CircosPlot: CircosPlot

In msraredon/Connectome: Single Cell Connectomics

CircosPlot

Description

Plotting function to make Circos plots using the circlize package, following the vignette by the Saeys Lab at: https://github.com/saeyslab/nichenetr/blob/master/vignettes/circos.md Note that this plotting type is incompatible with edges where the ligand and the receptor are the exact same gene.

Usage

CircosPlot(
  connectome,
  weight.attribute = "weight_sc",
  cols.use = NULL,
  min.z = NULL,
  lab.cex = 1,
  balanced.edges = T,
  edge.color.by.source = T,
  small.gap = 1,
  big.gap = 10,
  title = NULL,
  ...
)

Arguments

connectome	A connectomic object, ideally filtered to only edges of interest.
weight.attribute	Column to use to define edgeweights for network analysis. 'weight_sc' or 'weight_norm'. Defaults to 'weight_sc'. If 'weight_sc', function will automatically filter at min.z = 0 to remove negative source/sink values.
cols.use	Optional. Colors for plotting nodes.
min.z	Minimum z-score for ligand and receptor.
lab.cex	Text size for gene names
balanced.edges	Edges in this plot can change thickness along their length. This parameter decides whether to scale edges by a single edgeweight (chosen in weight.attribute) or by the separate cell-specific ligand and receptor values. Default balanced (TRUE). If FALSE, the edges will expand or contract to join ligand weight to receptor weight.
edge.color.by.source	Default TRUE - edges will be colored by their source cell type. If false, edges will be colored by receiving cell instead.
small.gap	Default 1. Amount of distance between sectors. If the number of edges is very large, this will have to be reduced in size.
big.gap	Default 10. Amount of distance between the source cells and the target cells (top and bottom arc of graph). If the number of edges is very large, this can be reduced in size in addition to 'small.gap'
title	Character string for title of plot.
...	Arguments passed to FilterConnectome

msraredon/Connectome documentation built on April 11, 2022, 9:16 a.m.