Merge pull request #22 from Qile0317/dev

CRAN 1.2.4

.Rbuildignore

@@ -18,3 +18,4 @@
 [.]yml$
 ^\.lintr$
 ^cran-comments\.md$
+^CITATION.cff$

CITATION.cff

@@ -0,0 +1,28 @@
+cff-version: "1.2.0"
+authors:
+- family-names: Yang
+  given-names: Qile
+  orcid: "https://orcid.org/0009-0005-0148-2499"
+doi: 10.5281/zenodo.13916956
+message: If you use this software, please cite our article in the
+  Journal of Open Source Software.
+preferred-citation:
+  authors:
+  - family-names: Yang
+    given-names: Qile
+    orcid: "https://orcid.org/0009-0005-0148-2499"
+  date-published: 2024-11-18
+  doi: 10.21105/joss.06868
+  issn: 2475-9066
+  issue: 103
+  journal: Journal of Open Source Software
+  publisher:
+    name: Open Journals
+  start: 6868
+  title: "APackOfTheClones: Visualization of clonal expansion with
+    circle packing"
+  type: article
+  url: "https://joss.theoj.org/papers/10.21105/joss.06868"
+  volume: 9
+title: "APackOfTheClones: Visualization of clonal expansion with circle
+  packing"

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: APackOfTheClones
 Type: Package
 Title: Visualization of Clonal Expansion for Single Cell Immune Profiles
-Version: 1.2.1
+Version: 1.2.4
 Authors@R: c(
     person(
         "Qile",
@@ -12,7 +12,7 @@ Authors@R: c(
     ))
 Maintainer: Qile Yang <qile.yang@berkeley.edu>
 Description: Visualize clonal expansion via circle-packing. 'APackOfTheClones' extends 'scRepertoire' to produce a publication-ready visualization of clonal expansion at a single cell resolution, by representing expanded clones as differently sized circles. The method was originally implemented by Murray Christian and Ben Murrell in the following immunology study: Ma et al. (2021) <doi:10.1126/sciimmunol.abg6356>.
-BugReports: https://github.com/Qile0317/APackOfTheClones/issues/
+BugReports: https://github.com/Qile0317/APackOfTheClones/issues
 Depends:
     R (>= 4.1.0)
 License: MIT + file LICENSE
@@ -42,7 +42,7 @@ Imports:
     Seurat,
     SeuratObject
 RoxygenNote: 7.3.2
-URL: https://qile0317.github.io/APackOfTheClones/
+URL: https://qile0317.github.io/APackOfTheClones/, https://github.com/Qile0317/APackOfTheClones, https://joss.theoj.org/papers/10.21105/joss.06868
 LinkingTo:
     Rcpp
 Roxygen: list(markdown = TRUE)

NEWS.md

@@ -1,3 +1,14 @@
+# APackOfTheClones 1.2.4
+
+## Additions
+
+- Update citation information as the tool has been published.
+
+## Changes
+
+- slightly improve README
+- Ensured all irrelevant files are not included in the package build to address CRAN submissions failures for the previous 2 patches.
+
 # APackOfTheClones 1.2.1
 
