JackStrawPlot: JackStraw Plot

In atakanekiz/Seurat3.0: Tools 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, dims = 1:5, reduction = "pca", xmax = 0.1,
  ymax = 0.3)

Arguments

object	Seurat object
dims	Dims to plot
reduction	reduction to pull jackstraw info from
xmax	X-axis maximum on each QQ plot.
ymax	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)

Omri Wurtzel

See Also

ScoreJackStraw

Examples

JackStrawPlot(object = pbmc_small)

atakanekiz/Seurat3.0 documentation built on May 26, 2019, 2:33 a.m.