plot.som {som}

Visualizing a SOM

Description

Plot the SOM in a 2-dim map with means and sd bars.

Usage

## S3 method for class 'som'
plot(x, sdbar=1, ylim=c(-3, 3), color=TRUE,
ntik=3, yadj=0.1, xlab="", ylab="", ...)

Arguments

x

a som object

sdbar

the length of sdbar in sd, no sdbar if sdbar=0

ylim

the range of y axies in each cell of the map

color

whether or not use color plotting

ntik

the number of tiks of the vertical axis

yadj

the proportion used to put the number of obs

xlab

x label

ylab

y label

...

other options to plot

Note

This function is not cleanly written. The original purpose was to mimic what GENECLUSTER does. The ylim is hardcoded so that only standardized data could be properly plotted.

There are visualization methods like umat and sammon in SOM\_PAK3.1, but not implemented here.

Author(s)

Jun Yan <[e-mail]>

Examples

foo <- som(matrix(rnorm(1000), 250), 3, 5)
plot(foo, ylim=c(-1, 1))