Rename from spatialNAcUtils to visiumStitched

DESCRIPTION

@@ -1,4 +1,4 @@
-Package: spatialNAcUtils
+Package: visiumStitched
 Title: Functions Useful for the spatial_NAc Project
 Version: 0.99.1
 Date: 2024-02-15

NEWS.md

@@ -1,10 +1,10 @@
-# spatialNAcUtils 0.99.1
+# visiumStitched 0.99.1
 
 BUG FIXES
 
 * `spot_plot()` correctly receives `colors` parameter when `is_discrete` is `FALSE`, and documentation describing this was fixed
 
-# spatialNAcUtils 0.99.0
+# visiumStitched 0.99.0
 
 NEW FEATURES
 

README.Rmd

@@ -13,52 +13,52 @@ knitr::opts_chunk$set(
 )
 ```
 
-# spatialNAcUtils
+# visiumStitched
 
 <!-- badges: start -->
-[![GitHub issues](https://img.shields.io/github/issues/LieberInstitute/spatialNAcUtils)](https://github.com/LieberInstitute/spatialNAcUtils/issues)
-[![GitHub pulls](https://img.shields.io/github/issues-pr/LieberInstitute/spatialNAcUtils)](https://github.com/LieberInstitute/spatialNAcUtils/pulls)
+[![GitHub issues](https://img.shields.io/github/issues/LieberInstitute/visiumStitched)](https://github.com/LieberInstitute/visiumStitched/issues)
+[![GitHub pulls](https://img.shields.io/github/issues-pr/LieberInstitute/visiumStitched)](https://github.com/LieberInstitute/visiumStitched/pulls)
 [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
-[![R-CMD-check-bioc](https://github.com/LieberInstitute/spatialNAcUtils/actions/workflows/check-bioc.yml/badge.svg)](https://github.com/LieberInstitute/spatialNAcUtils/actions/workflows/check-bioc.yml)
-[![Codecov test coverage](https://codecov.io/gh/LieberInstitute/spatialNAcUtils/branch/devel/graph/badge.svg)](https://app.codecov.io/gh/LieberInstitute/spatialNAcUtils?branch=devel)
+[![R-CMD-check-bioc](https://github.com/LieberInstitute/visiumStitched/actions/workflows/check-bioc.yml/badge.svg)](https://github.com/LieberInstitute/visiumStitched/actions/workflows/check-bioc.yml)
+[![Codecov test coverage](https://codecov.io/gh/LieberInstitute/visiumStitched/branch/devel/graph/badge.svg)](https://app.codecov.io/gh/LieberInstitute/visiumStitched?branch=devel)
 <!-- badges: end -->
 
-`spatialNAcUtils` is intended to provide re-usable functions helpful for various analyses in the [spatialNAc project](https://github.com/LieberInstitute/spatial_NAc). Code is maintained here in an R package for ease of use, and to ensure dependent `spatialNAc` code can easily refer to the latest functions here.
+`visiumStitched` is intended to provide re-usable functions helpful for various analyses in the [spatialNAc project](https://github.com/LieberInstitute/spatial_NAc). Code is maintained here in an R package for ease of use, and to ensure dependent `spatialNAc` code can easily refer to the latest functions here.
 
-For details, check the [documentation site](http://research.libd.org/spatialNAcUtils/).
+For details, check the [documentation site](http://research.libd.org/visiumStitched/).
 
 ## Installation instructions
 
-Get the latest stable `R` release from [CRAN](http://cran.r-project.org/). Then install `spatialNAcUtils` from [GitHub](https://github.com/LieberInstitute/spatialNAcUtils) using the following code:
+Get the latest stable `R` release from [CRAN](http://cran.r-project.org/). Then install `visiumStitched` from [GitHub](https://github.com/LieberInstitute/visiumStitched) using the following code:
 
 ```{r 'install', eval = FALSE}
 if (!requireNamespace("BiocManager", quietly = TRUE)) {
     install.packages("BiocManager")
 }
 
-BiocManager::install("LieberInstitute/spatialNAcUtils")
+BiocManager::install("LieberInstitute/visiumStitched")
 ```
 
 ## Citation
 
-Below is the citation output from using `citation('spatialNAcUtils')` in R. Please
-run this yourself to check for any updates on how to cite __spatialNAcUtils__.
+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('spatialNAcUtils')}
-print(citation("spatialNAcUtils"), bibtex = TRUE)
+```{r 'citation', eval = requireNamespace('visiumStitched')}
+print(citation("visiumStitched"), bibtex = TRUE)
 ```
 
-Please note that the `spatialNAcUtils` 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.
+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 `spatialNAcUtils` 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.
+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/spatialNAcUtils) is automatically updated thanks to `r BiocStyle::CRANpkg('pkgdown')`.
+* 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')`.
 

