plotNhoodGraph: Plot graph of neighbourhood
In MikeDMorgan/miloR: Differential neighbourhood abundance testing on a graph

plotNhoodGraph

R Documentation

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,
  is.da = FALSE,
  highlight.da = FALSE,
  ...
)

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
`is.da`	logical scalar that tells plotNhoodGraph to order nhoods by \|LFC\| which can help to visually emphasise which nhoods are DA.
`highlight.da`	logical or numeric scalar that emphasises the DA nhoods in the layout by adjusting the transparency of the non-DA nhoods. Can only be used if `is.da=TRUE`, otherwise will give a warning. If highlight.da is a numeric then it explicitly sets the transparency level (must be between 0 and 1). If highlight.da is logical then the transparency is set to 0.1
`...`	arguments to pass to `ggraph`