Plot Autofluorescence Identification Gate

This function plots the sample being used to identify intrusive autofluorescence in the single-stained controls. The input data are expected to be PCA projections of the unstained sample with an accompanying region to identify the low-autofluorescence cell region.

gate.af.identify.plot(gate.data, samp, gate.region, gate.bound.density, asp)

Arguments

gate.data

Matrix containing autofluorescence data points.

samp

Sample identifier.

gate.region

Dataframe containing region boundary information.

gate.bound.density

Density (e.g., from MASS:kde2d) information

asp

The AutoSpectral parameter list. Prepare using get.autospectral.param

Value

Saves the plot as a JPEG file in the specified directory.