samples: Format aesthetics for the biplot samples
In biplotEZ: EZ-to-Use Biplots

samples

R Documentation

Format aesthetics for the biplot samples

Description

This function allows the user to format the aesthetics for the samples.

Usage

samples (bp,  which = 1:bp$g, col = ez.col, pch = 16, cex = 1,
label = FALSE, label.name = NULL, label.col=NULL, label.cex = 0.75, 
label.side = "bottom", label.offset = 0.5,
connected=FALSE, connect.col = "black", connect.lty = 1, 
connect.lwd = 1, opacity = 1)

Arguments

`bp`	an object of class `biplot`.
`which`	a vector containing the groups or classes for which the samples should be displayed, with default `bp$g`.
`col`	the colour(s) for the samples, with default `blue`.
`pch`	the plotting character(s) for the samples, with default `16`.
`cex`	the character expansion(s) for the samples, with default `1`.
`label`	a logical value indicating whether the samples should be labelled, with default `FALSE`. Alternatively, specify `"ggrepel"` for non-overlapping placement of labels.
`label.name`	a vector of the same length as `which` with label names for the samples, with default `NULL`. If `NULL`, the `rownames(bp)` are used. Alternatively, a custom vector of length `n` should be used.
`label.col`	a vector of the same length as `which` with label colours for the samples, with default as the same colour of the sample points.
`label.cex`	a vector of the same length as `which` with label text expansions for the samples, with default `0.75`.
`label.side`	the side at which the label of the plotted point appears, with default `bottom`. Note that unlike the argument `pos` in `text()`, options are "`bottom`", "`left`", "`top`", "`right`" and not `1`, `2`, `3`, `4`.
`label.offset`	the offset of the label from the plotted point. See `?text` for a detailed explanation of the argument `offset`.
`connected`	a logical value indicating whether samples are connected in order of rows of the data matrix, with default `FALSE`.
`connect.col`	the colour of the connecting line, with default `black`.
`connect.lty`	the line type of the connecting line, with default `1`.
`connect.lwd`	the line width of the connecting line, with default `1`.
`opacity`	the opacity level of the plotted points, with default `1` for an opaque point.

Details

The arguments which, col, pch and cex are based on the specification of group.aes or classes. If no groups are specified, a single colour, plotting character and / or character expansion is expected. If g groups are specified, vectors of length g is expected, or values are recycled to length g.

The arguments label, label.cex, label.side and label.offset are based on the sample size n. A single value will be recycled n times or a vector of length n is expected.

Value

The object of class biplot will be appended with a list called samples containing the following elements:

`which`	a vector containing the groups or classes for which the samples (and means) are displayed.
`col`	the colour(s) of the samples.
`pch`	the plotting character(s) of the samples.
`cex`	the character expansion(s) of the plotting character(s) of the samples.
`label`	a logical value indicating whether samples are labelled.
`label.name`	the label names of the samples.
`label.col`	the label colours of the samples.
`label.cex`	the label text expansions of the samples.
`label.side`	the side at which the label of the plotted point appears..
`label.offset`	the offset of the label from the plotted point.
`connected`	a logical value indicating whether samples are connected in order of the rows of the data matrix.
`connect.col`	the colour of the connecting line.
`connect.lty`	the line type of the connecting line.
`connect.lwd`	the line width of the connecting line.
`opacity`	the opacity level of the plotted points.

Examples

biplot(iris[,1:4]) |> PCA() |> samples(col="purple",pch=15, opacity=0.5) |> plot()
biplot(iris[,1:4]) |> PCA() |> 
  samples(col="purple",pch=NA, opacity=0.5, label = TRUE) |> plot()
biplot(iris[,1:4]) |> PCA() |> 
  samples(col="purple",pch=NA, opacity=0.5, label = TRUE, 
          label.name = paste("s:",1:150, sep="")) |> 
  plot()
biplot(iris[,1:4]) |> PCA() |> 
  samples(col="purple",pch=NA, opacity=0.5, label = "ggrepel") |> plot()

biplotEZ documentation built on April 4, 2025, 2:20 a.m.