plotSwarmCircos: plotSwarmCircos

In jasonserviss/CIMseq: CIMseq is a software suite for analysis of scRNAseq data that has been produced using the cellular interactions by multiplet sequencing method

Description

plotSwarmCircos

Usage

plotSwarmCircos(swarm, ...)

## S4 method for signature 'CIMseqSwarm'
plotSwarmCircos(swarm, singlets, multiplets,
  classOrder = NULL, connectionClass = NULL, alpha = 0.05,
  weightCut = 0, label.cex = 1, legend = TRUE,
  theoretical.max = NULL, h.ratio = 0.5,
  pal = colorRampPalette(c("grey90", viridis::viridis(1)))(120)[20:110],
  nonSigCol = "grey90", classColour = NULL, gap.degree = NULL,
  clear = TRUE, ...)

Arguments

swarm	CIMseqSwarm; A CIMseqSwarm object.
...	additional arguments to pass on.
singlets	CIMseqSinglets; A CIMseqSinglets object.
multiplets	CIMseqMultiplets; A CIMseqMultiplets object.
classOrder	character; Order of the cell types / classes on the circos.
connectionClass	character; Vector of length 1 specifying the class / cell type to plot or NULL to plot all classes / cell types.
alpha	numeric; Vector of length 1 specifying the which p-values are considered significant.
weightCut	integer; Vector of length 1 specifying weights below which the p-value should not be calculated.
label.cex	numeric; Vector of length 1 between [0, 1] indicating the size of the cell type labels.
legend	logical; indicates if the legends should be plotted.
theoretical.max	integer; See estimateCells.
h.ratio	numeric; See circos.link.
pal	character; A vector including the colour pallete for the score colours.
nonSigCol	character; Vector of length 1 indicating the colours for non-significant connections.
classColour	character; Colours for the classes. Order should correspond to classOrder argument.
gap.degree	numeric; Controls the amount of space between the classes. See circos.par.
clear	logical; Should circos.clear be called when finished plotting?

Value

A ggplot object.

Author(s)

Jason T. Serviss

jasonserviss/CIMseq documentation built on Jan. 11, 2020, 4:42 a.m.