removed some fixmes, incremented minor ver

Qile0317 · Apr 16, 2024 · 77f5003 · 77f5003
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: APackOfTheClones
 Type: Package
 Title: Visualization of Clonal Expansion for Single Cell Immune Profiles
-Version: 1.1.0.9000
+Version: 1.2.0
 Authors@R: c(person("Qile", "Yang", email = "qile.yang@berkeley.edu", role = c("cre","aut","cph")))
 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>.

diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,4 @@
-# APackOfTheClones 1.1.0.9000 (development version)
+# APackOfTheClones 1.2.0
 
 ## Additions
 

diff --git a/R/ApotcClonalNetwork.R b/R/ApotcClonalNetwork.R
@@ -129,7 +129,6 @@ getSharedClones_error_handler <- function() {
 # output: a named list where each name is a clonotype, each element is a
 # numeric indicating which seurat cluster(s) its in. If exclude_unique_clones,
 # will filter out any clonotype with only length one. (not shared)
-# TODO FIXME make it based on ident
 get_shared_clones <- function(
     apotc_obj,
     zero_indexed = FALSE,

diff --git a/R/clusters.R b/R/clusters.R
@@ -69,7 +69,6 @@ update_clusterlist_df <- function(df, clusterlist) {
 
 }
 
-# FIXME
 # centroid finder for a matrix of [x, y, cluster]
 find_centroids <- function(xyc_df, ident_levels) {
 

diff --git a/R/get_clone_sizes.R b/R/get_clone_sizes.R
@@ -41,7 +41,7 @@
 #' countCloneSizes(combined_pbmc, "aa")
 #' countCloneSizes(combined_pbmc, "nt", orig.ident = c("P17B", "P17L"))
 #'
-countCloneSizes <- function( # FIXME
+countCloneSizes <- function(
     seurat_obj,
     clonecall = "strict",
     extra_filter = NULL,
@@ -173,7 +173,7 @@ count_raw_clone_sizes <- function(
 #' clustered_clone_sizes <- countCloneSizes(get(data("combined_pbmc")))
 #' mergeCloneSizes(clustered_clone_sizes)
 #'
-mergeCloneSizes <- function(clustered_clone_sizes, sort_decreasing = TRUE) { # FIXME
+mergeCloneSizes <- function(clustered_clone_sizes, sort_decreasing = TRUE) { 
 
     typecheck(clustered_clone_sizes, is_output_of_countCloneSizes)
     typecheck(sort_decreasing, is_a_logical, is.null)
-Original file line number
+Diff line change
@@ Expand Up / @@ -69,7 +69,6 @@ update_clusterlist_df <- function(df, clusterlist) { @@
     }
-    # FIXME
     # centroid finder for a matrix of [x, y, cluster]
     find_centroids <- function(xyc_df, ident_levels) {
@@ Expand Down @@