plotDR: Plotting tool for two and three dimensional data

In RDRToolbox: A package for nonlinear dimension reduction with Isomap and LLE.

Description

Creates two and three dimensional plots of (labeled) data. It uses the library "rgl" for rotatable 3D scatterplots.

Usage

plotDR(data, labels, axesLabels=c("x","y","z"), legend=FALSE, text, col, pch, ...)

Arguments

data	matrix with values to be plotted (rows correspond to samples, columns to features)
labels	vector containing labels of the classes within the data (optional)
axesLabels	vector containing labels for the axes of the plot
legend	logical value whether to automatically insert a legend into the plot
text	vector with (short) labels for each point (optional)
col	character vector of colours for each class (optional); see colors() to display a list of available colours
pch	character or integer value specifying the symbol when plotting points (see ?par or ?points for more info)
...	other common R plot parameters like for example las, cex or font to further customize the plot (see ?par for possible arguments); some parameters may only work with two dimensional plots

Details

It colours the data points according to given class labels (max. six classes when using default colours). A legend will be printed in the R console by default (for three dimensional plots, a legend is not supported).

Author(s)

Christoph Bartenhagen

Examples

## plot a two dimensional LLE embedding of a 1.000 dimensional dataset
d = generateData(samples=20, genes=1000, diffgenes=100, blocksize=10)
d_low = LLE(data=d[[1]], dim=2, k=5)
plotDR(data=d_low, labels=d[[2]])

## plot a two dimensional LLE embedding of a 1.000 dimensional dataset
## add axis labels, a legend and plot a text for each sample
d = generateData(samples=20, genes=1000, diffgenes=100, blocksize=10)
d_low = LLE(data=d[[1]], dim=2, k=5)
text = letters[1:20]
plotDR(data=d_low, labels=d[[2]], axesLabels=c("first component", "second component"), text=text, legend=TRUE)
## manually add a legend to the plot
plotDR(data=d_low, labels=d[[2]], axesLabels=c("first component", "second component"), text=text)
legend("topright", legend=c("class 1","class 2"), col=c("black", "red"), pch=1)

RDRToolbox documentation built on Nov. 8, 2020, 11:10 p.m.