README.md

@@ -1,76 +1,76 @@
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
-# spatialNAcUtils
+# visiumStitched
 
 <!-- badges: start -->
 
 [![GitHub
-issues](https://img.shields.io/github/issues/LieberInstitute/spatialNAcUtils)](https://github.com/LieberInstitute/spatialNAcUtils/issues)
+issues](https://img.shields.io/github/issues/LieberInstitute/visiumStitched)](https://github.com/LieberInstitute/visiumStitched/issues)
 [![GitHub
-pulls](https://img.shields.io/github/issues-pr/LieberInstitute/spatialNAcUtils)](https://github.com/LieberInstitute/spatialNAcUtils/pulls)
+pulls](https://img.shields.io/github/issues-pr/LieberInstitute/visiumStitched)](https://github.com/LieberInstitute/visiumStitched/pulls)
 [![Lifecycle:
 experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
-[![R-CMD-check-bioc](https://github.com/LieberInstitute/spatialNAcUtils/actions/workflows/check-bioc.yml/badge.svg)](https://github.com/LieberInstitute/spatialNAcUtils/actions/workflows/check-bioc.yml)
+[![R-CMD-check-bioc](https://github.com/LieberInstitute/visiumStitched/actions/workflows/check-bioc.yml/badge.svg)](https://github.com/LieberInstitute/visiumStitched/actions/workflows/check-bioc.yml)
 [![Codecov test
-coverage](https://codecov.io/gh/LieberInstitute/spatialNAcUtils/branch/devel/graph/badge.svg)](https://app.codecov.io/gh/LieberInstitute/spatialNAcUtils?branch=devel)
+coverage](https://codecov.io/gh/LieberInstitute/visiumStitched/branch/devel/graph/badge.svg)](https://app.codecov.io/gh/LieberInstitute/visiumStitched?branch=devel)
 <!-- badges: end -->
 
-`spatialNAcUtils` is intended to provide re-usable functions helpful for
+`visiumStitched` is intended to provide re-usable functions helpful for
 various analyses in the [spatialNAc
 project](https://github.com/LieberInstitute/spatial_NAc). Code is
 maintained here in an R package for ease of use, and to ensure dependent
 `spatialNAc` code can easily refer to the latest functions here.
 
 For details, check the [documentation
-site](http://research.libd.org/spatialNAcUtils/).
+site](http://research.libd.org/visiumStitched/).
 
 ## Installation instructions
 
 Get the latest stable `R` release from
-[CRAN](http://cran.r-project.org/). Then install `spatialNAcUtils` from
-[GitHub](https://github.com/LieberInstitute/spatialNAcUtils) using the
+[CRAN](http://cran.r-project.org/). Then install `visiumStitched` from
+[GitHub](https://github.com/LieberInstitute/visiumStitched) using the
 following code:
 
 ``` r
 if (!requireNamespace("BiocManager", quietly = TRUE)) {
     install.packages("BiocManager")
 }
 
-BiocManager::install("LieberInstitute/spatialNAcUtils")
+BiocManager::install("LieberInstitute/visiumStitched")
 ```
 
 ## Citation
 
-Below is the citation output from using `citation('spatialNAcUtils')` in
+Below is the citation output from using `citation('visiumStitched')` in
 R. Please run this yourself to check for any updates on how to cite
-**spatialNAcUtils**.
+**visiumStitched**.
 
 ``` r
-print(citation("spatialNAcUtils"), bibtex = TRUE)
-#> Warning in citation("spatialNAcUtils"): could not determine year for
-#> 'spatialNAcUtils' from package DESCRIPTION file
-#> To cite package 'spatialNAcUtils' in publications use:
+print(citation("visiumStitched"), bibtex = TRUE)
+#> Warning in citation("visiumStitched"): could not determine year for
+#> 'visiumStitched' from package DESCRIPTION file
+#> To cite package 'visiumStitched' in publications use:
 #> 
-#>   Eagles N (????). _spatialNAcUtils: Functions Useful for the
+#>   Eagles N (????). _visiumStitched: Functions Useful for the
 #>   spatial_NAc Project_. R package version 0.99.0.
 #> 
 #> A BibTeX entry for LaTeX users is
 #> 
 #>   @Manual{,
-#>     title = {spatialNAcUtils: Functions Useful for the spatial_NAc Project},
+#>     title = {visiumStitched: Functions Useful for the spatial_NAc Project},
 #>     author = {Nicholas J. Eagles},
 #>     note = {R package version 0.99.0},
 #>   }
 ```
 
-Please note that the `spatialNAcUtils` was only made possible thanks to
+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 `spatialNAcUtils` project is released with a
+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.
@@ -89,7 +89,7 @@ contributing to this project, you agree to abide by its terms.
   [codecov](https://codecov.io/gh) and
   *[covr](https://CRAN.R-project.org/package=covr)*.
 - The [documentation
-  website](http://LieberInstitute.github.io/spatialNAcUtils) is
+  website](http://LieberInstitute.github.io/visiumStitched) is
   automatically updated thanks to
   *[pkgdown](https://CRAN.R-project.org/package=pkgdown)*.
 - The code is styled automatically thanks to

dev/01_create_pkg.R

@@ -52,11 +52,11 @@ if (!requireNamespace("BiocStyle", quietly = TRUE)) {
 
 
 ## Package names have some properties. You can also use:
-available::available("spatialNAcUtils")
+available::available("visiumStitched")
 ## to check that your package name is not taken and that it doesn't have
 ## a meaning that you might not be aware of.
 
