plotSwarmCircos2: plotSwarmCircos2

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

Description

plotSwarmCircos2

Usage

plotSwarmCircos2(swarm, ...)

## S4 method for signature 'CIMseqSwarm'
plotSwarmCircos2(
  swarm,
  singlets,
  multiplets,
  classOrder = NULL,
  connectionClass = NULL,
  alpha = 0.05,
  weightCut = 0,
  expectedWeightCut = 0,
  label.cex = 1,
  legend = TRUE,
  pal = colorRampPalette(c("grey95", viridis::viridis(1)))(120)[30:120],
  nonSigCol = "grey95",
  h.ratio = 0.5,
  maxCellsPerMultiplet = Inf,
  depleted = FALSE,
  groups = NULL,
  multiplet.factor = NA,
  ...
)

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.
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.

Value

A ggplot object.

Author(s)

EngeLab

EngeLab/CIMseq documentation built on Jan. 25, 2022, 5 a.m.