ViewInterCircos: plot circle graph with communication profile

In ShellyCoder/cellcall: inference of intercellular networks from single-cell transcriptomics

plot circle graph with communication profile

Description

plot circle graph with communication profile

Usage

ViewInterCircos(
  object,
  font = 2,
  cellColor,
  lrColor = NULL,
  order.vector = NULL,
  trackhight1 = 0.05,
  linkcolor.from.sender = TRUE,
  linkcolor = NULL,
  arr.type = "big.arrow",
  arr.length = 0.04,
  DIY = TRUE,
  gap.degree = NULL,
  trackhight2 = 0.032,
  track.margin2 = c(0.01, 0.12),
  slot = "expr_l_r_log2_scale"
)

Arguments

object	a Cellwave objects
font	the size of font
cellColor	a color dataframe, rownames is cell type, value is color
lrColor	a color vector denotes the color of ligand and receptor, containing two elements, default is c('#D92E27', "#35C6F4")
order.vector	default is null, a celltype vector with the order you want in the circle graph
trackhight1	Height of the outer track
linkcolor.from.sender	logical value, whether the color of line correspond with color of sender cell
linkcolor	one color you want link to be, only if parameter linkcolor.from.sender=FALSE
arr.type	Type of the arrows, default value is big.arrow There is an additional option triangle
arr.length	Length of the arrows, measured in 'cm'. If arr.type is set to big.arrow, the value is percent to the radius of the unit circle.
DIY	logical value, if TRUE, the parameter object should be a dataframe, and set slot="expr_l_r_log2_scale". otherwise object should be a Cellwave objects.
gap.degree	between two neighbour sectors. It can be a single value or a vector. If it is a vector, the first value corresponds to the gap after the first sector.
trackhight2	Height of the inner track
track.margin2	affect current track
slot	plot the graph with the data of specific slot

ShellyCoder/cellcall documentation built on Oct. 11, 2023, 2:50 p.m.