find_ligands: Function findLigands

In kidcancerlab/rrrSingleCellUtils: A Set of Tools For Single Cell Analysis

Function findLigands

Description

Function findLigands

Usage

find_ligands(
  sobject,
  gset,
  receiver,
  senders,
  gset_spec = "human",
  rec_pct = 0.1,
  rec_spec = "human",
  send_pct = 0.1,
  send_spec = "human",
  stringency = "loose",
  d_plot = TRUE,
  lt_vis = TRUE,
  lr_vis = TRUE,
  n_best = 20
)

Arguments

sobject	A Seurat object containing all of the cells for analysis
gset	A character vector of gene symbols that represent genes altered in the target condition within the receiver cells, can come from findTarGenes function
receiver	The identity of the (single) cluster being stimulated by some ligand
senders	The identities of the cluster(s) producing the ligands
gset_spec	The species of the target gene set
rec_pct	A fraction between 0 and 1, the threshold for inclusion, receptors must be expressed in this fraction of receiver cells
rec_spec	The species of the receiver cells, "human" or "mouse"
send_pct	A fraction between 0 and 1, the threshold for inclusion, ligands must be expressed in this fraction of sender cells
send_spec	The species of the sender cells, "human" or "mouse"
stringency	Determine whether the ligand-receptor interactions are interpreted strictly (based on bona-fide interactions from the literature) or loosely (including predicted and inferred interaction) (must be either "strict" or "loose")
d_plot	Logical, to trigger output of a dotplot of ligands
lt_vis	Logical, to trigger output of a ligand-target visualization graph
lr_vis	Logical, to trigger output of a ligand-receptor visualization graph, weighted by downstream changes in gene expression
n_best	An integer, the number of top ligands to include on the graphs

Details

Identify ligands expressed by sender cells that activate target genes in receiver cells. published in https://doi.org/10.1038/s41592-019-0667-5 Note that this function will translate all murine genesets into their human orthologs for processing. Results of analyses using murine samples should be vetted and evaluated for legitimacy.

Value

A list containing the following objects: dotplots for 1. ligand dotplot 2. receptor dotplot (ggplot, if selected) 3. ligand-target graph (ggplot, if selected) 4. ligand-receptor interaction graph (ggplot, if selected) 5. ligand activity matrix (tibble) 6. ligand-target matrix for the prioritized ligands (tibble) 7. ligand-receptor interaction matrix (tibble)

Examples

## Not run: 
output <- find_ligands(combo, gset = targets_2,receiver = "Anchors",
                       senders = c("M1-like",
                                   "M2-like",
                                   "AlvMac",
                                   "DC"),
                       gset_spec = "human",
                       rec_spec = "human",
                       send_spec = "mouse")

## End(Not run)

kidcancerlab/rrrSingleCellUtils documentation built on April 17, 2025, 5:10 p.m.