plot.anacor: Plots for anacor solution

Description

These functions produce various plots for objects of class "anacor"

Usage

# S3 method for anacor
plot(x, plot.type = "jointplot", plot.dim = c(1,2), col.row = "cadetblue", 
col.column = "coral1", catlabels = list(label.row = TRUE, label.col = TRUE, 
col.row = "cadetblue", col.column = "coral1", cex = 0.8, pos = 3),
legpos = "top", arrows = c(FALSE, FALSE), conf = 0.95, wlines = 0, asp = 1, pch = 20, 
xlab, ylab, main, type, xlim, ylim, cex.axis2, ...)

Arguments

Object of class "anacor"

plot.type

Type of plot to be produced (details see below): 2-D and 3-D for "jointplot", "rowplot", and "colplot"; 2-D for "regplot", "graphplot", "benzplot", "transplot", and "orddiag".

plot.dim

Vector of length 2 with Dimensions to be plotted. For "regplot" a single value should be provided, for "transplot" more than two dimensions are allowed, and for "benzplot" this argument is ignored.

col.row

Color row categories

col.column

Color column categories

catlabels

Various parameter settings for labels

legpos

Position of the legend (for "transplot" only)

conf

Ellipsoid confidence level for "jointplot", "rowplot", and "colplot", assuming that the ellipse where computed in anacor(). If NULL, no ellipsoids are drawn.

arrows

Whether arrows from the origin to the row scores (first element) or column scores (second element) should be drawn.

wlines

For "graphplot" only: If 0, all lines are of the same thickness. For values > 0 line thickness indicates the strength of the pull

asp

Aspect ratio.

pch

Symbol for plotting points.

xlab

Label x-axis.

ylab

Label y-axis.

xlim

Scale x-axis.

ylim

Scale y-axis.

main

Plot title.

type

Whether points, lines or both should be plotted; for "regplot" and "transplot" only.

cex.axis2

For "regplot" only. The magnification to be used for the category labels in the scaled solution relative to the current setting of cex.

…

Additional graphical parameters.

Details

The following plot types are provided: "jointplot" plots row and column scores into the same device, "rowplot" and "colplot" plot the row scores and column scores, respectively, in separate devices. For these types of plots 3-dimensional versions are provided. The graph plot is an unlabeled version of the joint plot where the points are connected by lines. Options are provided (wlines) to steer the line thickness indicating the connection strength.

The regression plot ("regplot") provides two plots. First, the unscaled solution is plotted. A frequency grid for the row categories (x-axis) and column categories (y-axis) is produced. The regression line is based on the category weighted means of the relative frequencies: the blue line on the column-wise means on the x-axis and the column category on the y-axis, the red line is based on the row categories on the x-axis and the row-wise means on the y-axis. In a second device the scaled solution is plotted. The frequency grid is determined by the row scores (x-axis) and the column scores(y-axis). Now, instead of the row/column categories, the column scores (black line y-axis) and the row scores (red line x-axis) are used.

The transformation plot ("transplot") plots the row/column categories against the row/column scores. The Benzecri plot ("benzplot") plots the observed distances against the fitted distances. It is assumed that the CA result is Benzecri scaled. The ordination diagram ("orddiag") for CCA produces a joint plot and includes the column and row covariates based on intraset correlations.

References

De Leeuw, J. and Mair, P. (2009). Simple and Canonical Correspondence Analysis Using the R Package anacor. Journal of Statistical Software, 31(5), 1-18. https://www.jstatsoft.org/v31/i05/

Examples

Run this code

# NOT RUN {
## symmetric map
data(tocher)
res <- anacor(tocher)
plot(res, conf = NULL, main = "Symmetric Map")

## simple CA on Tocher data, asymmetric coordinates
res <- anacor(tocher, scaling = c("standard", "Benzecri"))
res

## Regression plots using Glass data
data(glass)
res <- anacor(glass)
plot(res, plot.type = "regplot", xlab = "fathers occupation", ylab = "sons occupation")


## Benzecri Plots for bitterling data
data(bitterling)
res1 <- anacor(bitterling, ndim = 2, scaling = c("Benzecri", "Benzecri"))
res2 <- anacor(bitterling, ndim = 5, scaling = c("Benzecri", "Benzecri"))
res2
plot(res1, plot.type = "benzplot", main = "Benzecri Distances (2D)")
plot(res2, plot.type = "benzplot", main = "Benzecri Distances (5D)")

## Column score plot,transformation plot, and ordination diagram for canonical CA
data(maxwell)
res <- anacor(maxwell$table, row.covariates = maxwell$row.covariates, 
scaling = c("Goodman", "Goodman"))
res
plot(res, plot.type = "colplot", xlim = c(-1.5,1), conf = NULL)
plot(res, plot.type = "transplot", legpos = "topright")
plot(res, plot.type = "orddiag")
# }