genes = genes)