added detail=FALSE arg for visualization

NEWS.md

@@ -2,6 +2,8 @@
 
 ## Additions
 
+- Add argument `detail` in `APOTCPlot` and `vizAPOTC` to allow user to plot a version of the clonal expansion plot where each cluster is just one large circle. Correspondingly added a subsection in `vignette("APackOfTheClones-shared")`.
+
 ## Changes
 
 # APackOfTheClones 1.1.0

R/APOTCPlot.R

@@ -86,6 +86,12 @@
 #' changed between the circle sizes on the left side of the legend and the
 #' numbers on the right. Useful to set to around 0.5 (or more / less) when there
 #' are particularly large clone sizes that may cover the numbers.
+#' @param detail logical. If `FALSE`, will only plot entire clusters as one
+#' large circle, which may be useful in cases where there are a high number
+#' of clones resulting in a large number of circles on the resulting ggplot,
+#' which has increased plotting times, and certain aspects of the plot needs
+#' to be finely adjusted with [AdjustAPOTC] or simply inspected. This should
+#' not be set to `FALSE` for the actual clonal expansion plot.
 #'
 #' @return A ggplot object of the APackOfTheClones clonal expansion plot of the
 #' seurat object. There is an additional 10th element in the object named
@@ -139,6 +145,8 @@ APOTCPlot <- function(
 	add_legend_background = TRUE,
 	add_legend_centerspace = 0,
 
+	detail = TRUE,
+
 	verbose = TRUE
 ) {
 	# handle varargs, run_id, and typecheck
@@ -151,7 +159,9 @@ APOTCPlot <- function(
 	apotc_obj <- getApotcData(seurat_obj, args$run_id)
 
 	# initialize plot
-	result_plot <- create_initial_apotc_plot(apotc_obj, res, linetype, alpha)
+	result_plot <- create_initial_apotc_plot(
+		apotc_obj, res, linetype, alpha, detail
+	)
 	result_plot_dimensions <- get_apotc_plot_dims(apotc_obj)
 
 	#set theme
@@ -180,7 +190,7 @@ APOTCPlot <- function(
 	}
 
 	if (isnt_empty(show_shared)) {
-		
+
 		# check only_link indexing
 		if (!is.null(only_link) &&
 			!is_valid_nonempty_cluster(apotc_obj, only_link)) {
@@ -234,7 +244,7 @@ APOTCPlot <- function(
 }
 
 APOTCPlot_error_handler <- function(args) {
-	
+
 	check_apotc_identifiers(args)
 	check_filtering_conditions(args)
 
@@ -266,6 +276,8 @@ APOTCPlot_error_handler <- function(args) {
 	typecheck(args$add_size_legend, is_a_logical)
 	check_legend_params(args)
 
+	typecheck(args$detail, is_a_logical)
+
 }
 
 # helpers for getting plot dimensions quickly

R/AdjustAPOTC.R

@@ -114,7 +114,7 @@ AdjustAPOTC <- function(
 	recolor_cluster = NULL,
 	new_color = NULL,
 
-	rename_label = NULL, # TODO add functionality to change all at once or modify all at once
+	rename_label = NULL,
 	new_label = NULL,
 	relocate_label = NULL,
 	label_relocation_coord = NULL,

R/ApotcClonalNetwork.R

@@ -116,7 +116,6 @@ 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 - allow filtering based on original clone size
 get_shared_clones <- function(
     apotc_obj,
     zero_indexed = FALSE,

R/Repulsion.R

@@ -1,3 +1,7 @@
+# cluster repulsion - the n body problem
+# FIXME the repulsion is too aggressive when clusters are super close, put upper bound on force based on clone scale
+# time complexity is O(mn^2) where m is the max number of iterations and n is the number of clusters(circles). n will never be that high so the timing isnt a problem
+
 # Functions defined in src/repulsion.cpp
 # - get_average_vector(vec_list)
 #     avg vector of a list of vectors

R/clusters.R

@@ -14,6 +14,8 @@ get_x_coords <- function(l) l[[1]]
 get_y_coords <- function(l) l[[2]]
 get_radii <- function(l) l[[3]]
 get_centroid <- function(l) l[[4]]
+get_centroid_x <- function(l) get_centroid(l)[1]
+get_centroid_y <- function(l) get_centroid(l)[2]
 get_cluster_radius <- function(l) l[[5]]
 get_clonotypes <- function(l) l$clonotype # not index due to legacy clusterlists
 
@@ -29,9 +31,19 @@ set_centroid <- function(l, v) {l$centroid <- v; l}
 set_cluster_radius <- function(l, v) {l$clRad <- v; l}
 set_clonotypes <- function(l, v) {l$clonotype <- v; l}
 
-# convert clusterlist to dataframe, assuming its valid
-# TODO allow get_abstract option to just get 1 large circle
-convert_to_dataframe <- function(clstr_list, seurat_cluster_index) {
+# convert clusterlist to dataframe, assuming its ***valid***
+convert_to_dataframe <- function(
+    clstr_list, seurat_cluster_index, detail = TRUE
+) {
+    if (!detail) {
+      return(data.frame(
+        "label" = paste("cluster", seurat_cluster_index),
+        "x" = get_centroid_x(clstr_list),
+        "y" = get_centroid_y(clstr_list),
+        "r" = get_cluster_radius(clstr_list)
+      ))
+    }
+
     data.frame(
         "label" = rep(
             paste("cluster", seurat_cluster_index),