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Bulk Cnet plot adjustments

Source: R/jamenrich-bulk-cnet-adjustments.R
bulk_cnet_adjustments.Rd

Bulk Cnet plot adjustments

Usage

bulk_cnet_adjustments(
  g,
  nodeset_adj,
  node_adj,
  apply_negative = TRUE,
  nodesets = NULL,
  ...
)

Arguments

g

igraph object expected to be a Cnet object with vertex attribute 'nodeType' containing values 'Gene' and 'Set'.

nodeset_adj

data.frame recognizing five colnames:

  • nodeset: character name of each nodeset

  • x,y: numeric x,y coordinate adjustments to add to existing coordinates

  • rotate_degrees: numeric angle in degrees to rotate existing nodes

  • percent_spacing: absolute spacing to enforce for nodes in the nodeset.

node_adj

data.frame recognizing five colnames:

  • node: character name of each node

  • x,y: numeric x,y coordinate adjustments to add to existing coordinates

  • label.dist: numeric value to add to existing label distance.

  • label.degree: numeric angle in degrees to add to the existing angle.

apply_negative

logical whether to allow shrinking nodeset spacing.

nodesets

list as output from get_cnet_nodesets(), or any list named by nodeset, containing character vector of node names.

...

additional arguments are ignored.

Value

igraph object after applying adjustments.

Details

This function applies a series of adjustments to nodesets and nodes in a Cnet igraph object. Nodesets are adjusted first, then nodes are adjusted afterward. This order is important because the x,y coordinates may be altered by nodeset first, before the node adjustment is applied.

All x,y coordinate adjustments are performed using scaled units, using the max x- or y-range for the plot layout. All Cnet igraph plots are assumed to use asp=1 to enforce aspect ratio 1, in order to maintain the intended visual distances used by the layout algorithms.

Therefore it is possible to expand a plot layout such that the overall scale is wider than before, thereby affecting the scaled unit space.

In any event, this function is intended to replicated the effect done by launch_shinycat().

See also

Other jam utility functions: ashape(), avg_angles(), avg_colors_by_list(), call_fn_ellipsis_deprecated(), cell_fun_bivariate(), collapse_mem_clusters(), colorRamp2D(), deconcat_df2(), display_colorRamp2D(), enrichList2geneHitList(), filter_mem_genes(), filter_mem_sets(), find_colname(), find_enrich_colnames(), get_hull_data(), get_igraph_layout(), gsubs_remove(), handle_igraph_param_list(), isColorBlank(), make_legend_bivariate(), make_point_hull(), mem_find_overlap(), order_colors(), rank_mem_clusters(), rotate_coordinates(), subgraph_jam(), subset_mem(), summarize_node_spacing(), xyAngle()