Seurat (version 2.3.4)

JackStrawPlot: JackStraw Plot

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.

Value

Returns a Seurat object where object@dr$pca@[e-mail] represents p-values for each PC and object@dr$pca@misc$jackstraw.plot stores the ggplot2 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.

Examples

# NOT RUN {
JackStrawPlot(object = pbmc_small)

# }