doctests and readme

DESCRIPTION

@@ -33,4 +33,4 @@ Imports:
     stats,
     utils
 RoxygenNote: 7.2.3
-URL: https://qile0317.github.io/APackOfTheClones/
+URL: https://qile0317.github.io/APackOfTheClones/

NEWS.md

@@ -27,13 +27,14 @@ All of which have documentation, including on the documentation site.
 Currently, Automated cluster repulsion uses a highly flawed mathematical formula loosely based on force directed graph drawing techniques, the resulting plots are not presentable and the function has been disabled temporarily
 
 ##  Future features/plans:
-* Customizable cluster coloration, not just based on the original Seurat/ggplot palette
-* User-controlled cluster shifting
-* Comprehensive cluster repulsion
-* better legends and optional legend border
-* automated optimization of the initial parameters of `clonal_expansion_plot`, especially the `clone_scale_factor`
-* BCR library integration
-* User vignette
-* Developer vignette
-* Submission to CRAN or Bioconductor
-* Rewrite of certain circle packing functions in `rust` to improve performance
+[ ] Customizable cluster coloration, not just based on the original Seurat/ggplot palette
+[ ] User-controlled cluster shifting
+[x] Comprehensive cluster repulsion
+[x] better legends and optional legend border
+[ ] automated optimization of the initial parameters of `clonal_expansion_plot`, especially the `clone_scale_factor`
+[ ] BCR library integration
+[x] User vignette
+[ ] Developer vignette
+[ ] Submission to CRAN or Bioconductor
+[ ] Rewrite of certain circle packing functions in `rust` or `c++` to improve performance
+[ ] Increase interoperability with `Seurat` and `scRepertoire`

R/clonal_expansion_plot.R

@@ -46,7 +46,6 @@ library(utils)
 #' @export
 #'
 #' @examples
-#' \donttest{
 #' library(Seurat)
 #' library(APackOfTheClones)
 #' data("mini_clonotype_data","mini_seurat_obj")
@@ -59,7 +58,6 @@ library(utils)
 #' integrated_seurat_object <- integrate_tcr(mini_seurat_obj, mini_clonotype_data)
 #' ball_pack_plot <- clonal_expansion_plot(integrated_seurat_object)
 #' ball_pack_plot
-#' }
 #'
 clonal_expansion_plot <- function(
   seurat_obj, tcr_df = "seurat_obj_already_integrated",

R/get_clone_sizes.R

@@ -27,15 +27,15 @@ get_clone_sizes <- function(integrated_seurat_obj, scale_factor = 0.001) {
 #' @export
 #' 
 #' @examples
-#' \donttest{
 #' library(Seurat)
 #' library(APackOfTheClones)
 #' data("mini_clonotype_data","mini_seurat_obj")
 #'
 #' # produce an integrated seurat_object
 #' integrated_seurat_object <- integrate_tcr(mini_seurat_obj, mini_clonotype_data)
 #' clonotype_counts <- count_clone_sizes(integrated_seurat_object)
-#' }
+#' clonotype_counts
+#' 
 count_clone_sizes <- function(integrated_seurat_obj) {
   if (is.null(integrated_seurat_obj@meta.data[["seurat_clusters"]])) {
     stop("A UMAP must first be run on the seurat object")

R/integration.R

@@ -32,14 +32,13 @@ library(utils)
 #' @import data.table
 #'
 #' @examples
-#' \donttest{
 #' library(Seurat)
 #' library(APackOfTheClones)
 #' data("mini_clonotype_data","mini_seurat_obj")
 #'
 #' # integrate the TCR data into new seurat object
 #' integrated_seurat_object <- integrate_tcr(mini_seurat_obj, mini_clonotype_data)
-#' }
+#' integrated_seurat_object
 #'
 #' @references atakanekiz (2019) Tutorial:Integrating VDJ sequencing data with Seurat. `https://www.biostars.org/p/384640/`
 #'

README.md

@@ -71,7 +71,11 @@ All exported functions has function level documentation which can be called with
 Currently, there is only one introductory vignette named `"Clonal_expansion_plotting"` which is a walkthrough on the clonal expansion visualization workflow. The vignette is ONLINE-ONLY and can be viewed at https://qile0317.github.io/APackOfTheClones/articles/
 
 ## Contributing
-`APackOfTheClones` is currently incomplete, and more features, tests, bugfixes, and documentation are to come. However, 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.
+`APackOfTheClones` is currently incomplete, and more features, tests, bugfixes, and documentation are to come. 
+
+There also are plans to refactor quite a bit of the codebase to increase inter-operability with both `Seurat` and `scRepertoire`.
+
+However, 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.