Create a PCA scatter plot — plot

Produces a ggplot2 scatter plot of PCA scores, with optional color and shape aesthetics mapped to sample metadata columns.

Usage

plot_pca(
  pca_result,
  color_by = NULL,
  shape_by = NULL,
  pcs = c(1, 2),
  point_size = 4
)

pca_result: Output from run_pca().
color_by: Column name from colData to map to point color. Default: NULL (no color mapping).
shape_by: Column name from colData to map to point shape. Default: NULL (no shape mapping).
pcs: Integer vector of length 2 specifying which PCs to plot. Default: c(1, 2).
point_size: Numeric point size. Default: 4.

A ggplot object.

Jared Andrews

data(airway, package = "airway")
result <- run_pca(airway, n_top = 50)
plot_pca(result, color_by = "dex")