View source: R/application_visualization.R
assign_ligands_to_celltype | R Documentation |
Assign ligands to a sender cell type, based on the strongest expressing cell type of that ligand. Ligands are only assigned to a cell type if that cell type is the only one to show an expression that is higher than the average + SD. Otherwise, it is assigned to "General".
assign_ligands_to_celltype(seuratObj, ligands, celltype_col, func.agg=mean, func.assign=function(x) mean(x) + sd(x), slot="data", condition_oi=NULL, condition_col=NULL)
seuratObj |
Seurat object |
ligands |
Vector of ligands to assign to cell types |
celltype_col |
Metadata column name in the Seurat object that contains the cell type information |
func.agg |
Function to use to aggregate the expression of a ligand across all cells in a cell type (default = mean) |
func.assign |
Function to use to assign a ligand to a cell type (default = mean + SD) |
condition_oi |
Condition of interest to subset the Seurat object (default = NULL) |
condition_col |
Metadata column name in the Seurat object that contains the condition of interest (default = NULL) |
slot |
Slot in the Seurat object to use (default = "data"). If "data", the normalized counts are first exponentiated before aggregation is performed |
A data frame of two columns, the cell type the ligand has been assigned to (ligand_type
) and the ligand name (ligand
)
## Not run:
assign_ligands_to_celltype(seuratObj = seuratObj, ligands = best_upstream_ligands[1:20],
celltype_col = "celltype", func.agg = mean, func.assign = function(x) {mean(x)+sd(x)},
slot = "data", condition_oi = "LCMV", condition_col = "aggregate")
## End(Not run)
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