PlotEmbed | R Documentation |
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.
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, ... )
embed |
The embedding from |
value |
The column of |
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 |
sdsv, sdsr, sdsg, sdsb |
Passed to |
clust |
Cluster labels (used as a factor) |
nbin, maxDens, fdens |
Parameters of density calculation, see |
limit |
Low/high offset for |
alpha |
Default alpha value of points |
fsom |
FlowSOM object |
data |
Data matrix, taken from |
col |
Overrides the computed point colors with exact supplied colors. |
cluster.colors |
Function to generate cluster colors, default |
expression.colors |
Function to generate expression color scale, default |
na.color |
Color to assign to |
plotf |
Plot function, defaults to |
... |
Extra params passed to the plot function |
EmbedSOM::PlotEmbed(cbind(rnorm(1e5),rnorm(1e5)))
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.