PlotEmbed: Helper function for plotting the embedding

In EmbedSOM: Fast Embedding Guided by Self-Organizing Map

Helper function for plotting the embedding

Description

Convenience plotting function. Takes the embed matrix which is the output of EmbedSOM(), together with a multitude of arguments that set how the plotting is done.

Usage

PlotEmbed(
  embed,
  value = 0,
  red = 0,
  green = 0,
  blue = 0,
  fr = PlotId,
  fg = PlotId,
  fb = PlotId,
  fv = PlotId,
  powr = 0,
  powg = 0,
  powb = 0,
  powv = 0,
  sdsr = 1,
  sdsg = 1,
  sdsb = 1,
  sdsv = 1,
  clust = NULL,
  nbin = 256,
  maxDens = NULL,
  fdens = sqrt,
  limit = NULL,
  alpha = NULL,
  fsom,
  data,
  col,
  cluster.colors = ClusterPalette,
  expression.colors = ExpressionPalette,
  na.color = grDevices::rgb(0.75, 0.75, 0.75, if (is.null(alpha)) 0.5 else alpha/2),
  plotf = PlotDefault,
  ...
)

Arguments

embed	The embedding from EmbedSOM(), or generally any 2-column matrix of coordinates
value	The column of data to use for coloring the plotted points
red, green, blue	The same, for individual RGB components
fv, fr, fg, fb	Functions to transform the values before they are normalized
powv, powr, powg, powb	Passed to corresponding NormalizeColor() calls as pow
sdsv, sdsr, sdsg, sdsb	Passed to NormalizeColor() as sds
clust	Cluster labels (used as a factor)
nbin, maxDens, fdens	Parameters of density calculation, see PlotData()
limit	Low/high offset for NormalizeColor() (obsolete&ignored, will be removed)
alpha	Default alpha value of points
fsom	FlowSOM object
data	Data matrix, taken from fsom parameter by default
col	Overrides the computed point colors with exact supplied colors.
cluster.colors	Function to generate cluster colors, default ClusterPalette()
expression.colors	Function to generate expression color scale, default ExpressionPalette()
na.color	Color to assign to NA values
plotf	Plot function, defaults to graphics::plot() slightly decorated with pch='.', cex=1
...	Extra params passed to the plot function

Examples

EmbedSOM::PlotEmbed(cbind(rnorm(1e5),rnorm(1e5)))

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