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Collapse Multienrichment clusters

Source: R/jamenrich-utils.R
collapse_mem_clusters.Rd

Collapse Multienrichment clusters

Usage

collapse_mem_clusters(
  mem,
  clusters,
  choose = NULL,
  per_cluster = Inf,
  byCols = c("composite_rank", "minp_rank", "gene_count_rank"),
  return_type = c("cnet", "Mem", "mem"),
  max_labels = 4,
  max_nchar_labels = 25,
  include_cluster_title = TRUE,
  cluster_color_min_fraction = 0.5,
  verbose = FALSE,
  ...
)

Arguments

mem

Mem or legacy list mem object

clusters

list named by cluster name, containing character vectors all of whose values should be present in sets(mem).

choose

character default NULL, passed to rank_mem_clusters() to choose a subset of clusters to return. Values must be found in names(clusters).

per_cluster

integer default 'Inf' with the maximum sets to include in each cluster. Use an integer like per_cluster=1 to choose one "exemplar" per cluster, ranked according to byCols which is described in rank_mem_clusters().

byCols

character vector of summary values to use when sorting sets within each cluster, passed to and described in rank_mem_clusters().

return_type

character default "cnet" with the output format:

  • "cnet" returns an igraph Cnet plot.

  • "Mem" returns a Mem object after collapsing by cluster.

  • "mem" returns legacy list mem output.

max_labels

integer default 4, the number of pathway labels to include in each cluster, ordered according to 'byCols'.

max_nchar_labels

integer default 25, max character length for each pathway label.

include_cluster_title

logical default TRUE, whether to include the cluster title as a prefix. For example if the cluster name is 'A' the new title would be: 'A: pathway 1; pathway 2; pathway 3; pathway 4'.

cluster_color_min_fraction

numeric value default 0.5, the fraction of pathways in a cluster which has "non blank" assigned color in enrichIMcolors() in order for the color to be assigned to the resulting node, in the case of Cnet output with return_type="cnet".

verbose

logical whether to print verbose output.

...

additional arguments are passed to cnet2mem() which includes thresholds used by apply_cnet_direction() such as direction_col_fn (color function applied to enrichIMdirection), gene_direction_col_fn (color function applied to geneIMdirection), and others. To avoid applying directional color to Set nodes (nodeType='Set') use direction_cutoff=100 and direction_max=101, which will consider any enrichIMdirection value at or below 100 to be non-directional.

Value

By default return_type="cnet" and this function returns an augmented Cnet plot. The labels of each cluster are defined by the input names(clusters), however an igraph attribute "set_labels" includes an abbreviated label of the top ranked sets for each cluster. This label is probably the closest thing to summarizing the composition of each cluster.

Details

This function is similar to rank_mem_clusters() in that it starts with mem results from multiEnrichMap() and a list of clusters of pathways/sets. Instead of ranking and choosing exemplars from each clusters, it simply collapses each cluster into one super-set that contains union of all genes.

It does also run rank_mem_clusters() in the event one would want to collapse only the top per_cluster entries for each cluster, but the default is to include them all.

See also

Other jam utility functions: ashape(), avg_angles(), avg_colors_by_list(), cell_fun_bivariate(), colorRamp2D(), curateIPAcolnames(), deconcat_df2(), display_colorRamp2D(), enrichList2geneHitList(), 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(), summarize_node_spacing(), with_ht_opts(), xyAngle()