norm_srsc: Jointl normalization of spatially resolved single cell data...

In jianhaizhang/spatialHeatmap: spatialHeatmap: Visualizing Spatial Assays in Anatomical Images and Large-Scale Data Extensions

Jointl normalization of spatially resolved single cell data and bulk data

Description

Jointl normalization of spatially resolved single cell data and bulk data

Usage

norm_srsc(cell, assay, bulk)

Arguments

cell	A Seurat object.
assay	The assay to use for normalization in the spatial single-cell data.
bulk	The bulk assay data.

Author(s)

Jianhai Zhang [e-mail]
Dr. Thomas Girke [e-mail]

References

Hao and Hao et al. Integrated analysis of multimodal single-cell data. Cell (2021) [Seurat V4] Stuart and Butler et al. Comprehensive Integration of Single-Cell Data. Cell (2019) [Seurat V3] Butler et al. Integrating single-cell transcriptomic data across different conditions, technologies, and species. Nat Biotechnol (2018) [Seurat V2] Satija and Farrell et al. Spatial reconstruction of single-cell gene expression data. Nat Biotechnol (2015) [Seurat V1] Pagès H, Lawrence M, Aboyoun P (2022). _S4Vectors: Foundation of vector-like and list-like containers in Bioconductor_. R package version 0.36.1, <https://bioconductor.org/packages/S4Vectors>. Morgan M, Obenchain V, Hester J, Pagès H (2021). SummarizedExperiment: SummarizedExperiment container. R package version 1.24. 0, https://bioconductor.org/packages/SummarizedExperiment. Amezquita R, Lun A, Becht E, Carey V, Carpp L, Geistlinger L, Marini F, Rue-Albrecht K, Risso D, Soneson C, Waldron L, Pages H, Smith M, Huber W, Morgan M, Gottardo R, Hicks S (2020). “Orchestrating single-cell analysis with Bioconductor.” _Nature Methods_, *17*, 137-145. <https://www.nature.com/articles/s41592-019-0654-x>.

Examples

library(Seurat); library(SummarizedExperiment)
# Bulk data. 
blk.mus <- readRDS(system.file("extdata/shinyApp/data", "bulk_mouse_cocluster.rds", package="spatialHeatmap"))
assay(blk.mus)[1:3, 1:5] 
# Spatial single-cell data.
# library(SeuratData)
# if (!'stxBrain' %in% InstalledData()$Dataset) InstallData("stxBrain")
# brain <- LoadData("stxBrain", type = "anterior1") 
# Joint normalization. 
# nor.lis <- norm_srsc(cell=brain, assay='Spatial', bulk=blk.mus) 
# Separate bulk and cell data. 
# srt.sc <- nor.lis$cell; bulk <- nor.lis$bulk 

jianhaizhang/spatialHeatmap documentation built on Nov. 28, 2024, 4:44 p.m.