Description Usage Arguments Details Value Author(s)
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).
1 2 | JackStrawPlot(object, PCs = 1:5, nCol = 3, score.thresh = 1e-05,
plot.x.lim = 0.1, plot.y.lim = 0.3)
|
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. |
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.
No value returned, just the PC plots.
Thanks to Omri Wurtzel for integrating with ggplot
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