Y-axis fix

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"),

NEWS

@@ -1,11 +1,12 @@
-CancerEvolutionVisualization 1.0.0 2022-08-03 (Dan Knight)
+CancerEvolutionVisualization 1.0.0 2022-09-01 (Dan Knight)
 
 ADDED
 * Documentation for default colour scheme
 
 UPDATE
 * Fixed discrepancies between documentation and code
 * Fixed bug related to referencing an uninitialized variable
+* Fixed y-axis positioning bug
 * Updated packaging/development dependencies
 
 

R/SRCGrob.R

@@ -40,15 +40,11 @@ SRCGrob <- function(
     gene.line.dist <- prep.gene.line.dist(gene.line.dist);
 
     yat <- prep.yat(yat);
-
-    yaxis.position <- if (is.null(yaxis2.label)) 'left' else {
-        if (!is.null(yaxis1.label)) 'both' else 'right';
-        };
+    yaxis.position <- get.y.axis.position(colnames(tree));
 
     inputs <- prep.tree(
         tree,
         genes,
-        yaxis.position,
         colour.scheme = colour.scheme
         );
 

R/prep.branch.lengths.R

@@ -1,4 +1,4 @@
-get.branch.length.colnames <- function(num.columns) {
+get.default.branch.length.colnames <- function(num.columns) {
         if (num.columns > 0) {
             sapply(
                 1:num.columns,
@@ -13,7 +13,7 @@ get.branch.length.colnames <- function(num.columns) {
 
 get.default.branch.lengths <- function(num.rows) {
     lengths <- data.frame(a = rep(1, times = num.rows));
-    colnames(lengths) <- get.branch.length.colnames(1);
+    colnames(lengths) <- get.default.branch.length.colnames(1);
 
     return(lengths);
     }
@@ -22,6 +22,10 @@ validate.branch.colname <- function(column.name) {
     grepl('length', column.name);
     }
 
+get.branch.length.colnames <- function(col.names) {
+    Filter(validate.branch.colname, col.names);
+    }
+
 validate.branch.length.values <- function(length.column) {
     return(tryCatch({
         numeric.values <- as.numeric(length.column);
@@ -76,7 +80,7 @@ prep.branch.lengths <- function(tree.df) {
 
     if (length(length.cols) > 0) {
         lengths.df <- data.frame(tree.df[, length.cols]);
-        colnames(lengths.df) <- get.branch.length.colnames(length(length.cols));
+        colnames(lengths.df) <- get.default.branch.length.colnames(length(length.cols));
 
         return(lengths.df);
     } else {

R/prep.tree.R

@@ -2,7 +2,6 @@ prep.tree <- function(
     tree.df,
     genes.df,
     bells = TRUE,
-    axis.type = 'left',
     colour.scheme
     ) {
 
@@ -143,3 +142,13 @@ check.parent.values <- function(node.names, parent.col) {
             }
         ));
     }
+
+get.y.axis.position <- function(tree.colnames) {
+    num.branch.length.cols <- length(get.branch.length.colnames(tree.colnames));
+
+    y.axis.position <- if (num.branch.length.cols == 1) 'left' else {
+        if (num.branch.length.cols > 1) 'both' else 'none';
+        };
+
+    return(y.axis.position);
+    }

tests/testthat/test-prep.branch.lengths.R

@@ -45,21 +45,21 @@ test_that(
     });
 
 test_that(
-    'get.branch.length.colnames returns the correct length', {
+    'get.default.branch.length.colnames returns the correct length', {
         expected.length <- 5;
 
         expect_length(
-            get.branch.length.colnames(expected.length),
+            get.default.branch.length.colnames(expected.length),
             expected.length
             );
     });
 
 test_that(
-    'get.branch.length.colnames handles length 0', {
+    'get.default.branch.length.colnames handles length 0', {
         expected.length <- 0;
 
         expect_length(
-            get.branch.length.colnames(expected.length),
+            get.default.branch.length.colnames(expected.length),
             expected.length
             );
     });

tests/testthat/test-prep.tree.R

@@ -205,3 +205,44 @@ test_that(
 
         expect_true(check.parent.values(node.names, parents));
     });
+
+test_that(
+    'get.y.axis.position handles a single branch length column', {
+        valid.colname <- 'length1';
+        cols <- c(valid.colname, 'invalid');
+
+        yaxis.position <- get.y.axis.position(cols);
+        expected.position <- 'left';
+
+        expect_equal(yaxis.position, expected.position);
+    });
+
+test_that(
+    'get.y.axis.position handles multiple valid branch length columns', {
+        valid.colnames <- sapply(
+            1:3,
+            FUN = function(x) {
+                paste0('length', x);
+                }
+            );
+
+        cols <- c(
+            valid.colnames,
+            'invalid.col'
+            );
+
+        yaxis.position <- get.y.axis.position(cols);
+        expected.position <- 'both';
+
+        expect_equal(yaxis.position, expected.position);
+    });
+
+test_that(
+    'get.y.axis.position handles no valid branch length columns', {
+        cols <- c('parent');
+
+        yaxis.position <- get.y.axis.position(cols);
+        expected.position <- 'none';
+
+        expect_equal(yaxis.position, expected.position);
+    });