plot_stability: Stability plot.

In MonashBioinformaticsPlatform/varistran: Variance Stabilizing Transformations appropriate for RNA-Seq expression data

Stability plot.

Description

Produce a ggplot object containing a plot of residual standard deviation against mean count.

Usage

plot_stability(y, x = NULL, design = NULL, bins = 20)

Arguments

y	Transformed counts matrix.
x	Optional, original counts matrix.
design	Matrix specifying a linear model with which to calculate residuals.
bins	Number points in the graph.

Details

Genes are partitioned evenly into "bins" bins by average expression level. Mean residual standard deviation is plotted against mean count.

If the variance stabilizing transformation has been successful, this plot should be close to a horizontal line. However it is normal for the standard deviation to drop off for counts below 5.

Value

A ggplot object.

This must be print()-ed to actually plot.

Author(s)

Paul Harrison

MonashBioinformaticsPlatform/varistran documentation built on June 9, 2025, 8:36 a.m.