plot_markers_to_clusters-ClusterSet-method: Map cell markers to clusters (hypergeometric/jaccard)

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

Map cell markers to clusters (hypergeometric/jaccard)

Description

Use jaccard index and hypergeometric to map a list of cell markers to gene clusters.

Usage

## S4 method for signature 'ClusterSet'
plot_markers_to_clusters(
  object,
  markers = NULL,
  gradient_palette = c("white", colors_for_gradient("De2")),
  background = NULL,
  cell_type_order = c("None", "hclust"),
  only_specific = FALSE,
  jaccard_scale = 10
)

Arguments

object	A ClusterSet object.
markers	A list of cell markers.
gradient_palette	A vector of colors for the gradient palette.
background	The background for hypergeometric test. Typically the list of genes annotated in the considered gene ontology (e.g. BP).
cell_type_order	The order of cell types. Can be "None" or "hclust". Not supported at the moment.
only_specific	Logical value indicating whether to show only specific markers.
jaccard_scale	The scale factor for Jaccard coefficient.

Value

A plot showing the relationship between markers and clusters.

Examples

load_example_dataset("8028126/files/pbmc3k_medium_clusters_enr")
library(clustermole)
m <- clustermole_markers(species = "hs")
markers <- split(m$gene[m$organ == "Blood" & m$species == "Human"], 
                 m$celltype[m$organ == "Blood" & m$species == "Human"])
plot_markers_to_clusters(pbmc3k_medium_clusters_enr, markers=markers)

dputhier/dbfmcl documentation built on Dec. 20, 2024, 1:59 a.m.