plotNhoodGraph: Plot graph of neighbourhood

In MarioniLab/miloR: Differential neighbourhood abundance testing on a graph

Plot graph of neighbourhood

Description

Visualize graph of neighbourhoods

Usage

plotNhoodGraph(
  x,
  layout = "UMAP",
  colour_by = NA,
  subset.nhoods = NULL,
  size_range = c(0.5, 3),
  node_stroke = 0.3,
  ...
)

Arguments

x	A Milo object
layout	this can be (a) a character indicating the name of the reducedDim slot in the Milo object to use for layout (default: 'UMAP') (b) an igraph layout object
colour_by	this can be a data.frame of milo results or a character corresponding to a column in colData
subset.nhoods	A logical, integer or character vector indicating a subset of nhoods to show in plot (default: NULL, no subsetting). This is necessary if testNhoods was run using subset.nhoods=....
size_range	a numeric vector indicating the range of node sizes to use for plotting (to avoid overplotting in the graph)
node_stroke	a numeric indicating the desired thickness of the border around each node
...	arguments to pass to ggraph

Value

a ggplot-class object

Author(s)

Emma Dann

Examples

NULL

MarioniLab/miloR documentation built on June 4, 2024, 11:55 a.m.