pcaEnrichment: Density plot of the principal components

Description Usage Arguments Value See Also Examples

View source: R/visualizations.R

Description

Density plot of the principal components

Usage

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pcaEnrichment(
  PCAout,
  PCx,
  PCy,
  colors = c("#0348A6", "#7AC5FF", "#C6FDEC", "#FFB433", "#FF4B20"),
  contours = TRUE,
  facet = NULL
)

Arguments

PCAout

The output of performPCA

PCx

The principal component graphed on the x-axis

PCy

The principal component graphed on the y-axis

colors

The color palette for the density plot

contours

Binary classifier to add contours to the density plot

facet

A parameter to separate the graph

Value

ggplot2 object of the results of PCA for the enrichment scores

See Also

performPCA for generating PCA results.

Examples

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ES2 <- readRDS(url(
"https://ncborcherding.github.io/vignettes/scone_enrichment_results.rds"))
PCA <- performPCA(enriched = ES2, groups = c("Type", "Cluster"))
pcaEnrichment(PCA, PCx = "PC1", PCy = "PC2", contours = TRUE)

ncborcherding/scone documentation built on Sept. 5, 2020, 1:11 a.m.