plot_graph: plot_graph

In clatworthylab/bowerbird: A single-cell package for Functional Annotation + Gene Module Summarization.

Description

Plot the geneset kNN network as a graph.

Usage

## S3 method for class '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 class '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.

Details

Just a ggraph wrapper to plot the graph.

Value

Returns a ggraph plot.

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)

clatworthylab/bowerbird documentation built on Dec. 19, 2021, 5:15 p.m.