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).
JackStrawPlot(object, PCs = 1:5, nCol = 3, score.thresh = 1e-05,
plot.x.lim = 0.1, plot.y.lim = 0.3)Seurat plot
Which PCs to examine
Number of columns
Threshold to use for the proportion test of PC significance (see Details)
X-axis maximum on each QQ plot.
Y-axis maximum on each QQ plot.
A ggplot object
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.