Hypergeometric test for cluster enrichment, e.g. to test whether a barcode is enriched in any cluster.

Takes a single cell object, a grouping variable, a factor within the group to test, and an ident class (i.e. clusters). Per level of ident performs hypergeometric testing for enrichment of group factor

Usage

plotClusterEnrichment(
  sc.obj = NULL,
  group = "barcode",
  factor = NULL,
  clusters = "seurat_clusters",
  threshold = 0.01,
  order = TRUE,
  plot = TRUE
)

Arguments

sc.obj

Single cell Seurat or SingleCellExperiment object containing clusters and group metadata.

group

a column of metadata (string). Default = `barcode`.

factor

a level of group to test for enrichment per cluster, e.g. a specific barcode (string).

clusters

a column of metadata defining the cluster identities of each cell (string). Default = `seurat_clusters`

threshold

P-value threshold for hypergeometric test (decimal). Default = `0.01`.

order

Order clusters in plot by -log10 P-value (boolean). Default = `TRUE`.

plot

Plot hypergeometric test results or return plot data (boolean). Default = `TRUE`.

Value

Returns a histogram of hypergeometric test results or underlying plot data

Details

plotClusterEnrichment

Hypergeometric test for enrichment of specific classes of cells in single cell RNA-seq clusters