Adjust Cnet node set
adjust_cnet_nodeset(
g,
set_nodes = NULL,
x = 0,
y = 0,
expand = 0,
percent_spacing = NULL,
rotate_degrees = 0,
cnet_nodesets = NULL,
verbose = FALSE,
...
)igraph Cnet plot, with vertex attribute nodeType that
contains values "Gene" and "Set", as produced by memIM2cnet().
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.
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.
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.
numeric value indicating the rotation in
degrees to adjust the node coordinates, relative to the center of
the coordinates.
list optional to provide the known nodesets
upfront, in order to avoid re-determining the nodesets.
logical indicating whether to print verbose output.
additional arguments are ignored.
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.
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()
# 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)
}