plot.DiffusionMap {destiny} | R Documentation

## 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 = 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, ...)

### 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)
`new_data` | A data set in the same format as `x` that is used to create `new_dcs <- dm_predict(dif, new_data)`
`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: `cluster_louvain` if igraph is installed)
`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. A vector is also possible. (default: red)
`pal` | Palette used to map the `col` vector to colors. (default: use `hcl.colors` for continuous and `palette()` for discrete data)
`pal_new` | Palette used to map the `col_new` vector to colors. (default: see `pal` argument)
`...` | Parameters passed to plot, scatterplot3d, or plot3d (if `interactive == TRUE`)
`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`, a `list(from = c(a, b), to = c(c, d))`), or an array of shape from|to \times dims \times min|max, i.e. 2 \times length(dims) \times 2. In case of 2d plotting, it should take and return a ggplot2 object.

### Details

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

### Value

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

### Examples

    data(guo)
    plot(DiffusionMap(guo))

[Package destiny version 3.1.0 Index]