plotPC: Plot Principal component (PC) Values (variation explained)...

In andreyshabalin/ramwas: Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms

Description

The function plotPCvalues plots PC values (variation explained).
The function plotPCvectors plots PC vectors (loadings).

Usage

plotPCvalues(values, n = 40, ylim = NULL, col = "blue")
plotPCvectors(eigenvector, i, col = "blue1")

Arguments

values	Vector of PC values.
n	Number of top PCs to plot.
ylim	Numeric vectors of length 2, giving the y coordinate range. Exactly as in Plotting Parameters.
col	Color of the plotted points.
eigenvector	The i-th eigenvector. See eigen.
i	Indicates loadings of which PC to plot.

Value

This function creates a PC plot and returns nothing (NULL).

Author(s)

Andrey A Shabalin [e-mail]

See Also

See vignettes: browseVignettes("ramwas").

Examples

# Sample data
# for 1000 observations and 10 samples
m = 1000
n = 10
data = matrix(rnorm(n*m), nrow = m)

# Covariance and eigenvalue decomposition
covmat = crossprod(data)
e = eigen(covmat)

# Plot PC values
plotPCvalues(e$values)

# Plot PC vectors
plotPCvectors(e$vectors[,1], 1)
plotPCvectors(e$vectors[,2], 2)

andreyshabalin/ramwas documentation built on Sept. 27, 2021, 7:25 p.m.