Robust Cell Type Decomposition (RCTD) is a computational method for deconvolving cell type mixtures in spatial transcriptomics data. RCTD learns cell type profiles from annotated RNA sequencing (RNA-seq) reference data and uses these profiles to identify cell types in spatial transcriptomic pixels while accounting for platform-specific effects.
This is a fork of Dylan Cable's original package, adapted to work with Bioconductor objects.
You can install the latest version of spacexr from Bioconductor:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("spacexr")
library(SpatialExperiment)
library(SummarizedExperiment)
library(spacexr)
# Spatial transcriptomics data
spatial_spe <- SpatialExperiment(
assay = your_spatial_counts, # genes x pixels matrix
spatialCoords = your_spatial_coordinates # x,y coordinates matrix
)
# Single-cell reference data
reference_se <- SummarizedExperiment(
assays = list(counts = your_reference_counts), # genes x cells matrix
colData = your_cell_annotations # cell type annotations df
)
# Configure and run RCTD
rctd_data <- createRctd(spatial_spe, reference_se)
results <- runRctd(rctd_data, rctd_mode = "doublet", max_cores = 4)
# Visualize results
plotAllWeights(results, title = "Cell Type Proportions")
For a detailed tutorial, please see the package vignette: browseVignettes("spacexr").
If you use this work for cell type estimation, please cite:
Cable, Dylan M., et al. "Robust decomposition of cell type mixtures in spatial transcriptomics." Nature Biotechnology 40.4 (2022): 517-526.
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