PlotData: Export a data frame for plotting with marker intensities and...
In EmbedSOM: Fast Embedding Guided by Self-Organizing Map

PlotData

R Documentation

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,
  pow = 0,
  sds = 1,
  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
`pow`, `sds`	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