<!-- README.md is generated from README.Rmd. Please edit that file --> # concordexR <!-- badges: start --> [](https://codecov.io/gh/pachterlab/concordexR) <!-- badges: end --> 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”](https://doi.org/10.1101/2023.06.28.546949). 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](https://github.com/) with: ``` r # 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 installation ``` Versions 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: ``` r if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install(version="devel") BiocManager::install("concordexR") ``` ## Example This is a basic example using concordex: ``` r library(SFEData) library(Voyager) #> Loading required package: SpatialFeatureExperiment #> #> Attaching package: 'SpatialFeatureExperiment' #> The following object is masked from 'package:base': #> #> scale library(scran) #> Loading required package: SingleCellExperiment #> Loading required package: SummarizedExperiment #> Loading required package: MatrixGenerics #> Loading required package: matrixStats #> #> Attaching package: 'MatrixGenerics' #> The following objects are masked from 'package:matrixStats': #> #> colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, #> colCounts, colCummaxs, colCummins, colCumprods, colCumsums, #> colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, #> colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, #> colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, #> colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, #> colWeightedMeans, colWeightedMedians, colWeightedSds, #> colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, #> rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, #> rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, #> rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, #> rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, #> rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, #> rowWeightedMads, rowWeightedMeans, rowWeightedMedians, #> rowWeightedSds, rowWeightedVars #> Loading required package: GenomicRanges #> Loading required package: stats4 #> Loading required package: BiocGenerics #> #> Attaching package: 'BiocGenerics' #> The following objects are masked from 'package:stats': #> #> IQR, mad, sd, var, xtabs #> The following objects are masked from 'package:base': #> #> anyDuplicated, aperm, append, as.data.frame, basename, cbind, #> colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, #> get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, #> match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, #> Position, rank, rbind, Reduce, rownames, sapply, setdiff, table, #> tapply, union, unique, unsplit, which.max, which.min #> Loading required package: S4Vectors #> #> Attaching package: 'S4Vectors' #> The following object is masked from 'package:utils': #> #> findMatches #> The following objects are masked from 'package:base': #> #> expand.grid, I, unname #> Loading required package: IRanges #> Loading required package: GenomeInfoDb #> Loading required package: Biobase #> Welcome to Bioconductor #> #> Vignettes contain introductory material; view with #> 'browseVignettes()'. To cite Bioconductor, see #> 'citation("Biobase")', and for packages 'citation("pkgname")'. #> #> Attaching package: 'Biobase' #> The following object is masked from 'package:MatrixGenerics': #> #> rowMedians #> The following objects are masked from 'package:matrixStats': #> #> anyMissing, rowMedians #> Loading required package: scuttle library(bluster) library(concordexR) ``` ``` r sfe <- McKellarMuscleData("small") #> see ?SFEData and browseVignettes('SFEData') for documentation #> loading from cache clusters <- quickCluster(sfe, min.size=2, d=15) ``` ``` r nbc <- calculateConcordex( sfe, clusters, n_neighbors=10, BLUSPARAM=KmeansParam(2) ) colData(sfe)[["shr"]] <- attr(nbc, "shrs") ``` ``` r plotSpatialFeature(sfe, features="shr") ``` <img src="man/figures/README-plot-shr-1.png" width="70%" /> ## 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} } ## Maintainer [Kayla Jackson](https://github.com/kayla-jackson)