3. Real Single-Cell Validation (Seurat Integration)
ImmuneSigR is designed to integrate seamlessly with
real-world scRNA-seq workflows. Below is an example of applying targeted
Plasma cell signatures to the PBMC 3k dataset.
(Note: The following code chunk is not evaluated during CRAN package building to avoid external data downloads, but you can run it locally in your R console).
library(Seurat)
library(SeuratData)
library(ggplot2)
# 1. Load and process pbmc3k dataset
data("pbmc3k")
pbmc <- UpdateSeuratObject(pbmc3k)
pbmc <- NormalizeData(pbmc) |> FindVariableFeatures() |> ScaleData() |> RunPCA() |> RunUMAP(dims = 1:10)
# 2. Extract expression matrix and define targets
expr_matrix_real <- as.matrix(pbmc[["RNA"]]$data)
real_targets <- c("Plasma cell_PMID_33208946", "Conventional Plasma cells_PMID_39406187")
# 3. Score using precise targets curated from literature
real_scores <- Score_ImmuneSigR(expr_matrix_real, target_cells = real_targets, min_genes = 5, method = "rank")
# 4. Add to metadata and visualize
pbmc <- AddMetaData(pbmc, metadata = real_scores)
score_cols <- colnames(real_scores)
p_umap <- FeaturePlot(pbmc, features = score_cols[1:2], ncol = 2, pt.size = 0.8) &
scale_colour_gradientn(colours = rev(RColorBrewer::brewer.pal(n = 11, name = "RdYlBu")))
# --- Plot Title Optimization (Publication Standard) ---
# Restructure "ImmuneSigR_CellName_PMID_xxxx_score" to "CellName Signature Score\n(PMID: xxxx)"
clean_titles <- gsub("^ImmuneSigR_(.+)_PMID_([0-9]+)_score$", "\\1 Signature Score\n(PMID: \\2)", score_cols[1:2])
p_umap[[1]] <- p_umap[[1]] + ggtitle(clean_titles[1]) + theme(plot.title = element_text(hjust = 0.5, size = 12, face = "bold"))
p_umap[[2]] <- p_umap[[2]] + ggtitle(clean_titles[2]) + theme(plot.title = element_text(hjust = 0.5, size = 12, face = "bold"))
# Display the plot
p_umap
