apply_nodeset_spacing: Apply minimum node spacing for each Cnet node set

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

Apply minimum node spacing for each Cnet node set

Description

Apply minimum node spacing for each Cnet node set

Usage

apply_nodeset_spacing(
  cnet,
  percent_spacing = 3,
  apply_negative = FALSE,
  metric = c("median", "minimum"),
  nodesets = NULL,
  tolerance = 1.05,
  cnet_nodesets = NULL,
  debug = FALSE,
  verbose = FALSE,
  ...
)

Arguments

cnet	igraph object that contains attribute "nodeType" and values nodeType=c("Gene", "Set"), consistent with use of get_cnet_nodeset() and adjust_cnet_nodeset(). The node layout is expected to be stored in igraph::graph_attr(cnet, "layout").
percent_spacing	numeric indicating the target spacing in relation to the maximum x-axis and y-axis span for the layout coordinates. For example percent_spacing=4 will require that the median spacing between nodes in each nodeset is at least 4 percent of the larger of the x-axis and y-axis ranges for the layout of input cnet.
apply_negative	logical indicating whether to shrink node spacing when the spacing is larger than the target ⁠percent spacing⁠. By default apply_negative=FALSE which allows nodes to exceed the spacing, and only adjusts node spacing when a nodeset is below this threshold.
metric	character string indicating the metric used to summarize nodeset spacing: "median" - takes the median spacing between nodes in the nodeset, so the end result has at least half nodes with percent_spacing distance, "typical distance between nodes". This option is useful when there may be one node pair close together, but most nodes have consistent distance from their nearest node neighbor. "minimum" - takes the minimum spacing between nodes in the nodeset, so the end result requires all nodes to have at least percent_spacing distance. function - a function can be provided which takes a numeric vector of node distances, and produces a single numeric summary value, which will be scaled relative to the maximum xy axis range. This option would allow using mean(), or a quantile function such as function(x){quantile(x, 0.3)}.
nodesets	character with optional subset of nodesets to adjust, or the default nodesets=NULL will adjust all nodesets. Values can be specified either in form or nodeset names, or any one or more members of a nodeset.
tolerance	numeric value used to apply a small tolerance to the distance threshold, for example the default tolerance=1.05 requires nodes to be more than 5% lower than the actual threshold before adjusting nodes. This additional activation threshold is experimental and may not be necessary. It is mainly intended to reduce calculations for nodesets that are only a small rounding error from being acceptable, which can happen when the overall plot range is adjusted during rounds of small node coordinate adjustments like with this function, nudge_igraph_node(), apply_nodeset_spacing(), or adjust_cnet_set_relayout_gene().
cnet_nodesets	list optional to provide the known nodesets upfront, in order to avoid re-determining the nodesets.
debug	logical indicating whether to print debug information without adjusting the nodeset spacing. This option is useful to see summary information about nodeset spacing before choosing the percent_spacing threshold.
verbose	logical indicating whether to print verbose output. The output includes text printed with debug=TRUE except that nodes are adjusted when debug=FALSE.
...	additional arguments are ignored.

Details

This function automates the process of spacing nodesets in a Cnet plot by calling adjust_cnet_nodeset() on all nodesets whose median nearest node distance is above or below a threshold.

By default nodes must be at least percent_spacing distance apart, relative to the maximum x-axis and y-axis layout coordinate range. Roughly speaking, nodes are clearly visible with distance between nodes of at least 3 percent of the coordinate range.

Nodes are not compressed down to this distance unless using the argument apply_negative=TRUE.

Note that this function does not detect when two clusters overlap. For other specific layout adjustments use adjust_cnet_nodeset(). In future, this function may attempt to re-position nodesets relative to each other, but that process tends to be iterative and is not guaranteed to have a solution.

When a nodeset contains only one node, there is no calculated distance so it is reported as NA when verbose=TRUE or debug=TRUE. However for internal purposes the nodeset is treated as if its nodeset spacing is exactly percent_spacing so that no subsequent adjustments are performed on the nodeset.

Value

igraph Cnet object, whose nodes are adjusted according to the arguments given.

See Also

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

jmw86069/multienrichjam documentation built on Feb. 7, 2024, 12:58 a.m.