EmbedSOM (version 1.9)

PlotEmbed: Helper function for plotting the embedding

Description

Takes the 'embed' object which is the output of EmbedSOM, together with a multitude of arguments that override 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, clust = NULL, nbin = 256,
  maxDens = NULL, fdens = sqrt, limit = 0.01, 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

value

The column of data to use for plotting the value

red, green, blue

The same for RGB components

fv, fr, fg, fb

Functions to transform the values before they are normalized

powv, powr, powg, powb

Adjustments of the value plotting

clust

Cluster labels (used as factor)

nbin, maxDens, fdens

Parameters of density calculation, see PlotData

limit

Low/high offset for NormalizeColor

alpha

Default alpha value

fsom

FlowSOM object

data

Data matrix, taken from fsom parameter by default

col

Different coloring, if supplied

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 slightly decorated 'graphics::plot'

...

Extra params passed to the plot function

Examples

# NOT RUN {
EmbedSOM::PlotEmbed(cbind(rnorm(1e5),rnorm(1e5)))
# }