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STged

R package supporting the paper "Precision gene expression deconvolution in spatial transcriptomics with STged".

STged integrates spatial correlation patterns of gene expression and intra-cell type expression similarity to achieve precise and robust deconvolution results. Implemented within a non-negative least-squares regression framework, STged models gene expression levels at each spot as a weighted linear combination of cell type-specific gene expression, with the weights corresponding to the respective cell type proportions. By incorporating a spatial neighborhood graph prior, STged captures spatial correlation structures in cell type expressions across spots. Moreover, it integrates cell type-specific gene expression information prior from scRNA-seq data to enhance accuracy.

Overview of STged

alt text

Install STged

In the STged, there are several Python modules and R packages are needed to install first.

  • Install Python dependencies
pip install squidpy
pip install numpy
pip install anndata
  • Install R dependencies
install.packages("Matrix", repos="http://R-Forge.R-project.org")
install.packages("nnls")
install.packages("MASS")
install.packages('reticulate')
  • Install STged
devtools::install_github("TJJjiajuan/STged")

Run the example

# Load the input data set
data(Fishplus)

# The path on the Windows platform on our computer
python_env <- 'C:/Users/visitor01/.conda/envs/stged/python.exe'

# We run STged as a toy examples
model.est = STged(sc_exp, sc_label, spot_exp, spot_loc, beta,
                  gene_det_in_min_cells_per = 0.01, expression_threshold = 0,
                  nUMI = 100, verbose = FALSE, clean.only = FALSE, depthscale = 1e6,  python_env,
                  truncate = TRUE, qt = 0.0001, knei =4,  methodL = "Square",
                  coord_type = "grid", lambda1 = NULL, lambda2 = NULL, cutoff = 0.05,
                  maxiter = 100, epsilon = 1e-5)

Tutorials

We provide a small example of how to run STged using the simulated FISHplus dataset. There are two ways to run STged: (1) step by step, or (2) using the main function.

Detailed Analysis and Reproducibility Guide

A tutorial with examples of the usage of STged is available at: STged-examples.html.

Contact

Please do not hesitate to contact Dr. Tu at tujiajuan@163.com for any clarifications regarding the content or operation of the archive.