kohonen (version 2.0.5)

plot.kohonen: Plot kohonen object

Description

Plot self-organising map, obtained from function kohonen. Several types of plots are supported.

Usage

## S3 method for class 'kohonen':
plot(x, type = c("codes", "changes", "counts",
                 "dist.neighbours", "mapping", "property", "quality"),
     classif = NULL, labels = NULL, pchs = NULL, main = NULL,
     palette.name = heat.colors, ncolors, bgcol = NULL,
     zlim = NULL, heatkey = TRUE, property, contin,
     whatmap = NULL, codeRendering = NULL, keepMargins = FALSE,
     heatkeywidth = .2, ...)

Arguments

x

kohonen object.

type

type of plot. (Wow!)

classif

classification object, as returned by predict.kohonen, or vector of unit numbers. Only needed if type equals "mapping" and "counts".

labels

labels to plot when type equals "mapping".

pchs

symbols to plot when type equals "mapping".

main

title of the plot.

palette.name

colors to use as unit background for "codes", "counts", "prediction", "property", and "quality" plotting types.

ncolors

number of colors to use for the unit backgrounds. Default is 20 for continuous data, and the number of distinct values (if less than 20) for categorical data.

bgcol

optional argument to colour the unit backgrounds for the "mapping" and "codes" plotting type. Defaults to "gray" and "transparent" in both types, respectively.

zlim

optional range for color coding of unit backgrounds.

heatkey

whether or not to generate a heatkey at the left side of the plot in the "property" and "counts" plotting types.

property

values to use with the "property" plotting type.

contin

whether or not the data should be seen as discrete (i.e. classes) or continuous in nature. Only relevant for the colour keys of plots of supervised networks.

whatmap

For supersom maps and a "codes" plot: what maps to show.

codeRendering

How to show the codes. Possible choices: "segments", "stars" and "lines".

keepMargins

if FALSE (the default), restore the original graphical parameters after plotting the kohonen map. If TRUE, one retains the map coordinate system so that one can add symbols to the plot, or map unit numbers using the <

heatkeywidth

width of the colour key; the default of 0.2 should work in most cases but in some cases, e.g. when plotting multiple figures, it may need to be adjusted.

...

other graphical parameters, e.g. colours of labels, or plotting symbols, in the "mapping" plotting type.

Details

Several different types of plots are supported: [object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

See Also

som, bdk, xyf

Examples

data(wines)
set.seed(7)

kohmap <- xyf(scale(wines), classvec2classmat(wine.classes),
              grid = somgrid(5, 5, "hexagonal"), rlen=100)
plot(kohmap, type="changes")
plot(kohmap, type="codes", main = c("Codes X", "Codes Y"))
plot(kohmap, type="counts")
plot(kohmap, type="quality")
plot(kohmap, type="mapping", 
     labels=wine.classes, col=wine.classes+1,
     main="mapping plot")
xyfpredictions <- classmat2classvec(predict(kohmap)$unit.predictions)
bgcols <- c("gray", "pink", "lightgreen")
plot(kohmap, type="mapping", col=wine.classes+1,
     pchs=wine.classes, bgcol=bgcols[as.integer(xyfpredictions)], 
     main="another mapping plot")