The goal of concordexR is to identify spatial homogeneous regions (SHRs) as defined in the recent manuscript, “Identification of spatial homogenous regions in tissues with concordex”. Briefly, SHRs are are domains that are homogeneous with respect to cell type composition. concordex relies on the the k-nearest-neighbor (kNN) graph to representing similarities between cells and uses common clustering algorithms to identify SHRs.
Installation
(Recommended) You can install the development version of concordexR from GitHub with:
# install.packages("devtools")
devtools::install_github("pachterlab/concordexR")
#> Using GitHub PAT from the git credential store.
#> Skipping install of 'concordexR' from a github remote, the SHA1 (046127e9) has not changed since last install.
#> Use `force = TRUE` to force installationVersions of the concordexR package that do not enable clustering spatial data into spatial homogeneous regions (SHRs) are available for Bioconductor versions 3.17-19. The most recent version of the package is slated to be released on Bioconductor version 3.20. You can install the Bioconductor development version with:
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(version="devel")
BiocManager::install("concordexR")Example
This is a basic example using concordex:
library(SFEData)
library(Voyager)
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library(scran)
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#> Loading required package: scuttle
library(bluster)
library(concordexR)
sfe <- McKellarMuscleData("small")
#> see ?SFEData and browseVignettes('SFEData') for documentation
#> loading from cache
clusters <- quickCluster(sfe, min.size=2, d=15)
nbc <- calculateConcordex(
sfe,
clusters,
n_neighbors=10,
BLUSPARAM=KmeansParam(2)
)
colData(sfe)[["shr"]] <- attr(nbc, "shrs")
plotSpatialFeature(sfe, features="shr")
Citation
If you’d like to use the concordexR package in your research, please cite our recent bioRxiv preprint
Jackson, K.; Booeshaghi, A. S.; Gálvez-Merchán, Á.; Moses, L.; Chari, T.; Pachter, L. Quantitative assessment of single-cell RNA-seq clustering with CONCORDEX. bioRxiv (Cold Spring Harbor Laboratory) 2023. https://doi.org/10.1101/2023.06.28.546949.
@article {Jackson2023.06.28.546949, author = {Jackson, Kayla C. and Booeshaghi, A. Sina and G{’a}lvez-Merch{’a}n, {’A}ngel and Moses, Lambda and Chari, Tara and Kim, Alexandra and Pachter, Lior}, title = {Identification of spatial homogeneous regions in tissues with concordex}, year = {2024}, doi = {10.1101/2023.06.28.546949}, publisher = {Cold Spring Harbor Laboratory}, URL = {https://www.biorxiv.org/content/early/2024/07/18/2023.06.28.546949}, journal = {bioRxiv} }