plot_pca_loadings: PCA loadings plot

In antonvsdata/amp: Smoothing Metabolomics Analyses

Description

Computes PCA using one of the methods provided in the Bioconductor package pcaMethods and plots the loadings of first principal components CITATION: When using this function, cite the pcaMethods package

Usage

plot_pca_loadings(object, all_features = FALSE, center = TRUE,
  scale = "uv", npc1 = 10, npc2 = 10, title = "PCA loadings",
  subtitle = NULL, ...)

Arguments

object	a MetaboSet object
all_features	logical, should all features be used? If FALSE (the default), flagged features are removed before visualization.
center	logical, should the data be centered prior to PCA? (usually yes)
scale	scaling used, as in pcaMethods::prep. Default is "uv" for unit variance
npc1, npc2	number of top feature to plot for first and second principal component
title, subtitle	the titles of the plot
...	additional arguments passed to pcaMethods::pca

Value

a ggplot object.

See Also

pca

Examples

plot_pca_loadings(merged_sample, npc1 = 5, npc2 = 5)

antonvsdata/amp documentation built on Jan. 8, 2020, 3:15 a.m.