EmbedSOM (version 1.9)

PlotData: Export a data frame for plotting with marker intensities and density.

Description

Export a data frame for plotting with marker intensities and density.

Usage

PlotData(embed, fsom, data = fsom$data, cols, names, normalize = cols,
  qlimit = 0, qlow = qlimit, qhigh = 1 - qlimit, pow = 0,
  vf = PlotId, density = "Density", densBins = 256,
  densLimit = NULL, fdens = sqrt)

Arguments

embed, fsom, data, cols

The embedding data, columns to select

names

Column names for output

normalize

List of columns to normalize using NormalizeColor, default all

qlimit, qlow, qhigh, pow

Parameters for the normalization

vf

Custom value-transforming function

density

Name of the density column

densBins

Number of bins for density calculation

densLimit

Upper limit of density (prevents outliers)

fdens

Density-transforming function; default sqrt