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
)

## Arguments

object | Seurat object |
---|

dims | Dims to plot |
---|

cols | 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 `brewer.pal.info` . By default, ggplot2 assigns colors. We also include a number of palettes from the pals package. See `DiscretePalette` for details. |
---|

reduction | reduction to pull jackstraw info from |
---|

xmax | X-axis maximum on each QQ plot. |
---|

ymax | Y-axis maximum on each QQ plot. |
---|

## Value

A ggplot object

## 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.

## See also

## Author

Omri Wurtzel

## Examples

#> Warning: Removed 83 rows containing missing values (geom_point).