Change error messages to indicate that all values are required in some methods.

.gitignore

@@ -5,7 +5,11 @@
 .RData
 .Ruserdata
 .Rproj.user
+.lintr
 
 vignettes/figures
 *.pdf
-*.html
+*.html
+
+*.code-workspace
+.vscode

R/create.clone.genome.distribution.plot.R

@@ -12,8 +12,14 @@ create.clone.genome.distribution.plot <- function(
     ) {
 
     # Preprocess ----------------------------------------------------------------------------------
-    if (!all(c('chr', 'pos', 'clone.id') %in% names(snv.df))) {
-        stop('snv.df does not contain at least one of chr, pos or clone.id columns')
+    required.cols <- c('chr', 'pos', 'clone.id');
+    missing.cols <- required.cols[!(required.cols %in% names(snv.df))];
+    if (length(missing.cols) != 0) {
+        stop(paste0(
+            'snv.df must contain the columns ',
+            oxford.comma.vector.concat(required.cols),
+            '; snv.df is missing ',
+            oxford.comma.vector.concat(missing.cols, paste(required.cols, collapse = ', ')), '.'));
         }
     if (is.null(clone.order)) {
         clone.order <- sort(unique(snv.df$clone.id));

R/data.frame.to.array.R

@@ -5,8 +5,14 @@ data.frame.to.array <- function(
     y.axis = 'ID'
     ) {
 
-    if (is.null(DF[[x.axis]]) | is.null(DF[[value]]) | is.null(DF[[y.axis]])) {
-        stop(paste('Dataframe does not contain one of the columns:', value, x.axis, y.axis));
+    required.cols <- c(value, x.axis, y.axis);
+    missing.cols <- required.cols[!(required.cols %in% names(DF))];
+    if (length(missing.cols) != 0) {
+        stop(paste0(
+            'Dataframe must contain the columns: ',
+            oxford.comma.vector.concat(required.cols),
+            '; Dataframe is missing ',
+            oxford.comma.vector.concat(missing.cols, paste(required.cols, collapse = ', ')), '.'));
         }
     arr <- reshape(
         data = DF[, c(x.axis, y.axis, value)],

R/utility.R

@@ -62,3 +62,19 @@ get.encoded.distance <- function(points) {
 
     return(encoded.distances);
     }
+
+
+oxford.comma.vector.concat <- function(vec, empty.value = '', flatten.empty.value = TRUE) {
+    if (length(vec) == 0) {
+        if (flatten.empty.value) {
+            oxford.comma.vector.concat(empty.value, flatten.empty.value = FALSE)
+            } else {
+                empty.value;
+                }
+    } else if (length(vec) == 1) {
+        paste(vec, collapse = ', ');
+        } else {
+            sep <- if (length(vec) > 2) ', and ' else ' and ';
+            paste(paste(head(vec, -1), collapse = ', '), tail(vec, 1), sep = sep);
+            }
+    }

tests/testthat/test-create.clone.genome.distribution.plot.R

@@ -0,0 +1,22 @@
+test_that('create.clone.genome.distribution.plot enforces data.frame columns', {
+    snv.df <- data.frame();
+    expect_error(
+        create.clone.genome.distribution.plot(snv.df),
+        'must contain the columns chr, pos, and clone.id; snv.df is missing chr, pos, and clone.id.'
+    );
+    snv.df <- data.frame(chr = 1);
+    expect_error(
+        create.clone.genome.distribution.plot(snv.df),
+        'must contain the columns chr, pos, and clone.id; snv.df is missing pos and clone.id.'
+    );
+    snv.df <- data.frame(chr = 1, pos = 1);
+    expect_error(
+        create.clone.genome.distribution.plot(snv.df),
+        'must contain the columns chr, pos, and clone.id; snv.df is missing clone.id.'
+    );
+    snv.df <- data.frame(clone.id = 1);
+    expect_error(
+        create.clone.genome.distribution.plot(snv.df),
+        'must contain the columns chr, pos, and clone.id; snv.df is missing chr and pos.'
+    );
+});

