JackStrawPlot: JackStraw Plot

In mayer-lab/SeuratForMayer2018: Seurat : R Toolkit for Single Cell Genomics

Description

Plots the results of the JackStraw analysis for PCA significance. For each PC, plots a QQ-plot comparing the distribution of p-values for all genes across each PC, compared with a uniform distribution. Also determines a p-value for the overall significance of each PC (see Details).

Usage

JackStrawPlot(object, PCs = 1:5, nCol = 3, score.thresh = 1e-05,
  plot.x.lim = 0.1, plot.y.lim = 0.3)

Arguments

object	Seurat plot
PCs	Which PCs to examine
nCol	Number of columns
score.thresh	Threshold to use for the proportion test of PC significance (see Details)
plot.x.lim	X-axis maximum on each QQ plot.
plot.y.lim	Y-axis maximum on each QQ plot.

Details

Significant PCs should show a p-value distribution (black curve) that is strongly skewed to the left compared to the null distribution (dashed line) The p-value for each PC is based on a proportion test comparing the number of genes with a p-value below a particular threshold (score.thresh), compared with the proportion of genes expected under a uniform distribution of p-values.

Value

A ggplot object

Author(s)

Thanks to Omri Wurtzel for integrating with ggplot

mayer-lab/SeuratForMayer2018 documentation built on May 25, 2019, 9:34 p.m.