-usethis::create_package("spatialNAcUtils")
+usethis::create_package("visiumStitched")
 ## This opens a new window in RStudio
 
 ## Note: If you create packages frequently, check the help file for

tests/testthat.R

@@ -7,6 +7,6 @@
 # * https://testthat.r-lib.org/articles/special-files.html
 
 library(testthat)
-library(spatialNAcUtils)
+library(visiumStitched)
 
-test_check("spatialNAcUtils")
+test_check("visiumStitched")

vignettes/spatialNAcUtils.Rmd → vignettes/visiumStitched.Rmd

@@ -1,5 +1,5 @@
 ---
-title: "Introduction to spatialNAcUtils"
+title: "Introduction to visiumStitched"
 author: 
   - name: Nicholas J. Eagles
     affiliation:
@@ -13,9 +13,9 @@ output:
     toc_depth: 2
     code_folding: show
 date: "`r doc_date()`"
-package: "`r pkg_ver('spatialNAcUtils')`"
+package: "`r pkg_ver('visiumStitched')`"
 vignette: >
-  %\VignetteIndexEntry{Introduction to spatialNAcUtils}
+  %\VignetteIndexEntry{Introduction to visiumStitched}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}  
 ---
@@ -45,43 +45,43 @@ bib <- c(
     rmarkdown = citation("rmarkdown")[1],
     sessioninfo = citation("sessioninfo")[1],
     testthat = citation("testthat")[1],
-    spatialNAcUtils = citation("spatialNAcUtils")[1]
+    visiumStitched = citation("visiumStitched")[1]
 )
 ```
 
 # Basics
 
-## Install `spatialNAcUtils`
+## Install `visiumStitched`
 
-`r Biocpkg("spatialNAcUtils")` is a `R` package available from [GitHub](https://github.com/LieberInstitute/spatialNAcUtils).
+`r Biocpkg("visiumStitched")` is a `R` package available from [GitHub](https://github.com/LieberInstitute/visiumStitched).
 It can be installed with the following commands in your `R` session:
 
 ```{r "install", eval = FALSE}
 if (!requireNamespace("remotes", quietly = TRUE)) {
     install.packages("remotes")
 }
 
-remotes::install("LieberInstitute/spatialNAcUtils")
+remotes::install("LieberInstitute/visiumStitched")
 ```
 
 ## Other documentation
 
-For now, `r Biocpkg("spatialNAcUtils")` doesn't have a demonstrative vignette as documentation.
-Please refer to the [Reference](http://research.libd.org/spatialNAcUtils/reference/index.html) for
+For now, `r Biocpkg("visiumStitched")` doesn't have a demonstrative vignette as documentation.
+Please refer to the [Reference](http://research.libd.org/visiumStitched/reference/index.html) for
 info about how to use its functions, and examples.
 
-## Citing `spatialNAcUtils`
+## Citing `visiumStitched`
 
-We hope that `r Biocpkg("spatialNAcUtils")` will be useful for your research. Please use the following information to cite the package and the overall approach. Thank you!
+We hope that `r Biocpkg("visiumStitched")` will be useful for your research. Please use the following information to cite the package and the overall approach. Thank you!
 
 ```{r "citation"}
 ## Citation info
-citation("spatialNAcUtils")
+citation("visiumStitched")
 ```
 
 # Reproducibility
 
-The `r Biocpkg("spatialNAcUtils")` package `r Citep(bib[["spatialNAcUtils"]])` was made possible thanks to:
+The `r Biocpkg("visiumStitched")` package `r Citep(bib[["visiumStitched"]])` was made possible thanks to:
 
 * R `r Citep(bib[["R"]])`
 * `r Biocpkg("BiocStyle")` `r Citep(bib[["BiocStyle"]])`
@@ -99,11 +99,11 @@ Code for creating the vignette
 ```{r createVignette, eval=FALSE}
 ## Create the vignette
 library("rmarkdown")
-system.time(render("spatialNAcUtils.Rmd", "BiocStyle::html_document"))
+system.time(render("visiumStitched.Rmd", "BiocStyle::html_document"))
 
 ## Extract the R code
 library("knitr")
-knit("spatialNAcUtils.Rmd", tangle = TRUE)
+knit("visiumStitched.Rmd", tangle = TRUE)
 ```
 
 Date the vignette was generated.