plot_graph

Plot the geneset kNN network as a graph.

# S3 method for BOWER
plot_graph(
  bower,
  colorby = "cluster",
  mode = c("default", "gsea"),
  gsea.slot = c("padj", "pval", "NES", "ES"),
  gsea.pval.cutoff = 0.25,
  node.size = "geneset_size",
  node.label = "labels",
  node.label.size = 3,
  title = NULL,
  title.size = 3,
  edge.width = "weight",
  edge.width.thickness.range = c(0, 1),
  edge.alpha = 0.25,
  dot_max = 8,
  guides.colour = FALSE
)

# S3 method for igraph
plot_graph(
  gr,
  colorby = "cluster",
  node.size = "geneset_size",
  node.label = "labels",
  node.label.size = 3,
  title = NULL,
  title.size = 3,
  edge.width = "weight",
  edge.width.thickness.range = c(0, 1),
  edge.alpha = 0.25,
  dot_max = 8,
  guides.colour = FALSE,
  ...
)

Arguments

bower	BOWER object
colorby	name of attribute for colors of nodes.
node.size	name of attribute for size of nodes or numerical value/vector.
node.label	name of attribute for colors of nodes.
node.label.size	size of node label.
edge.width	name of attribute for width of edges.
edge.width.thickness.range	scale for range of widths of edges.
edge.alpha	transparency of edges.
guides.colour	boolean. whether or not to display guide for vertex colour.
...	passed to ggraph::ggraph
node.max_size	maximum node size.

Value

Returns a ggraph plot.

Details

Just a ggraph wrapper to plot the graph.

Examples

gmt_file <- system.file("extdata", "h.all.v7.4.symbols.gmt", package = "bowerbird")
bwr <- bower(gmt_file)
bwr <- snn_graph(bwr)
bwr <- find_clusters(bwr)
bwr <- summarize_clusters(bwr, ncpus = 1)
plot_graph(bwr)
#> Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
#> Warning: Removed 41 rows containing missing values (geom_text).