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

In EmbedSOM: Fast Embedding Guided by Self-Organizing Map

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

EmbedSOM documentation built on July 5, 2022, 5:14 p.m.