 ## Additions
@@ -8,7 +19,7 @@
 ## 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

@@ -1,14 +1,13 @@
 # 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)
 [![Codecov test coverage](https://codecov.io/gh/Qile0317/APackOfTheClones/branch/main/graph/badge.svg)](https://app.codecov.io/gh/Qile0317/APackOfTheClones?branch=main)
 [![Documentation](https://img.shields.io/badge/docs-stable-blue.svg)](https://qile0317.github.io/APackOfTheClones/)
 [![Developmental Documentation](https://img.shields.io/badge/docs-dev-blue.svg)](https://qile0317.github.io/APackOfTheClones/dev/)
-[![DOI](https://zenodo.org/badge/551699219.svg)](https://doi.org/10.5281/zenodo.13916955)
 [![R Universe APackOfTheClones status badge](https://qile0317.r-universe.dev/badges/APackOfTheClones)](https://qile0317.r-universe.dev/APackOfTheClones)
 [![MIT license](https://img.shields.io/badge/license-MIT-green.svg)](https://github.com/Qile0317/APackOfTheClones/blob/main/LICENSE.md)
 <!-- badges: end -->
@@ -58,40 +57,18 @@ vizAPOTC(pbmc)
 vizAPOTC(pbmc, orig.ident = c("P17B", "P17L"), seurat_clusters = c(1, 3, 4))
 ```
 
-For finer control of the visualization / other parameters, the data for a run can be stored and adjusted with ```RunAPOTC()``` and ```AdjustAPOTC```, then visualized with ```APOTCPlot()```, like so:
-
-```R
-# using the same seurat object as before, run and store associated data,
-# identifying it with a run id. If not, one will be generated.
-pbmc <- RunAPOTC(pbmc, run_id = "default_run_1")
-
-# plot the corresponding data with the run_id. If not provided, will use the latest run.
-APOTCPlot(pbmc)
-
-# adjust the sizes of the clones and move the 2nd cluster to (0, 0). Run id this time was
-# left empty for no particular reason, but it will use "default_run_1" since its the latest
-pbmc <- AdjustAPOTC(
-    pbmc,
-    new_clone_scale_factor = 0.25,
-    relocate_cluster = 2,
-    relocation_coord = c(0, 0)
-)
-
-# one can also do another run with different parameters and a different id.
-pbmc <- RunAPOTC(pbmc, run_id = "run2", try_place = TRUE, repulse = FALSE)
-
-# plot both runs side by side
-library(cowplot)
-cowplot::plot_grid(
-    APOTCPlot(pbmc, run_id = "default_run_1"), APOTCPlot(pbmc, run_id = "run2")
-)
-
-```
+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://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>
+
 ## Documentation
 
 Comprehensive documentation, vignettes, and a changelog is deployed at <https://qile0317.github.io/APackOfTheClones/>
@@ -109,11 +86,9 @@ All exported functions have function level documentation.
 
 Github pull requests from forked branches are more than welcome as it is mostly a solo-project at the moment. For major changes, please open an issue first to discuss what you would like to change. Please also make sure to update tests as appropriate.
 
-An explanation of the algorithms will eventually be made publicly available in a either a pre-print or developer vignette.
-
 ## Contact
 
-Qile Yang - qile.yang \[at\] berkeley.edu
+Qile Yang - qile \[dot\] yang \[at\] berkeley.edu
 
 ## References
 

inst/CITATION

@@ -1,14 +1,15 @@
-citHeader("As of version 1.2.1, a paper for this package will tentatively be published in https://joss.theoj.org/papers/eb9d2b2fc3ffb1d440bd7120b66f1f71. Please check the citation information there first. If that is missing, please use the following:")
+citHeader("If using APackOfTheClones in your research work, please cite:")
 
 bibentry(
-  bibtype  = "manual",
+  bibtype  = "article",
   title    = "APackOfTheClones: Visualization of clonal expansion with circle packing",
   author   = "Qile Yang",
-  year     = 2023,
-  url      = "https://github.com/Qile0317/APackOfTheClones",
-  doi      = "10.32614/CRAN.package.APackOfTheClones",
-  textVersion = paste(
-    "Yang, Qile. 2023. APackOfTheClones: Visualization of clonal expansion with circle packing. ",
-    "URL https://github.com/Qile0317/APackOfTheClones, DOI 10.32614/CRAN.package.APackOfTheClones"
-  )
+  year     = 2024,
+  url      = "https://doi.org/10.21105/joss.06868",
+  doi      = "10.21105/joss.06868",
+  journal  = "Journal of Open Source Software",
+  volume   = 9,
+  number   = 103,
+  pages    = 6868,
+  textVersion = "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"
 )