View source: R/diffusionmap-plotting.r
plot.DiffusionMap | R Documentation |
If you want to plot the eigenvalues, simply plot(eigenvalues(dm)[start:end], ...)
plot.DiffusionMap(
x,
dims = 1:3,
new_dcs = if (!is.null(new_data)) dm_predict(x, new_data),
new_data = NULL,
col = NULL,
col_by = NULL,
col_limits = NULL,
col_new = "red",
pal = NULL,
pal_new = NULL,
...,
ticks = FALSE,
axes = TRUE,
box = FALSE,
legend_main = col_by,
legend_opts = list(),
interactive = FALSE,
draw_legend = !is.null(col_by) || (length(col) > 1 && !is.character(col)),
consec_col = TRUE,
col_na = "grey",
plot_more = function(p, ..., rescale = NULL) p
)
## S4 method for signature 'DiffusionMap,numeric'
plot(x, y, ...)
## S4 method for signature 'DiffusionMap,missing'
plot(x, y, ...)
x |
A DiffusionMap |
dims , y |
Diffusion components (eigenvectors) to plot (default: first three components; 1:3) |
new_dcs |
An optional matrix also containing the rows specified with |
new_data |
A data set in the same format as |
col |
Single color string or vector of discrete or categoric values to be mapped to colors.
E.g. a column of the data matrix used for creation of the diffusion map. (default: |
col_by |
Specify a |
col_limits |
If |
col_new |
If |
pal |
Palette used to map the |
pal_new |
Palette used to map the |
... |
Parameters passed to plot, scatterplot3d, or plot3d (if |
ticks |
logical. If TRUE, show axis ticks (default: FALSE) |
axes |
logical. If TRUE, draw plot axes (default: Only if |
box |
logical. If TRUE, draw plot frame (default: TRUE or the same as |
legend_main |
Title of legend. (default: nothing unless |
legend_opts |
Other colorlegend options (default: empty list) |
interactive |
Use plot3d to plot instead of scatterplot3d? |
draw_legend |
logical. If TRUE, draw color legend (default: TRUE if |
consec_col |
If |
col_na |
Color for |
plot_more |
Function that will be called while the plot margins are temporarily changed
(its |
If you specify negative numbers as diffusion components (e.g. plot(dm, c(-1,2))
), then the corresponding components will be flipped.
The return value of the underlying call is returned, i.e. a scatterplot3d or rgl object.
data(guo)
plot(DiffusionMap(guo))
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