Visualize the inferred signaling network of signaling pathways by aggregating all L-R pairs
netVisual_aggregate(
object,
signaling,
signaling.name = NULL,
color.use = NULL,
vertex.receiver = NULL,
sources.use = NULL,
targets.use = NULL,
top = 1,
remove.isolate = FALSE,
vertex.weight = NULL,
vertex.weight.max = NULL,
vertex.size.max = 15,
weight.scale = TRUE,
edge.weight.max = NULL,
edge.width.max = 8,
layout = c("hierarchy", "circle", "chord"),
thresh = 0.05,
from = NULL,
to = NULL,
bidirection = NULL,
vertex.size = NULL,
pt.title = 12,
title.space = 6,
vertex.label.cex = 0.8,
group = NULL,
cell.order = NULL,
small.gap = 1,
big.gap = 10,
scale = FALSE,
reduce = -1,
show.legend = FALSE,
legend.pos.x = 20,
legend.pos.y = 20,
...
)CellChat object
a signaling pathway name
alternative signaling pathway name to show on the plot
the character vector defining the color of each cell group
a numeric vector giving the index of the cell groups as targets in the first hierarchy plot
a vector giving the index or the name of source cell groups
a vector giving the index or the name of target cell groups.
the fraction of interactions to show
whether remove the isolate nodes in the communication network
The weight of vertex: either a scale value or a vector
the maximum weight of vertex; defualt = max(vertex.weight)
the maximum vertex size for visualization
whether scale the edge weight
the maximum weight of edge; defualt = max(net)
The maximum edge width for visualization
"hierarchy", "circle" or "chord"
threshold of the p-value for determining significant interaction
Deprecated. Use `sources.use`,`targets.use`
Deprecated. Use `vertex.weight`
Parameters below are set for "chord" diagram. Please also check the function `netVisual_chord_cell` for more parameters.
font size of the text
the space between the title and plot
The label size of vertex in the network
A named group labels for making multiple-group Chord diagrams. The sector names should be used as the names in the vector. The order of group controls the sector orders and if group is set as a factor, the order of levels controls the order of groups.
a char vector defining the cell type orders (sector orders)
Small gap between sectors.
Gap between the different sets of sectors, which are defined in the `group` parameter
scale each sector to same width; default = FALSE; however, it is set to be TRUE when remove.isolate = TRUE
if the ratio of the width of certain grid compared to the whole circle is less than this value, the grid is removed on the plot. Set it to value less than zero if you want to keep all tiny grid.
whether show the figure legend
adjust the legend position
other parameters (e.g.,vertex.label.cex, vertex.label.color, alpha.edge, label.edge, edge.label.color, edge.label.cex, edge.curved) passing to `netVisual_hierarchy1`,`netVisual_hierarchy2`,`netVisual_circle`. NB: some parameters might be not supported
an object of class "recordedplot"