mclm (version 0.2.7)

ca_help: Helpers for plotting ca objects

Description

The functions row_pcoord() and col_pcoord() retrieve the coordinates of the rows and columns of a ca object across all dimensions. The functions xlim4ca() and ylim4ca() return the range of values for the first and second dimensions.

Usage

row_pcoord(x, ...)
col_pcoord(x, ...)
xlim4ca(x, ...)
ylim4ca(x, ...)

Value

A matrix (for row_pcoord() and col_pcoord()) or a numeric vector (for xlim4ca() and ylim4ca()).

Arguments

x

An object of class ca.

...

Additional arguments (not implemented).

Functions

• row_pcoord(): Retrieve row principal coordinates for all dimensions

• col_pcoord(): Retrieve column principal coordinates for all dimensions

• xlim4ca(): Return range of first dimension for plotting

• ylim4ca(): Return range of second dimension for plotting

Details

In the output of row_pcoord(), each row corresponds to a row from the dataframe that ca::ca() was applied to, and each column corresponds to a principal component. In the output of col_pcoord(), each row corresponds to a column from the dataframe that ca::ca() was applied to, and each column corresponds to a principal component.

Examples

# traditional biplot from {ca}

library(ca)
data("author")
author_ca <- ca(author)
plot(author_ca)

# alternative plot with {mclm} tools
r_pc <- row_pcoord(author_ca)
c_pc <- col_pcoord(author_ca)
xlim <- xlim4ca(author_ca)
ylim <- ylim4ca(author_ca)
author_names <- as.factor(gsub(
                              "^.*?\\((.*?)\\)$", "\\1",
                             rownames(author), perl = TRUE))
plot(r_pc[,1], r_pc[,2], pch = 18,
    xlim = xlim, ylim = ylim, xlab = "", ylab = "",
    main = "authors and their alphabet",
    col = as.numeric(author_names))
abline(h = 0, col = "gray", lty = 3)
abline(v = 0, col = "gray", lty = 3)
text(c_pc[,1], c_pc[,2], colnames(author), col = "gray")
legend("topright",
       legend = levels(author_names),
       pch = rep(18, length(levels(author_names))),
       col = 1:length(levels(author_names)),
       title = "authors")