TopLigandsByIdent: Plot most active ligands in receiver cell type

In BlishLab/scriabin: Single-cell resolved interaction analysis through binning

Plot most active ligands in receiver cell type

Description

Plot most active ligands in receiver cell type

Usage

TopLigandsByIdent(
  seu,
  active_ligands = NULL,
  sender = NULL,
  receiver = NULL,
  group.by = "orig.ident",
  pearson.threshold = 0.1,
  ligands.display = 25,
  assay = "SCT"
)

Arguments

seu	A seurat object
active_ligands	The output of RankActiveLigands
sender	Character vector specifying the name of cells to consider as senders in the group.by meta.data column
receiver	Character vector specifying the name of cells to consider as receivers in the group.by meta.data column
group.by	Name of meta.data column to search for sender and receiver
pearson.threshold	Pearson coefficient for calculating the percentage of receiver cells with ligand activity (default: 0.1)
ligands.display	Number of top ligands to display, ranked by mean ligand activity (default: 25)
assay	Assay of Seurat object to calculate average expression

Value

A ggplot object

BlishLab/scriabin documentation built on Sept. 16, 2024, 1:19 a.m.