plotICA: Create multiple scatterplots from ICA

In nuno-agostinho/psichomics: Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation

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 diag logical, whether or not the main diagonal is plotted (scatter plot of variables against themselves).

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)

nuno-agostinho/psichomics documentation built on Feb. 11, 2024, 11:16 p.m.