plotSphereLogFC {cydar} | R Documentation |
Visualize hyperspheres in low-dimensional space, coloured by log-fold change in abundance for each hypersphere.
plotSphereLogFC(x, y, logFC, max.logFC=NULL, zero.col=0.8, length.out=100, pch=16, ...) # Deprecated - all arguments passed to plotSphereLogFC. plotCellLogFC(...)
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 |
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.
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
.
Aaron Lun
# 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)