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
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
No value returned, just the PC plots.
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.