Merge pull request #119 from uclahs-cds/dendrogram

Dendrogram mode

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: CancerEvolutionVisualization
 Title: Publication Quality Phylogenetic Tree Plots
-Version: 2.1.0
-Date: 2024-08-05
+Version: 3.0.0
+Date: 2024-08-28
 Authors@R: c(
 	person("Paul Boutros", role = "cre", email = "[email protected]"),
 	person("Adriana Salcedo", role = "aut"),

NAMESPACE

@@ -6,7 +6,7 @@ import(BoutrosLab.plotting.general)
 importFrom("graphics", "par", "strheight", "strwidth")
 importFrom("grDevices", "dev.list", "rainbow")
 importFrom("utils", "read.table", "vi", "head")
-importFrom("stats", "setNames", "aggregate", "reshape")
+importFrom("stats", "median", "setNames", "aggregate", "reshape")
 importFrom("grDevices", "col2rgb")
 
 export(SRCGrob)

NEWS.md

@@ -1,19 +1,21 @@
-# CancerEvolutionVisualization 2.1.0 (2024-08-05)
+# CancerEvolutionVisualization 3.0.0 (2024-08-28)
 
 ## Added
+* Dendrogram mode
 * Optional "spread" column to control node/branch spacing
 * Plotting functions to visualize the distribution of clones across the genome.
-* Documentation for heatmaps and clone-genome distirbution plor
-* Option to disable node drawing with node-by-node control 
+* Documentation for heatmaps and clone-genome distribution plot
+* Option to disable node drawing with node-by-node control
 
 ## Update
 * Fixed angle calculation bug where child angles do not follow
   their parent angle, instead moving "downward" at 0 degrees.
 * Updated package metadata and README
+* Split angle handling for `radial` and `dendrogram` modes to optimized each
 * Set default parameters for heatmaps, defaulting too BPG defaults unless necessary
 * Updated changelog format to NEWS.md Markdown format
 * Refactored use of plyr/dplyr and stringr functions to remove dependencies
-
+* Set default parameters for heatmaps, defaulting to BPG defaults unless necessary
 
 # CancerEvolutionVisualization 2.0.1 (2023-11-17)
 
@@ -207,5 +209,4 @@
 # CancerEvolutionVisualization 0.0.0 (2021-09-13)
 
 INITIAL FEATURES
-
-- Tree, CNA, and SNV input sampling
+* Tree, CNA, and SNV input sampling

R/add.nodes.R

@@ -85,7 +85,7 @@ add.normal <- function(clone.out, node.radius, label.cex, normal.cex = 1) {
         'N',
         x = unit(0.5, 'npc'),
         y = unit(0.5, 'npc'),
-        name = 'ormal.label',
+        name = 'normal.label',
         just = 'center',
         gp = gpar(
             col = 'black',