Plot PCA scores from a pca_audit result

Source: R/pca_audit.R

Produces a ggplot2 scatter plot of two principal component score axes, optionally colored by a sample-metadata column. This is a purely visual convenience: the statistical results returned by pca_audit do not depend on this function being called.

plot_pca_audit(pca_result, pc_x = 1, pc_y = 2, color_by = NULL)

Arguments

pca_result

An object of class "rnaSentry_pca" as returned by pca_audit.

pc_x, pc_y

Integers selecting the two PC axes to plot. Defaults to 1 and 2.

color_by

Optional character. Name of a sample-metadata column in the original colData(se) to color points by.

Value

A ggplot object.

Examples

library(SummarizedExperiment)
set.seed(2)
counts <- matrix(rpois(240, lambda = 200), nrow = 20, ncol = 12,
                  dimnames = list(paste0("gene", 1:20), paste0("S", 1:12)))
coldata <- DataFrame(batch = factor(rep(c("B1", "B2"), each = 6)),
                      row.names = paste0("S", 1:12))
se <- SummarizedExperiment(assays = list(counts = counts), colData = coldata)
res <- pca_audit(se, batch_col = "batch")
plot_pca_audit(res)