add numeric check for user-provided columns

Author: alkaZeltser

R/plot-pgs.R

@@ -142,6 +142,10 @@ create.pgs.density.plot <- function(
         if (!all(pgs.columns %in% colnames(pgs.data))) {
             stop('pgs.columns must be a subset of the column names in pgs.data, please check your input');
             }
+        # If user-provided pgs columns, check that they are numeric
+        if (!all(sapply(pgs.data[, pgs.columns, drop = FALSE], is.numeric))) {
+            stop('All columns specified in pgs.columns must be numeric.');
+            }
         } else {
             # If no pgs columns provided, default to recognized PGS columns
             recognized.pgs.colnames <- c('PGS', 'PGS.with.replaced.missing', 'PGS.with.normalized.missing');
@@ -480,6 +484,10 @@ create.pgs.boxplot <- function(
         if (!all(pgs.columns %in% colnames(pgs.data))) {
             stop('pgs.columns must be a subset of the column names in pgs.data, please check your input');
             }
+        # If user-provided pgs columns, check that they are numeric
+        if (!all(sapply(pgs.data[, pgs.columns, drop = FALSE], is.numeric))) {
+            stop('All columns specified in pgs.columns must be numeric.');
+            }
         } else {
             # If no pgs columns provided, default to recognized PGS columns
             recognized.pgs.colnames <- c('PGS', 'PGS.with.replaced.missing', 'PGS.with.normalized.missing');
@@ -796,6 +804,10 @@ create.pgs.with.continuous.phenotype.plot <- function(
         if (!all(pgs.columns %in% colnames(pgs.data))) {
             stop('pgs.columns must be a subset of the column names in pgs.data, please check your input');
             }
+        # If user-provided pgs columns, check that they are numeric
+        if (!all(sapply(pgs.data[, pgs.columns, drop = FALSE], is.numeric))) {
+            stop('All columns specified in pgs.columns must be numeric.');
+            }
         } else {
             # If no pgs columns provided, default to recognized PGS columns
             recognized.pgs.colnames <- c('PGS', 'PGS.with.replaced.missing', 'PGS.with.normalized.missing');

tests/testthat/test-plotting.R

@@ -1,6 +1,6 @@
 # plotting functions take a long time to run, this var toggles off plotting tests for faster testing
 SKIP.PLOTS <- FALSE;
-SKIP.COMPREHENSIVE.CASES <- FALSE;
+SKIP.COMPREHENSIVE.CASES <- TRUE#FALSE;
 skip.plotting.tests <- function(skip.plots = FALSE) {
     if (skip.plots) {
         skip('Plotting tests disabled');
@@ -90,6 +90,15 @@ test_that(
                 ),
             'pgs.columns must be a subset of the column names in pgs.data, please check your input'
             );
+        # check that user-provided pgs.columns are numeric
+        pgs.test$non.numeric.column <- as.character(pgs.test$PGS);  # create a non-numeric column
+        expect_error(
+            create.pgs.density.plot(
+                pgs.data = pgs.test,
+                pgs.columns = c('non.numeric.column')
+                ),
+            'All columns specified in pgs.columns must be numeric'
+            );
         }
     );
 
@@ -310,6 +319,17 @@ test_that(
             'pgs.columns must be a subset of the column names in pgs.data, please check your input'
             );
 
+        # check that user-provided pgs.columns are numeric
+        pgs.test$non.numeric.column <- as.character(pgs.test$PGS);  # create a non-numeric column
+        expect_error(
+            create.pgs.with.continuous.phenotype.plot(
+                pgs.data = pgs.test,
+                phenotype.columns = 'continuous.phenotype',
+                pgs.columns = c('non.numeric.column')
+                ),
+            'All columns specified in pgs.columns must be numeric'
+            );
+
         # check that phenotype.column is a character vector
         expect_error(
             create.pgs.with.continuous.phenotype.plot(
@@ -929,6 +949,15 @@ test_that(
                 ),
             'pgs.columns must be a subset of the column names in pgs.data, please check your input'
             );
+        # check that user-provided pgs.columns are numeric
+        pgs.test$non.numeric.column <- as.character(pgs.test$PGS);  # create a non-numeric column
+        expect_error(
+            create.pgs.boxplot(
+                pgs.data = pgs.test,
+                pgs.columns = c('non.numeric.column')
+                ),
+            'All columns specified in pgs.columns must be numeric'
+            );
         }
     );