plot.DPT {destiny} | R Documentation |
Plots diffusion components from a Diffusion Map and the accompanying Diffusion Pseudo Time (DPT
)
plot.DPT(x, root = NULL, paths_to = integer(0L), dcs = 1:2, divide = integer(0L), w_width = 0.1, col_by = "dpt", col_path = rev(palette()), col_tip = "red", ..., col = NULL, legend_main = col_by) ## S4 method for signature 'DPT,numeric' plot(x, y, ...) ## S4 method for signature 'DPT,missing' plot(x, y, ...)
x |
A |
paths_to |
Numeric Branch IDs. Are used as target(s) for the path(s) to draw. |
dcs |
The dimensions to use from the DiffusionMap |
divide |
If |
w_width |
Window width for smoothing the path (see |
col_by |
Color by 'dpt' (DPT starting at |
col_path |
Colors for the path or a function creating n colors |
col_tip |
Color for branch tips |
... |
Graphical parameters supplied to |
col |
See |
legend_main |
See |
y, root |
Root branch ID. Will be used as the start of the DPT. (default: lowest branch ID)
(If longer than size 1, will be interpreted as |
The return value of the underlying call is returned, i.e. a scatterplot3d or rgl object for 3D plots.
data(guo_norm) dm <- DiffusionMap(guo_norm) dpt <- DPT(dm) plot(dpt) plot(dpt, 2L, col_by = 'branch') plot(dpt, 1L, 2:3, col_by = 'num_cells') plot(dpt, col_by = 'DPT3')