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, dims = 1:5, cols = NULL, reduction = "pca", xmax = 0.1, ymax = 0.3 )
Dims to plot
Vector of colors, each color corresponds to an individual PC. This may also be a single character or numeric value corresponding to a palette as specified by
reduction to pull jackstraw info from
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.
data("pbmc_small") JackStrawPlot(object = pbmc_small)#> Warning: Removed 83 rows containing missing values (geom_point).