cmp_to_a_list: Map a user list to a ClusterSet and display various metrics...

In dputhier/scigenex: The scigenex package (Single-Cell Informative GENe Explorer)

Map a user list to a ClusterSet and display various metrics related to overlap with internaly stored clusters

Description

Map a user list to a ClusterSet and display various metrics related to overlap with internaly stored clusters

Usage

cmp_to_a_list(
  object = NULL,
  user_list = NULL,
  name_user_list = "user list",
  background = NULL,
  colors = c("#ED7931", "#3C78AE"),
  module = c("clust_size", "overlap_size", "percent_overlap", "percent_covered",
    "jacard_stat", "hypergeom"),
  as.list = FALSE
)

Arguments

object	A ClusterSet object
user_list	A set of elements to be compared to clusters stored in the object.
name_user_list	A name for the user list.
background	A background(e.g. all the gene of the genome).
colors	A set of colors.
module	The analyses to be performed.
as.list	Whether a list of plot should be returned (default to a patchwork).

Value

A patchwork representing the various metrics (or a list of diagram).

Examples

set.seed(124)
load_example_dataset("7871581/files/pbmc3k_medium_clusters")
user_list <- sample(row_names(pbmc3k_medium_clusters), 100)
cmp_to_a_list(pbmc3k_medium_clusters, user_list, background=user_list)

dputhier/scigenex documentation built on Feb. 28, 2025, 1:24 a.m.