Specialized plot() function for KGX graphs

Specialized plot() function for KGX graphs

# S3 method for class 'tbl_kgx'
plot(
  x,
  ...,
  layout = "auto",
  node_color = pcategory,
  node_shape = pcategory,
  node_size = NULL,
  node_alpha = 0.9,
  edge_color = predicate,
  edge_linetype = NULL,
  edge_alpha = 0.5,
  max.overlaps = 10,
  bundle = FALSE,
  palettes = monarch_palettes(),
  layer_args = list(theme_bw = list(), theme = list(axis.text = ggplot2::element_blank(),
    axis.ticks = ggplot2::element_blank(), axis.title = ggplot2::element_blank(),
    legend.key = ggplot2::element_blank(), panel.background = ggplot2::element_blank(),
    panel.border = ggplot2::element_blank(), panel.grid = ggplot2::element_blank()),
    scale_edge_color_manual = list(values = palettes$edges$discrete, na.value = "grey"),
    scale_edge_color_gradientn = list(colors = palettes$continuous[3:1], na.value =
    "grey"), scale_color_manual = list(values = palettes$nodes$discrete, 
     na.value =
    "grey"), scale_shape_manual = list(values = palettes$nodes$shape, na.value = 19),
    scale_edge_fill_manual = list(values = palettes$nodes$discrete, na.value = "grey",
    guide = "none"), geom_edge_fan = list(aes(color = {
     {
         edge_color
    
    }
 }, linetype = {
     {
         edge_linetype
     }
 }), arrow = arrow(length =
    unit(2, "mm"), type = "open"), end_cap = circle(2.5, "mm"), edge_alpha = edge_alpha,
    show.legend = FALSE), geom_edge_loop = list(aes(color = {
     {
         edge_color

        }
 }), arrow = arrow(length = unit(2, "mm"), type = "open"), end_cap =
    circle(2.5, "mm"), edge_alpha = edge_alpha), geom_edge_bundle_force2 = list(aes(color
    = {
     {
         edge_color
     }
 }, linetype = {
     {
         edge_linetype

        }
 }), edge_alpha = edge_alpha), geom_edge_density = NULL, geom_node_point =
    list(aes(color = {
     {
         node_color
     }
 }, shape = {
     {
        
    node_shape
     }
 }, size = {
     {
         node_size
     }
 }), alpha =
    node_alpha), geom_node_label = list(aes(label = str_wrap(name, 20)), box.padding =
    0.4, min.segment.length = 0, size = 2, repel = TRUE, segment.colour = alpha("black",
    edge_alpha), segment.linetype = "dotted", fill = "#FFFFFF88"))
)

Arguments

x

A tbl_kgx graph.

...

Arguments passed on to ggraph::ggraph

graph

The object containing the graph. See Details for a list of supported classes. Or a layout_ggraph object as returned from create_layout in which case all subsequent arguments is ignored.

layout

The layout to use for the plot. Default is "sugiyama".

node_color

The column to use for node color. Default is "pcategory".

node_shape

The column to use for node shape. Default is "pcategory".

node_size

The column to use for node size. Default is NULL.

node_alpha

The alpha value for nodes. Default is 0.9.

edge_color

The column to use for edge color. Default is "predicate".

edge_linetype

The column to use for edge linetype. Default is NULL.

edge_alpha

The alpha value for edges. Default is 0.5.

max.overlaps

Exclude text labels when they overlap too many other things. For each text label, we count how many other text labels or other data points it overlaps, and exclude the text label if it has too many overlaps. Defaults to 10.

bundle

Whether to bundle edges with geom_edge_bundle_force2. Default is FALSE.

palettes

A named list of discrete/continuous palettes for nodes/edges Default is monarch_palettes.

layer_args

A named list of arguments for each ggplot layer.

Examples

filename <- system.file("extdata", "eds_marfan_kg.tar.gz", package = "monarchr")
g <- file_engine(filename) |>
          fetch_nodes(query_ids = "MONDO:0007525") |>
          expand(predicates = "biolink:has_phenotype",
                 categories = "biolink:PhenotypicFeature")|>
          expand(categories = "biolink:Gene")
plot(g)
#> Using "sugiyama" as default layout
#> Warning: ggrepel: 45 unlabeled data points (too many overlaps). Consider increasing max.overlaps