plot_PCA: PCA, screeplot and PERMANOVA test
In vari-bbc/bbcRNA: Bulk RNA-seq workflow for VAI BBC

Description Usage Arguments Value See Also

Runs PCA on normalized counts. Makes PCA and scree plots. Tests for significant clustering based on specific variables using PERMANOVA and Euclidean distances.

plot_PCA(
  x,
  norm_cts_type = "edger",
  assay_name = "norm_log_cpm",
  color_by = colnames(colData(x))[[1]],
  shape_by = colnames(colData(x))[[1]],
  adonis = TRUE,
  adonis_by = colnames(colData(x))[[1]]
)

`x`	A BbcSE object.
`norm_cts_type`	"edger" or "deseq2"
`assay_name`	Name of assay from the 'norm_cts' slot. Option was implemented with the idea of being able to plot batch-corrected data.
`color_by`	colData column to color by for PCA plot
`shape_by`	colData column to shape by for PCA plot
`adonis`	logical for whether vegan::adonis should be run. If TRUE, adonis() will be run with Euclidean distance calculated from the same normalized counts as used for PCA.
`adonis_by`	colData column to test using PERMANOVA. May be a vector of values; in this case, each variable is tested sequentially using adonis().

A list containing ggplot objects for 1. PCA 2. scree plot 3. prcomp()$x merged with meta data. Handy if visualizations of >PC2 are needed 4. a list of output from vegan::adonis()

adonis

vari-bbc/bbcRNA documentation built on Nov. 10, 2020, 11:09 p.m.