rank_mem_clusters: Rank Multienrichment clusters

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

Rank Multienrichment clusters

Description

Rank Multienrichment clusters

Usage

rank_mem_clusters(
  mem,
  clusters,
  choose = NULL,
  per_cluster = Inf,
  byCols = c("composite_rank", "minp_rank", "gene_count_rank"),
  verbose = FALSE,
  ...
)

Arguments

mem	list object output from multiEnrichMap()
clusters	list containing set names, that must match colnames(mem$memIM) and rownames(mem$enrichIM).
choose	optional vector indicating which clusters to return. If an integer vector, it refers to the elements in the input clusters. If a character vector, it must contain values in names(clusters). When choose is NULL, all clusters are returned.
per_cluster	integer vector with the number of entries to return for each cluster. Values will be recycled to the length of the clusters to be returned, defined by choose or by length(clusters) when choose is NULL.
byCols	character vector used to sort the resulting data.frame within each cluster. This argument is passed directly to jamba::mixedSortDF().
verbose	logical indicating whether to print verbose output.
...	additional arguments are ignored.

Details

This function takes list output from multiEnrichMap(), and a list of clusters, and returns a data.frame that contains several rank order metrics. It is intended to be used with column clusters following mem_gene_path_heatmap(), see examples.

The argument per_cluster is intended to make it convenient to pick the top exemplar pathways, especially when argument byCols is defined so that it sorts by the rank columns.

The argument choose is intended to make it easy to retrieve pathways from specific clusters.

Value

data.frame sorted by the criteria defined by byCols, with colname "set" to indicate the pathway/set name.

See Also

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(), mem_find_overlap(), order_colors(), rotate_coordinates(), subgraph_jam(), subset_mem(), summarize_node_spacing(), xyAngle()

Examples

## Start with mem
# mem <- multiEnrichMap(...);
# gp_hm <- mem_gene_path_heatmap(mem, column_split=4);
## Retrieve clusters from the Heatmap output, there should be 4 clusters
# clusters <- heatmap_column_order(gp_hm)
# clusters_df <- rank_mem_clusters(mem, clusters)

jmw86069/multienrichjam documentation built on Nov. 3, 2024, 10:29 p.m.