plotSphereLogFC {cydar}R Documentation

Plot changes in hypersphere abundance

Description

Visualize hyperspheres in low-dimensional space, coloured by log-fold change in abundance for each hypersphere.

Usage

plotSphereLogFC(x, y, logFC, max.logFC=NULL, zero.col=0.8, 
    length.out=100, pch=16, ...)

# Deprecated - all arguments passed to plotSphereLogFC.
plotCellLogFC(...)

Arguments

x, y

A numeric vector of coordinates for each hypersphere.

logFC

A numeric vector of log-fold changes for each hypersphere.

max.logFC

A numeric scalar specifying the maximum absolute log-fold change.

zero.col

A numeric scalar between 0 and 1, specifying the greyscale intensity to represent a log-fold change of zero.

length.out

An integer scalar specifying the resolution of the colour bar.

pch, ...

Additional arguments to pass to plot.

Details

Each hypersphere is represented by a point in the two-dimensional embedding, coloured from blue (negative log-FC) to grey (zero log-FC) to red (positive log-FC). The darkness of the grey colour is set with zero.col.

If max.logFC is not NULL, extreme values in logFC are winsorized to lie within [-max.logFC, max.logFC]. This preserves the resolution of colours for smaller log-fold changes.

Value

A plot of the low-dimensional embedding of the hypersphere locations is made on the current graphics device. A vector of colours of length length.out is returned, containing the colour gradient used for the log-fold changes. The vector names contains the numeric values associated with each colour. This can be used to construct a colour bar with createColorBar.

Author(s)

Aaron Lun

See Also

createColorBar

Examples

# Making up some coordinates.
x <- rnorm(100)
y <- rnorm(100) 

# Log-FC plot and colour bar.
logFC <- rnorm(100)
out <- plotSphereLogFC(x, y, logFC)

out <- plotSphereLogFC(x, y, logFC, max.logFC=0.5)
plot(0,0, type="n", axes=FALSE, ylab="", xlab="", ylim=c(-1, 1), xlim=c(-1, 0.5))
createColorBar(out) 
text(-0.6, 0, srt=90, "Log-FC", cex=1.2)

[Package cydar version 1.6.1 Index]