nudge_igraph_node: Nudge igraph layout by node

In jmw86069/multienrichjam: Analysis and Visualization of Multiple Gene Set Enrichments

Nudge igraph layout by node

Description

Nudge igraph layout by node

Usage

nudge_igraph_node(
  g,
  nodes = NULL,
  x = 0,
  y = 0,
  nodes_xy = NULL,
  use_grep = FALSE,
  aspect = 1,
  debug = FALSE,
  verbose = FALSE,
  ...
)

Arguments

g	igraph object that contains layout coordinates stored as graph attribute "layout", for example graph_attr(g, "layout").
nodes	character vector indicating which nodes in g should be nudged.
x, y	numeric values indicating the amount to move each node defined by nodes. These values are relative to the x- and y-axis ranges of the layout coordinates, and based upon aspect below.
nodes_xy	list alternative to using arguments ⁠nodes,x,y⁠. This argument assumes a list of numeric adjustments to x and y, where the names(nodes_xy) are node names. For example: ⁠nodes_xy=list(APOE=c(x=0.05, y=-0.01), GAPDH=c(x=0.1, y=0.0)⁠ however the numeric vector does not need to contain names.
use_grep	logical indicating whether to match values in nodes to V(g)$name and V(g)$label using jamba::provigrep(), which follows case-insensitive grep(). When use_grep=FALSE the values in either V(g)$name or V(g)$label must be identical to nodes.
aspect	numeric indicating the aspect ratio of the output plot. Any value other than aspect=1 will use the observed x-axis and y-axis range of the layout coordinates. When aspect=1 then the highest of x-axis and y-axis ranges is used for the relative x and y adjustment. Note that igraph::plot() does not maintain aspect ratio 1 by default, but jam_igraph() does maintain aspect ratio 1 and is preferred.
debug	logical indicating whether to plot the layout before and after adjustment, drawing arrows to indicate the movement of particular nodes. This plot is very basic, using base R plot(), and is only intended as a quick visual review.
verbose	logical indicating whether to print verbose output.
...	additional arguments are ignored.

See Also

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

jmw86069/multienrichjam documentation built on Nov. 3, 2024, 10:29 p.m.