SigScore: Calculate Signature Score for Cell Clusters

In CAESAR.Suite: CAESAR: a Cross-Technology and Cross-Resolution Framework for Spatial Omics Annotation

Calculate Signature Score for Cell Clusters

Description

This function calculates a signature score for cell clusters based on the embeddings of cells and genes in a Seurat object. The score measures how well the genes linked to specific clusters are separated in the embedding space. The function also supports returning a weighted mean score across all clusters.

Usage

SigScore(seu, reduction, label, gclink, return.mean = TRUE)

Arguments

seu	A Seurat object containing the single-cell RNA-seq data.
reduction	A character string specifying the name of the dimensional reduction to use (e.g., "caesar").
label	A character string specifying the column name in the Seurat object's metadata that contains the cell type or cluster labels.
gclink	A data frame with two columns: 'gene' and 'cluster', where 'gene' corresponds to gene names and 'cluster' corresponds to the associated cell cluster.
return.mean	Logical, indicating whether to return the weighted mean signature score across all clusters. If FALSE, returns the score for each gene-cluster pair. Default is TRUE.

Details

The function computes the distance between gene embeddings and cell embeddings using a custom distance metric. It then calculates a score for each gene-cluster pair by evaluating how well the genes associated with a specific cluster are ordered in proximity to the cells of that cluster. The score is normalized between 0 and 1, where 1 indicates perfect separation.

Value

If return.mean = TRUE, a numeric value representing the weighted mean signature score across all clusters. If return.mean = FALSE, a numeric vector containing the signature score for each gene-cluster pair.

Examples

library(Seurat)
data(toydata)

seu <- toydata$seu

seu$cluster <- Idents(seu)

gclink <- data.frame(
    gene = c(
        "FBLN1", "CCDC80", "LYPD3", "MLPH", "HOXD9", "EGFL7",
        "HAVCR2", "IGSF6", "KRT5", "KRT6B", "CD79A", "DERL3",
        "CAV1", "AVPR1A", "CD3G", "CD3D"
    ),
    cluster = c(
        "CAFs", "CAFs", "Cancer Epithelial", "Cancer Epithelial",
        "Endothelial", "Endothelial", "Myeloid", "Myeloid",
        "Normal Epithelial", "Normal Epithelial", "Plasmablasts",
        "Plasmablasts", "PVL", "PVL", "T-cells", "T-cells"
    )
)

score <- SigScore(
    seu, reduction = "caesar", label = "cluster", gclink = gclink,
    return.mean = TRUE
)
print(score)

score <- SigScore(
    seu, reduction = "caesar", label = "cluster",
    gclink = gclink, return.mean = FALSE
)
print(score)

CAESAR.Suite documentation built on April 3, 2025, 10:32 p.m.