Color edges by nodegroups

Color edges by nodegroups

Usage

color_edges_by_nodegroups(
  g,
  nodegroups = NULL,
  nodegroup_colors = NULL,
  edge_alpha = NULL,
  Crange = NULL,
  Lrange = NULL,
  darkFactor = 1,
  sFactor = 1,
  naColor = "grey",
  verbose = FALSE,
  ...
)

Arguments

g

igraph object that contains vertex node attribute "color" as seen with igraph::vertex_attr(g, "color").

nodegroups

list or communities object that references nodes in g and assigns one or more to nodegroups. Default NULL calls get_cnet_nodeset(), passing '...' for customization.

nodegroup_colors

character or default NULL which assigns categorical colors by colorjam::rainbowJam().

edge_alpha

numeric of default NULL uses 1, with opacity where 0 is transparent, 1 is completely solid.

Crange, Lrange

numeric ranges passed to colorjam::rainbowJam() to restrict the chroma and luminance of categorical colors. Default NULL uses the defaults in colorjam::rainbowJam().

darkFactor, sFactor

numeric default 1 each, used to darken and saturate colors, respectively. When either contain values other than 1, it calls jamba::makeColorDarker().

naColor

character color, default 'grey', used for edges that for any reason were not assigned to a nodegroup, to prevent them from becoming NA.

verbose

logical indicating whether to print verbose output.

...

additional arguments are passed to colorjam::blend_colors().

Value

igraph object with edge color attribute updated to represent the result of blending node colors, seen by igraph::edge_attr(g)$color.

Details

This function is analogous to color_nodes_by_nodegroups(), and in fact uses the same nodegroup color strategy. However, by default 'Set' nodes are not colored, and therefore edges are only colored using the nodegroup.

Using filter_set_only=FALSE, which is passed to get_cnet_nodeset(), will assign 'Set' nodes to their own nodegroups, giving them colors. At that point, edges will blend colors for the 'Set' and 'Gene' nodes.

See also

Other jam igraph utilities: color_edges_by_nodes(), color_nodes_by_nodegroups(), get_cnet_nodeset(), jam_igraph(), launch_shinycat(), subgraph_jam()

Examples

cnet1 <- make_cnet_test()
igraph::vertex_attr(cnet1, "shape") <- "circle";
cnet2 <- color_nodes_by_nodegroups(cnet1)
cnet3 <- color_edges_by_nodegroups(cnet2)
jam_igraph(cnet3)


cnet2b <- color_nodes_by_nodegroups(cnet1, filter_set_only=FALSE)
cnet3b <- color_edges_by_nodegroups(cnet2b, filter_set_only=FALSE)
jam_igraph(cnet3b)