clusterPlotSOMmap: Plot self-organising map

In BioMedR: Generating Various Molecular Representations for Chemicals, Proteins, DNAs, RNAs and Their Interactions

Description

Plot self-organising map

Usage

clusterPlotSOMmap(x, index = NULL, main = NULL, label = NULL, pchs = 46,
  bgcol = NULL, cols = "red", lwds = 2, keepMargins = FALSE, ...)

Arguments

x	Kohonen object.
index	The location of the user's objective data
main	Title of the plot.
label	Labels to plot.
pchs	Symbols to plot.
bgcol	Optional argument to colour the unit backgrounds for the "mapping" and "codes" plotting type. Defaults to "gray" and "transparent" in both types, respectively.
cols	A specification for the default number color.
lwds	The number width, a positive number, defaulting to 1.
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 identify function.
...	other graphical parameters.

Details

Plot self-organising map, obtained from function kohonen. shows where objects are mapped. It needs the classif argument, and a labels or pchs argument.

Value

plot mapping

Author(s)

Min-feng Zhu <[e-mail]>,

Examples

data(som.bcl)

clusterPlotSOMmap(som.bcl, pchs = 1)
idx = unique(som.bcl$unit.classif[1:80])
bgcols <- c("gray", "lightgreen")
index = rep(1, 5 * 5)
index[idx]  = 2
bgcol = bgcols[as.integer(index)]
label = c()
for (i in 1:length(idx)) {
  label[i] = length(which(som.bcl$unit.classif[1:80] == idx[i]))
  }

clusterPlotSOMmap(som.bcl, index = idx, label = label, bgcol = bgcol)

BioMedR documentation built on July 5, 2019, 9:03 a.m.