PlotLigandTargetAlluvium: Plot connections between ligands and predicted target genes...

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

Plot connections between ligands and predicted target genes This function plots an alluvium displaying ligand-target linkages. If you consider a subset of receiver_cells, and a set of ligands_of_interest, perhaps those expressed by a particular sender cell type of interest, this function will find the top n_targets target genes predicted to be upregulated by those ligands. The only target genes shown are those that also appear in the individual cell's gene signature.

Description

Plot connections between ligands and predicted target genes This function plots an alluvium displaying ligand-target linkages. If you consider a subset of receiver_cells, and a set of ligands_of_interest, perhaps those expressed by a particular sender cell type of interest, this function will find the top n_targets target genes predicted to be upregulated by those ligands. The only target genes shown are those that also appear in the individual cell's gene signature.

Usage

PlotLigandTargetAlluvium(
  seu,
  signature_matrix = NULL,
  active_ligands = active_ligands,
  receiver_cells = NULL,
  ligands_of_interest = NULL,
  n_targets = 250
)

Arguments

seu	A seurat object
signature_matrix	The output of GenerateCellSignature
active_ligands	The output of RankActiveLigands
receiver_cells	Character vector of receiver cells to query
ligands_of_interest	Ligands to plot
n_targets	Top ligand-target gene linkages for each ligand to plot

Value

A ggplot object

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