plotPCA-methods: Ploting PCA

In isglobal-brge/rexposome: Exposome exploration and outcome data analysis

Ploting PCA

Description

Methdo to draw a plot for PCA contained in an ExposomePCA

Usage

plotPCA(
  object,
  set,
  cmpX = 1,
  cmpY = 2,
  show.exposures = FALSE,
  show.samples = FALSE,
  phenotype
)

Arguments

object	An onbject of class ExposomePCA
set	Group ("all", "samples" or "exposures") taht will be ploted.
cmpX	(default: 1) component to be placed at X axis
cmpY	(default: 2) component to be placed at Y axis
show.exposures	(default: FALSE) If set to true, labels indicating the exposures are shown.
show.samples	(default: FALSE) If set to true, labels indicating the samples are shown.
phenotype	If set is set to "samples" can be used to color samples by phenotype

Value

An object of class ggplot or an object of class gtable if argument set was set to "all".

See Also

pca to compite PCA on an ExposomeSet, plotPCA to plot the PCA, ExposomePCA as main class

Examples

data("exposome")
epca <- pca(expo[3:7, 1:100])
# A grid with exposures space, samples space and explained variance
plotPCA(epca, set = "all")
# Only exposures space
plotPCA(epca, set = "exposures") + ggplot2::theme(legend.position = "bottom")
# Only samples space
plotPCA(epca, set = "samples")
# Only samples space but coloured by phenotype
plotPCA(epca, set = "samples", phenotype = "sex") +
ggplot2::theme(legend.position = "bottom")

isglobal-brge/rexposome documentation built on Feb. 4, 2023, 12:35 p.m.