se_pca_plot: Run PCA and return a plot

In amcdavid/GeneseeBulk: Pipeline, analysis functions and markdown templates for bulk RNAseq

Run PCA and return a plot

Description

Run PCA and return a plot

Usage

se_pca_plot(object, ntop = 500, aes_point, aes_label, print_plot = TRUE)

Arguments

object	SummarizedExperiment
ntop	use this many variable genes
aes_point	a call to aes evaluated in the context of the colData for the geom_point, eg aes(color = treatment).
aes_label	a call to aes evaluated in the context of the colData for the geom_textrepel, eg aes(label = sample_id).
print_plot	logical

Value

list with elements pca_dat, containing colData plus PC1, PC2, pca output of prcomp and plot.

amcdavid/GeneseeBulk documentation built on March 26, 2022, 4:58 a.m.