tests/testthat/test-data.frame.to.array.R

@@ -0,0 +1,22 @@
+test_that('data.frame.to.array enforces data.frame columns', {
+    DF <- data.frame();
+    expect_error(
+        data.frame.to.array(DF),
+        'Dataframe must contain the columns: CCF, SNV.id, and ID; Dataframe is missing CCF, SNV.id, and ID.'
+    );
+    DF <- data.frame(CCF = 1);
+    expect_error(
+        data.frame.to.array(DF),
+        'Dataframe must contain the columns: CCF, SNV.id, and ID; Dataframe is missing SNV.id and ID.'
+    );
+    DF <- data.frame(CCF = 1, SNV.id = 1);
+    expect_error(
+        data.frame.to.array(DF),
+        'Dataframe must contain the columns: CCF, SNV.id, and ID; Dataframe is missing ID.'
+    );
+    DF <- data.frame(SNV.id = 1);
+    expect_error(
+        data.frame.to.array(DF),
+        'Dataframe must contain the columns: CCF, SNV.id, and ID; Dataframe is missing CCF and ID.'
+    );
+});

tests/testthat/test-utility.R

@@ -76,3 +76,67 @@ test_that(
 
         expect_equal(order(result), expected.order);
     });
+
+test_that(
+    'oxford.comma.vector.concat returns `empty.value` when input is empty', {
+        vec <- NULL;
+        expect_equal(oxford.comma.vector.concat(vec), '');
+        expect_equal(oxford.comma.vector.concat(vec, 'default'), 'default');
+        vec <- c(NULL);
+        expect_equal(oxford.comma.vector.concat(vec), '');
+        expect_equal(oxford.comma.vector.concat(vec, 'default'), 'default');
+        vec <- c(NULL, NULL);
+        expect_equal(oxford.comma.vector.concat(vec), '');
+        expect_equal(oxford.comma.vector.concat(vec, 'default'), 'default');
+        vec <- c();
+        expect_equal(oxford.comma.vector.concat(vec), '');
+        expect_equal(oxford.comma.vector.concat(vec, 'default'), 'default');
+    });
+
+test_that(
+    'oxford.comma.vector.concat returns `empty.value` in correct format when input is empty', {
+        vec <- NULL;
+        expect_equal(oxford.comma.vector.concat(vec, flatten.empty.value = FALSE), '');
+        expect_equal(oxford.comma.vector.concat(vec, 'default', flatten.empty.value = FALSE), 'default');
+        vec <- c(NULL);
+        expect_equal(oxford.comma.vector.concat(vec, flatten.empty.value = FALSE), '');
+        expect_equal(oxford.comma.vector.concat(vec, 'default', flatten.empty.value = FALSE), 'default');
+        vec <- c(NULL, NULL);
+        expect_equal(oxford.comma.vector.concat(vec, flatten.empty.value = FALSE), '');
+        expect_equal(oxford.comma.vector.concat(vec, 'default', flatten.empty.value = FALSE), 'default');
+        vec <- c();
+        expect_equal(oxford.comma.vector.concat(vec, flatten.empty.value = FALSE), '');
+        expect_equal(oxford.comma.vector.concat(vec, 'default', flatten.empty.value = FALSE), 'default');
+
+        vec <- c();
+        vec.default <- NULL;
+        expect_null(oxford.comma.vector.concat(vec, vec.default, flatten.empty.value = FALSE));
+        vec <- c();
+        vec.default <- c(1, 2, 3);
+        expect_equal(oxford.comma.vector.concat(vec, vec.default), '1, 2, and 3');
+        expect_equal(oxford.comma.vector.concat(vec, vec.default, flatten.empty.value = FALSE), c(1, 2, 3));
+    });
+
+test_that(
+    'oxford.comma.vector.concat returns grammatically correct oxford comma', {
+        vec <- c(1);
+        expect_equal(oxford.comma.vector.concat(vec), '1');
+        vec <- c(1, 2);
+        expect_equal(oxford.comma.vector.concat(vec), '1 and 2');
+        vec <- c(1, 2, 3);
+        expect_equal(oxford.comma.vector.concat(vec), '1, 2, and 3');
+        vec <- c(1, 2, 3, 4);
+        expect_equal(oxford.comma.vector.concat(vec), '1, 2, 3, and 4');
+    });
+
+test_that(
+    'oxford.comma.vector.concat returns grammatically correct oxford comma for flattened default value', {
+        vec.default <- c(1);
+        expect_equal(oxford.comma.vector.concat(NULL, vec.default), '1');
+        vec.default <- c(1, 2);
+        expect_equal(oxford.comma.vector.concat(NULL, vec.default), '1 and 2');
+        vec.default <- c(1, 2, 3);
+        expect_equal(oxford.comma.vector.concat(NULL, vec.default), '1, 2, and 3');
+        vec.default <- c(1, 2, 3, 4);
+        expect_equal(oxford.comma.vector.concat(NULL, vec.default), '1, 2, 3, and 4');
+    });