Adjust Cnet node set

Adjust Cnet node set

Usage

adjust_cnet_nodeset(
  g,
  set_nodes = NULL,
  x = 0,
  y = 0,
  percent_spacing = NULL,
  expand = 0,
  rotate_degrees = 0,
  cnet_nodesets = NULL,
  verbose = FALSE,
  ...
)

Arguments

g

igraph Cnet plot, with vertex attribute nodeType that contains values "Gene" and "Set", as produced by memIM2cnet().

set_nodes

character vector of one or more set names, which are defined here as the names of the nodes with nodeType="Set" to which each node with nodeType="Gene" is connected. For example set_nodes=c("A", "B") will return all Gene nodes that are connected only to Set nodes "A" and "B". Alternatively, one can refer to a cluster by the node name of one member of the cluster, as a convenience option.

x, y

numeric indicating the relative amount to move nodes in the node set, based upon the overall range of x and y values in the layout coordinates.

percent_spacing

numeric within node spacing as percentage of the max x/y layout ranges. This option is preferred to expand when trying to keep nodeset spacing consistent for the overall layout. As a general rule, use summarize_node_spacing(g)$nearest_within with column 'Median' to determine node spacing for each nodeset, then adjust each nodeset to relatively consistent median spacing.

expand

numeric the relative amount to expand node coordinates, where expand=0 does no expansion, expand=1 will expand coordinates 100% of the distance to the center of the cluster, twice the original distance; and expand=-1 will expand coordinates to half the distance to the center.

rotate_degrees

numeric value indicating the rotation in degrees to adjust the node coordinates, relative to the center of the coordinates.

cnet_nodesets

list optional to provide the known nodesets upfront, in order to avoid re-determining the nodesets. Otherwise get_cnet_nodesets() is called, which for large networks may introduce a small time lag.

verbose

logical indicating whether to print verbose output.

...

additional arguments are ignored.

Details

This function is intended to help adjust a node set, defined as a set of "Gene" nodes that all connect to the same "Set" nodes. These nodes are usually clustered together in a Cnet plot, and can be manipulated as a group using this function. Use get_cnet_nodeset(g) to get all node sets from a Cnet igraph object.

Specifically, this function can be used to expand, rotate, and move the cluster of nodes in a Cnet network layout. The purpose is usually to help the visual clarity of the plot, and to reduce node label overlaps.

See also

Other jam cnet igraph functions: adjust_cnet_set_relayout_gene(), apply_cnet_direction(), apply_nodeset_spacing(), get_cnet_nodeset(), make_cnet_test(), nudge_igraph_node(), rotate_igraph_layout()

Examples

# the examples below are for internal data
# and will be rewritten to work with example data
if (1 == 2) {
g <- mem_dmjdm_gp_20_plots_jikl$cnet_collapsed_set;
set_nodes <- c("J", "L")
g2 <- adjust_cnet_nodeset(g, set_nodes=c("J", "L"), expand=0.5)

jam_igraph(g)
g2 <- adjust_cnet_nodeset(g, set_nodes=c("I", "K", "L"), x=0.01, y=-0.01, expand=0.2)
g2 <- adjust_cnet_nodeset(g2, set_nodes=c("I", "J", "K", "L"), x=-0.08, y=-0.05, expand=0.2)
g2 <- adjust_cnet_nodeset(g2, set_nodes=c("I", "L"), x=-0.05, y=0.05, expand=0.3)
g2 <- adjust_cnet_nodeset(g2, set_nodes=c("I", "J", "L"), x=-0.02, y=0.03, expand=0.3)
g2 <- adjust_cnet_nodeset(g2, set_nodes=c("I", "K"), x=0.03, y=0.09, expand=0.)
g2 <- adjust_cnet_nodeset(g2, set_nodes=c("I", "J", "K"), x=0.02, y=-0.01, expand=0.)
g2 <- adjust_cnet_nodeset(g2, set_nodes=c("I", "J"), x=0.01, y=-0.00, expand=0.1)
g2 <- adjust_cnet_nodeset(g2, set_nodes=c("J"), x=-0.03, y=-0.02, expand=0.)
jam_igraph(g2)
}