CircosDiff: CircosDiff

In msraredon/Connectome: Single Cell Connectomics

CircosDiff

Description

Currently in beta testing. A Circos Plot for a differential edgelist made using DifferentialConnectome. Note that negative log fold changes cannot be plotted; therefore, this plot uses the 'score' for the differential comparison, which is always positive in proportion to perturbation.

Usage

CircosDiff(
  differential.connectome,
  features = NULL,
  sources.include = NULL,
  targets.include = NULL,
  min.score = NULL,
  min.pct = NULL,
  verbose = T,
  infinity.to.max = T,
  edge.color.by.source = T,
  cols.use = NULL,
  lab.cex = 1,
  title = NULL,
  small.gap = 1,
  big.gap = 10
)

Arguments

differential.connectome	A differential connectome, made with DifferentialConnectome. May be filtered as desired prior to plotting.
features	Gene of interest. Output will be limited to edges including these specific genes.
sources.include	Source nodes of interest. Output will be limited to edges coming from these sources.
targets.include	Target nodes of interest. Output will be limited to edges landing on these targets.
min.score	Default NULL. Will limit output to edges with a differential score greater than this value.
min.pct	Default NULL. Threshold to return clusterwise observations for both ligand and receptor. Only needs to be satisfied in connect.1 OR in connect.2.
verbose	Whether to output feedback to user
infinity.to.max	Default TRUE. If TRUE, will create a pseudo value to replace values of "Inf"
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.
cols.use	Optional. Colors for plotting nodes.
lab.cex	Text size for gene names
title	Character string for title of plot.
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'

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