Specialized plot() function for KGX graphs

Specialized plot() function for KGX graphs

# S3 method for class 'tbl_kgx'
plot(
  g,
  ...,
  layout = "auto",
  node_color = pcategory,
  node_shape = namespace,
  edge_color = predicate,
  edge_linetype = primary_knowledge_source,
  node_label = name,
  plot_ids = FALSE,
  label_size = 2,
  fan_strength = 2,
  edge_alpha = 0.9,
  node_alpha = 0.9
)

Arguments

g

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 "auto" as used by ggraph.

node_color

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

node_shape

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

edge_color

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

edge_linetype

The column to use for edge line type. Default is "primary_knowledge_source".

node_label

The column to use for node labels. Defaults to "name".

plot_ids

Whether to show node IDs in node labels. Defaults to FALSE.

label_size

Size of node label text. Default is 2.

fan_strength

Fan strength in ggraph's geom_edge_fan, Default is 2.

edge_alpha

Alpha value for edges, default 0.9.

node_alpha

Alpha value for nodes, default 0.9.

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