mem_find_overlap: Find best overlap threshold for EnrichMap
In jmw86069/jamenrich: Analysis and Visualization of Multiple Gene Set Enrichments

mem_find_overlap

R Documentation

Find best overlap threshold for EnrichMap

Description

Find best overlap threshold for EnrichMap

Usage

mem_find_overlap(
  mem,
  overlap_range = c(0.1, 0.99),
  overlap_count = 2,
  node_fraction = 0.5,
  max_cutoff = 0.4,
  debug = FALSE,
  ...
)

Arguments

`mem`	`list` output from `multiEnrichMap()`
`overlap_range`	numeric range of Jaccard overlap values
`overlap_count`	numeric value passed to `mem_multienrichplot()` which is used to filter the multienrichmap by Jaccard overlap and by overlap_count.
`max_cutoff`	numeric value between 0 and 1, to define the maximum fraction of nodes in the largest connected component, compared to the total number of non-singlet nodes.
`debug`	logical indicating whether to return full debug data, which is used internally to determine the best overlap cutoff to use.

Details

This function implements a straightforward approach to determine a reasonable Jaccard overlap threshold for EnrichMap data. It finds the overlap threshold at which the first connected component is no more than max_cutoff fraction of the whole network. This fraction is defined as the number of nodes in the largest connected component, divided by the total number of non-singlet nodes. When all nodes are connected, this fraction == 1.

We found empirically that a max_cutoff=0.4, the point at which the largest connected component contains no more than 40% of all nodes, seems to be a reasonably good place to start.

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(), handle_igraph_param_list(), isColorBlank(), make_legend_bivariate(), make_point_hull(), order_colors(), rank_mem_clusters(), rotate_coordinates(), subgraph_jam(), subset_mem(), summarize_node_spacing(), xyAngle()