handle_igraph_param_list: Handle igraph attribute parameter list
In jmw86069/jamenrich: Analysis and Visualization of Multiple Gene Set Enrichments

handle_igraph_param_list

R Documentation

Handle igraph attribute parameter list

Description

Handle igraph attribute parameter list, internal function for jam_igraph()

Usage

handle_igraph_param_list(
  x,
  attr,
  factor_l,
  i_values = NULL,
  attr_type = c("node", "vertex", "edge"),
  verbose = FALSE,
  ...
)

Arguments

`x`	`igraph` object
`attr`	`character` name of the attribute to update in `x`.
`factor_l`	`list` or `numeric` vector or `function`: `list` of `numeric` vectors where `names(factor_l)` correspond to attribute names, and the names of numeric vectors are attribute values The attribute names and attribute values are used to match relevant entities of type `attr_type`. For matching entities, attribute values are used as defined by attribute name `attr`, and are multiplied by the matching numeric value in `factor_l`. `numeric` vector which is directly multiplied by `i_values` to produce an adjusted output vector `i_values`. `function` which is used to modify `i_values` by calling `factor_l(i_values)` to produce adjusted output `i_values`.
`i_values`	`vector` of attribute values that represent the current attribute values in `x` for the attribute `attr`.
`attr_type`	`character` string indicating the type of entity being adjusted in `x`: `"node"` or `"vertex"` refers to `igraph::vertex_attr()` `"edge"` refers to `igraph::edge_attr()`
`...`	additional arguments are ignored.

Details

This mechanism is intended to help update igraph attributes in bulk operations by the attribute values associated with nodes or edges. Most commonly, the argument factor_l is multiplied by numeric attributes to scale attribute values, for example label font size, or node size.

For example:

handle_igraph_param_list(x,
   attr="size",
   factor_l=list(nodeType=c(Gene=1, Set=2)),
   i_values=rep(1, igraph::vcount(x)),
   attr_type="node")

This function call will match node attribute nodeType, the size of nodes with attribute value nodeType="Set" are multiplied size * 2, nodeType="Gene" are multiplied size * 1.

Value

vector of attribute values representing attr.

Other jam utility functions: 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(), get_hull_data(), get_igraph_layout(), gsubs_remove(), 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()