plotICA {psichomics}R Documentation

Create multiple scatterplots from ICA

Description

Create multiple scatterplots from ICA

Usage

plotICA(ica, components = seq(10), groups = NULL, ...)

Arguments

ica

Object resulting from performICA()

components

Numeric: independent components to plot

groups

Matrix: groups to plot indicating the index of interest of the samples (use clinical or sample groups)

...

Arguments passed on to pairsD3::pairsD3

group

a optional vector specifying the group each observation belongs to. Used for tooltips and colouring the observations.

subset

an optional vector specifying a subset of observations to be used for plotting. Useful when you have a large number of observations, you can specify a random subset.

labels

the names of the variables (column names of x used by default).

cex

the magnification of the plotting symbol (default=3)

width

the width (and height) of the plot when viewed externally.

col

an optional (hex) colour for each of the levels in the group vector.

big

a logical parameter. Prevents inadvertent plotting of huge data sets. Default limit is 10 variables, to plot more than 10 set big=TRUE.

theme

a character parameter specifying whether the theme should be colour colour (default) or black and white bw.

opacity

numeric between 0 and 1. The opacity of the plotting symbols (default 0.9).

tooltip

an optional vector with the tool tip to be displayed when hovering over an observation. You can include basic html.

leftmar

space on the left margin

topmar

space on the bottom margin

Value

Multiple scatterplots as a pairsD3 object

See Also

Other functions to analyse independent components: performICA()

Examples

data <- scale(USArrests)
ica  <- fastICA::fastICA(data, n.comp=4)
plotICA(ica)

# Colour by groups
groups <- NULL
groups$sunny <- c("California", "Hawaii", "Florida")
groups$ozEntrance <- c("Kansas")
groups$novel <- c("New Mexico", "New York", "New Hampshire", "New Jersey")
plotICA(ica, groups=groups)
[Package psichomics version 1.20.2 Index]