Collapse Multienrichment clusters
Arguments
- cluster_color_min_fraction
numeric
value between 0 and 1 used to define the cnet colors for each cluster. The number of significant pathways is calculated per cluster for each enrichment usingmem$enrichIMcolors
, and the fraction of significant pathways versus the max number per enrichment is used to filter. For example a cluster with 10 pathways, might have 8 significant pathways in one enrichment result, and 3 significant pathways in another enrichment result. The fraction for each enrichment is8/8 == 1
for the first enrichment, and3/8 = 0.375
for the second enrichment. Whencluster_color_min_fraction=0.5
(default) the first enrichment color would be included, but not the second enrichment color. The intent is to represent enrichment colors that have at least half (0.5
) the pathways of the most representative (max) enrichment color. Therefore, a cluster with only one significant pathway from a given enrichment would typically not be representive of that enrichment, and its enrichment color would not be included.
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()
,
bulk_cnet_adjustments()
,
call_fn_ellipsis_deprecated()
,
cell_fun_bivariate()
,
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()