destiny (version 2.0.4)

plot.DiffusionMap: 3D or 2D plot of diffusion map

Description

If you want to plot the eigenvalues, simply plot(eigenvalues(dm)[start:end], ...)

Usage

plot.DiffusionMap(x, dims, new_dcs = NULL, col = NULL, col_by = NULL,
  col_limits = NULL, col_new = "red", pal = NULL, ..., mar = 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) NULL)
# S4 method for DiffusionMap,numeric
plot(x, y, ...)
# S4 method for DiffusionMap,missing
plot(x, y, ...)

Arguments

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 y and plotted. (default: no more points)

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: par('fg'))

col_by

Specify a dataset(x) or phenoData(dataset(x)) column to use as color

col_limits

If col is a continuous (=double) vector, this can be overridden to map the color range differently than from min to max (e.g. specify c(0, 1))

col_new

If new_dcs is given, it will take on this color. (default: red)

pal

Palette used to map the col vector to colors. (default: use cube_helix for continuous and palette() for discrete data)

...

Parameters passed to plot, scatterplot3d, or plot3d (if interactive == TRUE)

mar

Bottom, left, top, and right margins (default: par(mar))

ticks

logical. If TRUE, show axis ticks (default: FALSE)

axes

logical. If TRUE, draw plot axes (default: Only if ticks is TRUE)

box

logical. If TRUE, draw plot frame (default: TRUE or the same as axes if specified)

legend_main

Title of legend. (default: nothing unless col_by is given)

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 col_by is given or col is given and a vector to be mapped)

consec_col

If col or col_by refers to an integer column, with gaps (e.g. c(5,0,0,3)) use the palette color consecutively (e.g. c(3,1,1,2))

col_na

Color for NA in the data. specify NA to hide.

plot_more

Function that will be called while the plot margins are temporarily changed (its p argument is the rgl or scatterplot3d instance or NULL, its rescale argument is NULL or of the shape list(from = c(a, b), to = c(c,d)))

Value

The return value of the underlying call is returned, i.e. a scatterplot3d or rgl object.

Details

If you specify negative numbers as diffusion components (e.g. plot(dm, c(-1,2))), then the corresponding components will be flipped.

Examples

data(guo)
plot(DiffusionMap(guo))