Plotting a PCoA

Source: R/plotgg.r

Function for plotting results of PCO.

# S3 method for PCO
plotgg(x, components = c("PCo1", "PCo2"), shape = NULL,
  col = NULL, fill = NULL, point_size = 2)

Arguments

x

A PCO 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 PCO 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 PCO 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 PCO object.
point_size

point_size

Value

A ggplot2 object of the PCoA plot.

See also

PCO

Examples

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

# distfun <- function(x) vegan::vegdist(x,method="bray") #requires vegan package
distfun <- dist

Dat.pco <- PCO(Dat,dim=2,distfun=distfun)
plotgg(Dat.pco)
plotgg(Dat.pco,shape="fraction",point_size=3)
plotgg(Dat.pco,shape="fraction",col="accession",point_size=4)