PlotData {EmbedSOM} | R Documentation |
Export a data frame for plotting with marker intensities and density.
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)
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 |