plotSphereIntensity {cydar} | R Documentation

## Plot cell or hypersphere data

### Description

Visualize cells or hyperspheres in low-dimensional space, coloured by marker intensities or log-fold changes.

### Usage

    plotSphereIntensity(x, y, intensity, irange=NULL,
        col.range=viridis(100), pch=16, ...)

    # Deprecated - all parameters passed to plotCellIntensity.
    plotCellIntensity(...)

### Arguments

`x, y` | A numeric vector of coordinates for each hypersphere.
`intensity` | A numeric vector specifying the marker intensities for each hypersphere.
`irange` | A numeric vector of length 2, specifying the upper and lower bound for the intensities.
`col.range` | A vector of colours specifying the colour scale to be used for increasing intensity. More values represent a higher-resolution scale.
`pch, ...` | Additional arguments to pass to `plot`.

### Details

Each hypersphere is represented by a point in the two-dimensional embedding, colored using the viridis colour scheme, i.e., purple (low intensity) to green (medium) to yellow (high). If `irange` is not `NULL`, extreme values in `intensity` will be winsorized to lie within `irange`. This preserves the resolution of colours for smaller changes at low intensities. Users should consider using `intensityRanges` to define appropriate values of `irange` for each marker.

### Value

A plot of the low-dimensional embedding of the hypersphere locations is made on the current graphics device. A vector of colours equal to `col.range` is returned, containing the colour gradient used for the intensities. The vector names contain the numeric values associated with each colour. This can be used to construct a colour bar with `createColorBar`.

### Author(s)

Aaron Lun

### See Also

`viridis`, `intensityRanges`, `createColorBar`

### Examples

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

    # Intensity plot and colour bar.
    intensities <- rgamma(100, 2, 2)
    out <- plotSphereIntensity(x, y, intensities)

    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, "Intensity", cex=1.2)

[Package cydar version 1.10.0 Index]