update links

NEWS.md

@@ -18,7 +18,7 @@
 ## Changes
 
 - The main change in this patch is a minor alteration in the circle packing algorithm that should result in packings acting slightly more consistent across different physical systems. This may result in slightly different circle placements in the clonal expansion plot, but the overall structure should remain the same. This is pretty much only noticeable in the case of extremely small testing datasets, which is why this is a patch version. However, it is very possible that the same seurat object will produce a slightly different packing than before.
-- updated citation information upon calling `citation("APackOfTheClones")`: the package as of this patch version is undergoing review in the [journal of open source software](https://joss.theoj.org/papers/eb9d2b2fc3ffb1d440bd7120b66f1f71).
+- updated citation information
 - Updated the `combined_pbmc` dataset to be up-to-date with the latest version of `Seurat`.
 - Spelling & minor fixes / updates to various functions, documentation.
 - Removed package startup deprecation message for returning users of version `0.1.x`.

README.md

@@ -1,7 +1,7 @@
 # APackOfTheClones <img src="man/figures/logo.png" width="20%" align="right" />
 
 <!-- badges: start -->
-[![JOSS status](https://joss.theoj.org/papers/eb9d2b2fc3ffb1d440bd7120b66f1f71/status.svg)](https://joss.theoj.org/papers/eb9d2b2fc3ffb1d440bd7120b66f1f71)
+[![DOI](https://joss.theoj.org/papers/10.21105/joss.06868/status.svg)](https://doi.org/10.21105/joss.06868)
 [![CRAN status](https://www.r-pkg.org/badges/version/APackOfTheClones)](https://CRAN.R-project.org/package=APackOfTheClones)
 [![Downloads](https://cranlogs.r-pkg.org/badges/grand-total/APackOfTheClones?color=brightgreen)](https://www.r-pkg.org/pkg/APackOfTheClones)
 [![R-CMD-check](https://github.com/Qile0317/APackOfTheClones/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/Qile0317/APackOfTheClones/actions/workflows/R-CMD-check.yaml)
@@ -57,17 +57,17 @@ vizAPOTC(pbmc)
 vizAPOTC(pbmc, orig.ident = c("P17B", "P17L"), seurat_clusters = c(1, 3, 4))
 ```
 
-Additional features and use-cases are covered in the vignettes and documentation, including options to store seperate runs with different parameters on the same seurat object, highlighting clonotypes, getting shared clonotypes across clusters, displaying links between them, and more.
+Additional features and use-cases are covered in the vignettes and documentation, including options to store separate runs with different parameters on the same seurat object, highlighting clonotypes, getting shared clonotypes across clusters, displaying links between them, and more.
 
 ### Package conventions
 
 Most exported functions are named with `camelCase` with the exception of those that modify Seurat objects having `PascalCase` to mimic their conventions. All function arguments follow `snake_case`.
 
 ## Please Cite
 
-If you use `APackOfTheClones` in your work, please cite the corresponding [publication](https://joss.theoj.org/papers/eb9d2b2fc3ffb1d440bd7120b66f1f71) with the output of `citation("APackOfTheClones")`:
+If you use `APackOfTheClones` in your work, please cite the corresponding [publication](https://doi.org/10.21105/joss.06868) with the output of `citation("APackOfTheClones")`:
 
-> Yang, Q., (2024). APackOfTheClones: Visualization of clonal expansion with circle packing. Journal of Open Source Software, 9(103), 6868, https://doi.org/10.21105/joss.06868
+> Yang, Q., (2024). APackOfTheClones: Visualization of clonal expansion with circle packing. Journal of Open Source Software, 9(103), 6868, <https://doi.org/10.21105/joss.06868>
 
 ## Documentation