The width of edges represent the strength of the communication.
netVisual_hierarchy1(
net,
vertex.receiver,
color.use = NULL,
title.name = NULL,
sources.use = NULL,
targets.use = NULL,
remove.isolate = FALSE,
top = 1,
weight.scale = FALSE,
vertex.weight = 20,
vertex.weight.max = NULL,
vertex.size.max = 15,
edge.weight.max = NULL,
edge.width.max = 8,
alpha.edge = 0.6,
label.dist = 2.8,
space.v = 1.5,
space.h = 1.6,
shape = NULL,
label.edge = FALSE,
edge.curved = 0,
margin = 0.2,
vertex.label.cex = 0.6,
vertex.label.color = "black",
arrow.width = 1,
arrow.size = 0.2,
edge.label.color = "black",
edge.label.cex = 0.5,
vertex.size = NULL
)a weighted matrix defining the signaling network
a numeric vector giving the index of the cell groups as targets in the first hierarchy plot
the character vector defining the color of each cell group
alternative signaling pathway name to show on the 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.
whether remove the isolate nodes in the communication network
the fraction of interactions to show
whether rescale the edge weights
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
the maximum weight of edge; defualt = max(net)
The maximum edge width for visualization
the transprency of edge
the distance between labels and dot position
the space between different columns in the plot
the space between different rows in the plot
The shape of the vertex, currently <U+201C>circle<U+201D>, <U+201C>square<U+201D>, <U+201C>csquare<U+201D>, <U+201C>rectangle<U+201D>, <U+201C>crectangle<U+201D>, <U+201C>vrectangle<U+201D>, <U+201C>pie<U+201D> (see vertex.shape.pie), <U+2018>sphere<U+2019>, and <U+201C>none<U+201D> are supported, and only by the plot.igraph command. <U+201C>none<U+201D> does not draw the vertices at all, although vertex label are plotted (if given). See shapes for details about vertex shapes and vertex.shape.pie for using pie charts as vertices.
whether label edge
Specifies whether to draw curved edges, or not. This can be a logical or a numeric vector or scalar. First the vector is replicated to have the same length as the number of edges in the graph. Then it is interpreted for each edge separately. A numeric value specifies the curvature of the edge; zero curvature means straight edges, negative values means the edge bends clockwise, positive values the opposite. TRUE means curvature 0.5, FALSE means curvature zero
The amount of empty space below, over, at the left and right of the plot, it is a numeric vector of length four. Usually values between 0 and 0.5 are meaningful, but negative values are also possible, that will make the plot zoom in to a part of the graph. If it is shorter than four then it is recycled.
The label size of vertex
The color of label for vertex
The width of arrows
the size of arrow
The color for single arrow
The size of label for arrows
Deprecated. Use `vertex.weight`
an object of class "recordedplot"