plotPcElbow: Plot principal component elbow

In acidgenomics/pointillism: Single-cell RNA-seq toolkit

Plot principal component elbow

Description

Calculate the principal component (PC) cutoff using a heuristic approach.

Usage

plotPcElbow(object, ...)

## S4 method for signature 'Seurat'
plotPcElbow(object, minPct = 0.01, maxCumPct = 0.9)

Arguments

object	Object.
minPct	numeric(1) (0-1). Minimum percent standard deviation.
maxCumPct	numeric(1) (0-1). Maximum cumulative percen standard deviation.
...	Additional arguments.

Details

Automatically return the smallest number of PCs that match the minSD, minPct, and maxCumPct cutoffs.

Value

ggplot. Elbow point is saved in attr(object, "elbow").

Note

Updated 2023-08-16.

See Also

• Seurat::PCElbowPlot().

• monocle3::plot_pc_variance_explained().

Examples

data(Seurat, package = "AcidTest")

## Seurat ====
object <- Seurat
plotPcElbow(object)

acidgenomics/pointillism documentation built on Oct. 18, 2023, 4:11 p.m.