plot.smacof {smacof}

2D SMACOF plots

Description

These methods provide various 2D plots for SMACOF models.

Usage

## S3 method for class 'smacof'
plot(x, plot.type = "confplot", plot.dim = c(1,2), sphere = TRUE, 
                      bubscale = 1, col = 1, label.conf = list(label = TRUE, pos = 3, 
                      col = 1, cex = 0.8), hull.conf = list(hull = FALSE, col = 1, 
                      lwd = 1, ind = NULL), shepard.x = NULL, identify = FALSE, 
                      type = "p", pch = 20, cex = 0.5, asp = 1, main, xlab, ylab, 
                      xlim, ylim, col.hist = NULL, ...)

## S3 method for class 'smacofR'
plot(x, plot.type = "confplot", what = c("both", "columns", "rows"), 
                       plot.dim = c(1,2), col.rows = hcl(0), col.columns = hcl(240), 
                       label.conf.rows = list(label = TRUE, pos = 3, 
                       col = hcl(0, l = 50), cex = 0.8), 
                       label.conf.columns = list(label = TRUE, pos = 3, 
                       col = hcl(240, l = 50), cex = 0.8),  
                       shepard.x = NULL, col.dhat = NULL, type = "p", pch = 20,
                       cex = 0.5, asp = 1, main, xlab, ylab, xlim, ylim, ...)

## S3 method for class 'smacofID'
plot(x, plot.type = "confplot", plot.dim = c(1,2), bubscale = 1, 
                        col = 1, label.conf = list(label = TRUE, pos = 3, col = 1, 
                        cex = 0.8), identify = FALSE, type = "p", pch = 20,  cex = 0.5, 
                        asp = 1, plot.array, main, xlab, ylab, xlim, ylim, ...)

Arguments

x

Object of class "smacof", "smacofR", and "smacofID" (see details)

plot.type

String indicating which type of plot to be produced: "confplot", "resplot" "Shepard", "stressplot", "bubbleplot" "histogram" (see details)

plot.dim

Vector with dimensions to be plotted.

main

Plot title.

xlab

Label of x-axis.

ylab

Label of y-axis.

xlim

Scale x-axis.

ylim

Scale y-axis.

type

What type of plot should be drawn (see also plot).

pch

Plot symbol.

cex

Symbol size.

asp

Aspect ratio.

col

Point color.

sphere

In case of spherical smacof, whether sphere should be plotted or not.

bubscale

Scaling factor (size) for the bubble plot.

label.conf

List with arguments for plotting the labels of the configurations in a configuration plot (logical value whether to plot labels or not, label position, label color). If pos = 5 labels are placed away from the nearest point.

hull.conf

Option to add convex hulls to a configuration plot. Hull index needs to be provided.

shepard.x

Shepard plot only: original data (e.g. correlation matrix) can be provided for plotting on x-axis.

identify

If TRUE, the identify() function is called internally that allows to add configuration labels by mouse click.

what

For unfolding only: Whether row coordinates, column coordinates, or both should be plotted.

col.rows

Row colors in unfolding configuration plot.

col.columns

Column colors in unfolding configuration plot.

col.dhat

Shepard plot only: color specification of the dhats. For row conditional transformations in unfolding a vector of the length of the number of rows should be specified.

label.conf.rows

List with arguments for plotting the labels of the row configurations in an unfolding configuration plot (logical value whether to plot labels or not, label position, label color).

label.conf.columns

List with arguments for plotting the labels of the columns configurations in an unfolding configuration plot (logical value whether to plot labels or not, label position, label color).

col.hist

Color of the borders of the histogram.

plot.array

Array arrangements of plots for individual difference models (see details).

...

Further plot arguments passed: see plot for detailed information.

Details

mds() and smacofSym() create an object of class "smacof", unfolding(), prefscal(), and smacofRect() produce "smacofR", and smacofIndDiff() generates "smacofID".

Plot description:

- Configuration plot (plot.type = "confplot"): Plots the MDS configuration.

- Residual plot (plot.type = "resplot"): Plots the disparities (d-hats) distances against the fitted distances.

- Shepard diagram (plot.type = "Shepard"): Diagram with the observed dissimilarities against the fitted distances including (isotonic) regression line.

- Stress decomposition plot (plot.type = "stressplot"): Plots the stress contribution in of each observation. Note that it rescales the stress-per-point (SPP) from the corresponding smacof function to percentages (sum is 100). The higher the contribution, the worse the fit.

- Bubble plot (plot.type = "bubbleplot", not available for rectangular SMACOF): Combines the configuration plot with the point stress contribution. The larger the bubbles, the worse the fit.

- Histogram (plot.type = "histogram": gives a weighted histogram of the dissimilarities. For optional arguments, see wtd.hist.

For smacofIndDiff() the residual plot, Shepard diagram, and stress plot are based on the sum of the residuals across individuals/ways. The configuration plot represents the group stimulus space (i.e., joint configuration). If plot.array is not specified, it produces a Shepard plot of the distances summed across subjects, if plot.array = 0 it produces a sqrt(nsubjects) times sqrt(nsubjects) array of graph panels, if plot.array = 3 it produces 3x3 arrays of graph panels, if plot.array = c(2, 3) it produces 2x3 arrays of graph panels, and if plot.array = c(3, 2, 5) produces 3x2 arrays of panels (only the first two values are used).

See Also

plot.procr

Examples

## 2D plots for simple MDS
data(trading)
res <- mds(trading)
plot(res, plot.type = "confplot")
plot(res, plot.type = "confplot", label.conf = list(pos = 5)) ## avoid overlapping labels
plot(res, plot.type = "Shepard")
plot(res, plot.type = "stressplot")
plot(res, plot.type = "resplot")
plot(res, plot.type = "bubbleplot")
plot(res, plot.type = "histogram")

## Add convex hulls to configuration plot
r <- cor(PVQ40, use = "pairwise.complete.obs")
diss <- sim2diss(r, method = "corr") 
res <- mds(delta = diss, type = "ordinal") 
codes <- substring(colnames(PVQ40), 1, 2)  ## supplementary variable
plot(res, hull.conf = list(hull = TRUE, ind = codes, col = "coral1", lwd = 2))

## Shepard plots
ekmanD <- sim2diss(ekman)
fit1 <- mds(ekmanD, type = "ordinal")
plot(fit1, plot.type = "Shepard")
plot(fit1, plot.type = "Shepard", shepard.x = ekman)  ## original data on x-axis

## Joint configuration plot and row/column stressplots for unfolding
data(breakfast)
res <- unfolding(breakfast)
plot(res, plot.type = "confplot")
plot(res, plot.type = "stressplot")