# escheR
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The goal of escheR is to create an unified multi-dimensional spatial visualizations for spatially-resolved transcriptomics data following Gestalt principles.
Our preprint describing the innovative visualization is available from [bioRxiv](https://www.biorxiv.org/content/10.1101/2023.03.18.533302).
# Installation
You can install the latest release version of `escheR` from Bioconductor. with using the following code will install version of the `nnSVG` package from Bioconductor. Additional details are shown on the [Bioconductor](https://bioconductor.org/packages/escheR) page.
```{r install_bioc, eval=FALSE}
if (!require("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("escheR")
```
The latest development version can also be installed from the `devel` version of Bioconductor or from [GitHub](https://github.com/boyiguo1/escheR) following
```{r install_github, eval = FALSE}
if (!require("devtools")) install.packages("devtools")
devtools::install_github("boyiguo1/escheR")
```
If you have R version before v4.3 and would like to install `escheR`, you can follow
```{r pre-R4.3, eval = FALSE}
if (!require("devtools")) install.packages("devtools")
devtools::install_github("boyiguo1/escheR@pre-R4.3")
```
> WARNING: The purpose of having the branch `pre-R4.3` is to allow users to use `escheR` before the formal release of R 4.3 and during the early stage of R 4.3 release. This branch will not update with any further development passing [`escheR v0.99.6`](https://github.com/boyiguo1/escheR/blob/devel/NEWS.md). We recommend users to update their R versions up to date.
# Input data format
To use `escheR`, we assume the input data are provided as a [`SpatialExperiment`](https://bioconductor.org/packages/release/bioc/html/SpatialExperiment.html) Bioconductor object. For people whose data are stored as a [`Seurat`](https://satijalab.org/seurat/articles/spatial_vignette.html) object, we advise to convert to a `SpatialExperiment` object before applying the workflow below.
# Tutorial
Please find an end-to-end tutorial at [https://boyiguo1.github.io/escheR/](https://boyiguo1.github.io/escheR/articles/SRT_eg.html)
# Citation
Our preprint describing `escheR` is available from bioRxiv:
* Guo B, Hicks SC (2023). “escheR: Unified multi-dimensional visualizations with Gestalt principles.” _bioRxiv_. doi:10.1101/2023.03.18.533302
# Acknowledgement
## Development tools
- Continuous code testing is possible thanks to [GitHub
actions](https://www.tidyverse.org/blog/2020/04/usethis-1-6-0/)
through *[biocthis](https://lcolladotor.github.io/biocthis/)*,
- The [documentation
website](https://boyiguo1.github.io/escheR/) is
automatically updated thanks to
*[pkgdown](https://CRAN.R-project.org/package=pkgdown)*.
- The code is styled automatically thanks to
*[styler](https://CRAN.R-project.org/package=styler)*.
- The documentation is formatted thanks to
*[devtools](https://CRAN.R-project.org/package=devtools)* and
*[roxygen2](https://CRAN.R-project.org/package=roxygen2)*.
