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README.md
<!-- README.md is generated from README.Rmd. Please edit that file --> # concordexR <!-- badges: start --> [![codecov](https://codecov.io/gh/pachterlab/concordexR/branch/main/graph/badge.svg?token=FSASJPR4T5)](https://codecov.io/gh/pachterlab/concordexR) <!-- badges: end --> The goal of concordexR is to identify spatial homogeneous regions (SHRs) as defined in the recent manuscrpt["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 You can install the development version of concordexR from [GitHub](https://github.com/) with: ``` r # install.packages("devtools") devtools::install_github("pachterlab/concordexR") ``` ## Example This is a basic example using concordex: ``` r library(concordexR) ``` ``` r res <- calculateConcordex(g$index, labels = iris$Species, k = 10, return.map = TRUE) ``` ``` r plotConcordexSim(res) ``` <img src="man/figures/README-unnamed-chunk-3-1.png" width="70%" /> ``` r heatConcordex(res) ``` <img src="man/figures/README-unnamed-chunk-4-1.png" width="70%" />