From a148b556c424d3af01c50e943e1731d4d380ce3f Mon Sep 17 00:00:00 2001
From: Dan Knight <danknight@mednet.ucla.edu>
Date: Thu, 1 Sep 2022 12:16:17 -0700
Subject: [PATCH 1/5] Function to get the root node from tree input

---
 R/prep.tree.R | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/R/prep.tree.R b/R/prep.tree.R
index 0b45152..caa32fd 100644
--- a/R/prep.tree.R
+++ b/R/prep.tree.R
@@ -143,3 +143,16 @@ check.parent.values <- function(node.names, parent.col) {
             }
         ));
     }
+
+get.root.node <- function(tree) {
+    valid.values <- as.character(c(-1, 0));
+    candidates <- which(is.na(tree$parent) | tree$parent %in% valid.values);
+
+    if (length(candidates) > 1) {
+        stop('More than one root node detected.');
+    } else if (length(candidates) == 0) {
+        stop('No root node provided.');
+        }
+
+    return(candidates);
+    }

From 891eb42312ae8ed16a059a1339e9fd5f40c927a7 Mon Sep 17 00:00:00 2001
From: Dan Knight <danknight@mednet.ucla.edu>
Date: Thu, 1 Sep 2022 12:16:40 -0700
Subject: [PATCH 2/5] Add root node check to tree prep

---
 R/prep.tree.R | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/R/prep.tree.R b/R/prep.tree.R
index caa32fd..ede2d90 100644
--- a/R/prep.tree.R
+++ b/R/prep.tree.R
@@ -10,6 +10,9 @@ prep.tree <- function(
         stop('No parent column provided');
         }
 
+    # Error on invalid tree structure
+    get.root.node(tree.df);
+
     if ('angle' %in% colnames(tree.df)) {
         message(paste(
             'Overriding branch angles will be supported in a future version.',

From 7ad982693a08f6de31a7f6034776a38a894fae5f Mon Sep 17 00:00:00 2001
From: Dan Knight <danknight@mednet.ucla.edu>
Date: Thu, 1 Sep 2022 12:23:07 -0700
Subject: [PATCH 3/5] Unit tests for root node prep

---
 tests/testthat/test-prep.tree.R | 48 +++++++++++++++++++++++++++++++++
 1 file changed, 48 insertions(+)

diff --git a/tests/testthat/test-prep.tree.R b/tests/testthat/test-prep.tree.R
index 8589879..bfe8d00 100644
--- a/tests/testthat/test-prep.tree.R
+++ b/tests/testthat/test-prep.tree.R
@@ -205,3 +205,51 @@ test_that(
 
         expect_true(check.parent.values(node.names, parents));
     });
+
+test_that(
+    'get.root.node handles valid NA root', {
+        parent <- c(2, NA, 1);
+        expected.root <- which(is.na(parent));
+
+        tree <- data.frame(parent = parent);
+        root <- get.root.node(tree);
+        
+        expect_equal(root, expected.root);
+    });
+
+test_that(
+    'get.root.node handles valid -1 root', {
+        parent <- c(2, -1, 1);
+        expected.root <- which(parent == -1);
+
+        tree <- data.frame(parent = parent);
+        root <- get.root.node(tree);
+        
+        expect_equal(root, expected.root);
+    });
+
+test_that(
+    'get.root.node handles valid 0 root', {
+        parent <- c(2, 0, 1);
+        expected.root <- which(parent == 0);
+
+        tree <- data.frame(parent = parent);
+        root <- get.root.node(tree);
+        
+        expect_equal(root, expected.root);
+    });
+
+test_that(
+    'get.root.node handles multiple root nodes', {
+        root.parent <- -1;
+        tree <- data.frame(parent = rep(root.parent, 2));
+
+        expect_error(get.root.node(tree), regexp = 'root')
+    });
+
+test_that(
+    'get.root.node handles a missing root node', {
+        tree <- data.frame(parent = 1:3);
+
+        expect_error(get.root.node(tree), regexp = 'root')
+    });
\ No newline at end of file

From a92bc20df630a68970bfed9c6228386434b19b5b Mon Sep 17 00:00:00 2001
From: Dan Knight <danknight@mednet.ucla.edu>
Date: Thu, 1 Sep 2022 12:25:11 -0700
Subject: [PATCH 4/5] Update changelog

---
 DESCRIPTION | 2 +-
 NEWS        | 3 ++-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 19afa1b..72237f2 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: CancerEvolutionVisualization
 Title: Function to Generate Publication Quality Phylogenetic Tree Plots
 Version: 1.0.0
-Date: 2022-08-03
+Date: 2022-09-01
 Authors@R: c(
 	person("Paul Boutros", role = "cre", email = "PBoutros@mednet.ucla.edu"),
 	person("Adriana Salcedo", role = "aut"),
diff --git a/NEWS b/NEWS
index 823c714..b0b4bb2 100644
--- a/NEWS
+++ b/NEWS
@@ -1,7 +1,8 @@
-CancerEvolutionVisualization 1.0.0 2022-08-03 (Dan Knight)
+CancerEvolutionVisualization 1.0.0 2022-09-01 (Dan Knight)
 
 ADDED
 * Documentation for default colour scheme
+* Checks for valid tree structure (root node)
 
 UPDATE
 * Fixed discrepancies between documentation and code

From db001eac7cb5389c6d1254a680869f05860502d3 Mon Sep 17 00:00:00 2001
From: Dan Knight <danknight@mednet.ucla.edu>
Date: Thu, 1 Sep 2022 12:26:18 -0700
Subject: [PATCH 5/5] Fix linting errors

---
 tests/testthat/test-prep.tree.R | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/tests/testthat/test-prep.tree.R b/tests/testthat/test-prep.tree.R
index bfe8d00..44a1ed2 100644
--- a/tests/testthat/test-prep.tree.R
+++ b/tests/testthat/test-prep.tree.R
@@ -213,7 +213,7 @@ test_that(
 
         tree <- data.frame(parent = parent);
         root <- get.root.node(tree);
-        
+
         expect_equal(root, expected.root);
     });
 
@@ -224,7 +224,7 @@ test_that(
 
         tree <- data.frame(parent = parent);
         root <- get.root.node(tree);
-        
+
         expect_equal(root, expected.root);
     });
 
@@ -235,7 +235,7 @@ test_that(
 
         tree <- data.frame(parent = parent);
         root <- get.root.node(tree);
-        
+
         expect_equal(root, expected.root);
     });
 
@@ -252,4 +252,4 @@ test_that(
         tree <- data.frame(parent = 1:3);
 
         expect_error(get.root.node(tree), regexp = 'root')
-    });
\ No newline at end of file
+    });