PlotEmbed {EmbedSOM} | R Documentation |
Takes the 'embed' object which is the output of EmbedSOM, together with a multitude of arguments that override how the plotting is done.
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, ...)
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 |
EmbedSOM::PlotEmbed(cbind(rnorm(1e5),rnorm(1e5)))