plotSphereLogFC: Plot changes in hypersphere abundance

In MarioniLab/cydar: Using Mass Cytometry for Differential Abundance Analyses

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="grey80",
    left.col="blue", right.col="red",length.out=100, pch=16, ...)

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 string specifying the colour to use at a log-fold change of zero.
left.col	A string specifying the colour to use at the most negative log-fold change.
right.col	A string specifying the colour to use at the most positive log-fold change.
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 name 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)

MarioniLab/cydar documentation built on Sept. 7, 2024, 6:24 a.m.