plotgg.PCA: Plot a PCA

In surh/AMOR: Abundance Matrix Operations in R

Plot a PCA

Description

Function for plotting results of PCA.

Usage

## S3 method for class 'PCA'
plotgg(
  x,
  components = c("PC1", "PC2"),
  shape = NULL,
  col = NULL,
  fill = NULL,
  biplot = FALSE,
  biplot_color = "grey21",
  point_size = 2
)

Arguments

x	A PCA object.
components	Vector of length 2 indicating which components to plot.
shape	String indicating which variable to use as aestetics mapping for shape. Must correspond to a column header in the Map attribute of the PCA object.
col	String indicating which variable to use as aestetics mapping for color. Must correspond to a column header in the Map attribute of the PCA object.
fill	String indicating which variable to use as aestetics mapping for fill. Must correspond to a column header in the Map attribute of the PCA object.
biplot	Logical indicating whether the loadings should be plotted as well.
biplot_color	Color to use for the loadings in a biplot
point_size	size for the points in the plot

Value

A ggplot2 object of the PCA plot.

Author(s)

Sur from Dangl Lab.

See Also

PCA

Examples

data(Rhizo)
data(Rhizo.map)
Dat <- create_dataset(Rhizo,Rhizo.map)
Dat.pca <- PCA(Dat)

plotgg(PCA(Dat$Tab),point_size=6)
plotgg(Dat.pca,point_size=4)
plotgg(Dat.pca,shape="fraction",point_size=3)
plotgg(Dat.pca,col="accession")
plotgg(Dat.pca,col="accession",shape="fraction",point_size=4,biplot=TRUE)
p1 <- plotgg(Dat.pca,col="accession",components=c("PC2","PC3"),shape="fraction",biplot=TRUE,biplot_color="pink",point_size=6)
p1

surh/AMOR documentation built on Feb. 21, 2023, 6:31 a.m.