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README.Rmd
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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# visiumStitched <img src="man/figures/logo.png" align="right" />
<!-- badges: start -->
[](https://zenodo.org/doi/10.5281/zenodo.13012339)
[](https://github.com/LieberInstitute/visiumStitched/issues)
[](https://github.com/LieberInstitute/visiumStitched/pulls)
[](https://lifecycle.r-lib.org/articles/stages.html#stable)
[](https://github.com/LieberInstitute/visiumStitched/actions/workflows/check-bioc.yml)
[](https://app.codecov.io/gh/LieberInstitute/visiumStitched?branch=devel)
[](https://bioconductor.org/checkResults/release/bioc-LATEST/visiumStitched)
[](https://bioconductor.org/checkResults/devel/bioc-LATEST/visiumStitched)
[](http://bioconductor.org/packages/stats/bioc/visiumStitched/)
[](https://support.bioconductor.org/tag/visiumStitched)
[](https://bioconductor.org/packages/release/bioc/html/visiumStitched.html#since)
[](http://bioconductor.org/checkResults/devel/bioc-LATEST/visiumStitched/)
[](https://bioconductor.org/packages/release/bioc/html/visiumStitched.html#since)
<!-- badges: end -->
`visiumStitched` provides helper functions for working with multiple Visium
capture areas that overlap each other. This package was developed along with
the companion example use case data available from
https://github.com/LieberInstitute/visiumStitched_brain. `visiumStitched`
prepares `SpaceRanger` (10x Genomics) output files so you can stitch the images
from groups of capture areas together with `Fiji`. Then `visiumStitched` builds
a `SpatialExperiment` object with the stitched data and makes an artificial
hexagonal grid enabling the seamless use of spatial clustering methods that rely
on such grid to identify neighboring spots, such as `PRECAST` and `BayesSpace`.
The `SpatialExperiment` objects created by `visiumStitched` are compatible with
`spatialLIBD`, which can be used to build interactive websites for stitched
`SpatialExperiment` objects (check the
[example human brain data](https://libd.shinyapps.io/visiumStitched_brain)).
`visiumStitched` also enables casting `SpatialExperiment` objects as `Seurat`
objects.
For details, check the
[documentation site](http://research.libd.org/visiumStitched/).
## Example data processed with visiumStitched
Here is example human brain data from
[LieberInstitute/visiumStitched_brain](https://github.com/LieberInstitute/visiumStitched_brain)
that was stitched together using `visiumStitched`. The resulting data can be
accessed and visualized with
[`spatialLIBD`](https://research.libd.org/spatialLIBD/) version 1.17.8 or newer.
```{r "example_visiumStitched_brain"}
## Check that you have a recent version of spatialLIBD installed
stopifnot(packageVersion("spatialLIBD") >= "1.17.8")
## Download the spot-level data, which is a SpatialExperiment object
spe <- spatialLIBD::fetch_data(type = "visiumStitched_brain_spe")
## Explore the stitched data
spe
## Show clustering results from PRECAST at k = 8
spatialLIBD::vis_clus(
spe,
clustervar = "precast_k8",
is_stitched = TRUE
)
```
## Installation instructions
Get the latest stable `R` release from [CRAN](http://cran.r-project.org/). Then
install `visiumStitched` from Bioconductor using the following code:
```{r 'install', eval = FALSE}
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("visiumStitched")
```
## Citation
Below is the citation output from using `citation('visiumStitched')` in R.
Please run this yourself to check for any updates on how to cite
__visiumStitched__.
```{r 'citation', eval = requireNamespace('visiumStitched')}
print(citation("visiumStitched"), bibtex = TRUE)
```
Please note that the `visiumStitched` was only made possible thanks to many
other R and bioinformatics software authors, which are cited either in the
vignettes and/or the paper(s) describing this package.
## Code of Conduct
Please note that the `visiumStitched` project is released with a
[Contributor Code of Conduct](http://bioconductor.org/about/code-of-conduct/).
By contributing to this project, you agree to abide by its terms.
## Development tools
* Continuous code testing is possible thanks to [GitHub actions](https://www.tidyverse.org/blog/2020/04/usethis-1-6-0/) through `r BiocStyle::CRANpkg('usethis')`, `r BiocStyle::CRANpkg('remotes')`, and `r BiocStyle::CRANpkg('rcmdcheck')` customized to use [Bioconductor's docker containers](https://www.bioconductor.org/help/docker/) and `r BiocStyle::Biocpkg('BiocCheck')`.
* Code coverage assessment is possible thanks to [codecov](https://codecov.io/gh) and `r BiocStyle::CRANpkg('covr')`.
* The [documentation website](http://LieberInstitute.github.io/visiumStitched) is automatically updated thanks to `r BiocStyle::CRANpkg('pkgdown')`.
* The code is styled automatically thanks to `r BiocStyle::CRANpkg('styler')`.
* The documentation is formatted thanks to `r BiocStyle::CRANpkg('devtools')` and `r BiocStyle::CRANpkg('roxygen2')`.
For more details, check the `dev` directory.
This package was developed using `r BiocStyle::Biocpkg('biocthis')`.