plot_gr {flowGraph} | R Documentation

## Plots a cell hierarchy.

### Description

Plots a cell hierarchy given the output from `fg_plot`, a list of nodes and edges.

### Usage

    plot_gr(
      gr,
      main = NULL,
      show_bgedges = TRUE,
      colour_palette = NULL,
      label_coloured = TRUE,
      shiny_plot = FALSE,
      interactive = FALSE,
      visNet_plot = TRUE,
      colour_edges = FALSE,
      ...
    )

### Arguments

`gr` | A list containing data frames `e` and `v`.
`main` | A string containing the plot title. If this is set to NULL, the function will look for a plot title in the `main` slot of `gr`; otherwise, this defaults to "".
`show_bgedges` | A logical variable indicating whether or not edges not specified for plotting should be plotted as light grey in the background. If this is `NULL`, the function will look for a `show_bgedges` in the `show_bgedges` slot of `gr`; otherwise, this defaults to `TRUE`.
`colour_palette` | A colour palette e.g. the default palette if the user sets this to `NULL` is `c('blue','cyan','yellow','red')`.
`label_coloured` | A logical indicating whether to colour the node labels using the same colours as the nodes in the non-interactive plot.
`shiny_plot` | A logical indicating whether this plot is made for shiny; users don't need to change this.
`interactive` | A logical variable indicating whether the plot should be an interactive plot; see package `ggiraph`.
`visNet_plot` | A logical variable indicating if an interactive plot is chosen, if function should output a visNetwork plot; if set to `FALSE`, ggplot's girafe will be used instead.
`colour_edges` | A logical variable indicating whether to colour edges if plotting a node feature summary.
`...` | Other parameters for `ggplot` if `interactive` is set to `FALSE`; other parameters for `plot_ly` if `interactive` is set to `TRUE`.

### Value

A `ggplot` object if `interactive` is set to `FALSE`; a `ggiraph` object if `interactive` is set to `TRUE`.

### See Also

`flowGraph-class` `fg_plot` `get_phen_meta` `ggdf` `fg_get_feature` `fg_get_summary`

### Examples

     no_cores <- 1
     data(fg_data_pos2)
     fg <- flowGraph(fg_data_pos2$count, class=fg_data_pos2$meta$class,
                     no_cores=no_cores)

     # fg <- fg_summary(fg, no_cores=no_cores, class="class", control="control",
     #                  overwrite=FALSE, test_name="t_byLayer", diminish=FALSE)

     gr_summary <- fg_plot(
       fg, type="node", p_thres=.05, show_bgedges=TRUE,
       path=NULL) # set path to a full path to save plot as a PNG

     plot_gr(gr_summary, main=gr_summary$main, show_bgedges=TRUE)

     plot_gr(gr_summary, main=gr_summary$main, show_bgedges=TRUE, interactive=TRUE)

[Package flowGraph version 1.2.0 Index]