multiIntHist: multiIntHist

In cydar: Using Mass Cytometry for Differential Abundance Analyses

Description

Generate intensity histograms from multiple batches.

Usage

multiIntHist(collected, cols=NULL, xlab="Intensity", ylab="Density",
    lwd=2, lty=1, pch=16, cex=2, ...) 

Arguments

collected	A list of numeric vectors, where each vector contains intensities for a given marker from all cells of a single batch.
cols	A vector of R colours of the same length as collected, to be used in colouring the histograms.
xlab, ylab	Strings specifying the x- and y-axis labels.
lwd, lty	Parameters for plotting the histogram traces.
pch, cex	Parameters for plotting the frequency of zeroes.
...	Other arguments to pass to plot.

Details

A histogram is constructed for the set of intensities from each batch, and the histogram outline is plotted with the specified parameters. The frequency of intensities at zero (or negative values) is indicated with a single point at an intensity of zero. This ensures that the number of events at zero and small non-zero intensities can be distinguished.

The process is repeated for all batches so that intensity distributions can be compared between batches. If cols=NULL, the rainbow colour palette is automatically used to generate the colour for each batch. Some small jitter is added to the zero points so that they do not completely overlap each other.

Value

Histogram traces representing the intensity distributions are produced on the current graphics device.

Author(s)

Aaron Lun

See Also

normalizeBatch

Examples

multiIntHist(list(rgamma(1000, 1, 1), rgamma(1000, 2, 1), rgamma(1000, 1, 2)))

cydar documentation built on April 17, 2021, 6:01 p.m.