Add test cases

DESCRIPTION

@@ -31,5 +31,7 @@ Suggests:
     shiny,
     biomaRt,
     pwalign,
-    Biostrings
+    Biostrings,
+    testthat (>= 3.0.0)
 VignetteBuilder: knitr
+Config/testthat/edition: 3

tests/testthat.R

@@ -0,0 +1,12 @@
+# This file is part of the standard setup for testthat.
+# It is recommended that you do not modify it.
+#
+# Where should you do additional test configuration?
+# Learn more about the roles of various files in:
+# * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
+# * https://testthat.r-lib.org/articles/special-files.html
+
+library(testthat)
+library(geneviewer)
+
+test_check("geneviewer")

tests/testthat/test-GC_chart.R

@@ -0,0 +1,292 @@
+
+# GC_chart
+test_that("GC_chart works with valid data", {
+  # Run function
+  chart <- GC_chart(geneviewer::ophA_clusters, group = "class", cluster = "cluster", height = "200px")
+
+  # Check result
+  expect_s3_class(chart, "htmlwidget")
+  expect_true("x" %in% names(chart))
+  expect_true("data" %in% names(chart$x))
+  expect_equal(nrow(chart$x$data), nrow(geneviewer::ophA_clusters))
+})
+
+test_that("GC_chart throws error for missing columns", {
+  # Create test data
+  genes_data <- data.frame(
+    start = c(10, 50, 90),
+    end = c(40, 80, 120)
+  )
+
+  # Test for missing group column
+  expect_error(
+    GC_chart(genes_data, group = "group"),
+    "group column not found in data"
+  )
+
+  # Test for missing cluster column
+  expect_error(
+    GC_chart(genes_data, cluster = "cluster"),
+    "cluster column not found in data"
+  )
+})
+
+test_that("GC_chart filters rows with NA in start or end columns", {
+
+  genes_data <- data.frame(
+    start = c(10, NA, 90, 130),
+    end = c(40, 80, NA, 160),
+    group = c('A', 'A', 'B', 'B')
+  )
+
+  expect_warning(
+    chart <- GC_chart(genes_data, group = "group"),
+    "Rows with NA values in 'start' or 'end' columns have been filtered out"
+  )
+
+  expect_equal(nrow(chart$x$data), 2)
+})
+
+# GC_title
+test_that("GC_title updates cluster title and subtitle correctly with ophA_clusters data", {
+  # Load ophA_clusters data
+  data("ophA_clusters", package = "geneviewer")
+
+  # Generate a GC chart
+  chart <- GC_chart(ophA_clusters, cluster = "cluster", group = "class", height = "400px")
+
+  # Add a title and subtitle to the chart
+  updated_chart <- GC_title(
+    GC_chart = chart,
+    title = "OphA Cluster Analysis",
+    subtitle = "Key Functional Clusters",
+    show = TRUE,
+    height = "50px",
+    style = list(backgroundColor = "#e0f7fa"),
+    titleFont = list(fontSize = "18px", fontWeight = "bold", fill = "#004d40"),
+    subtitleFont = list(fontSize = "14px", fontStyle = "italic", fill = "#00796b")
+  )
+
+  # Assertions
+  expect_s3_class(updated_chart, "htmlwidget")
+
+  # Check if the title section is updated correctly
+  expect_true("title" %in% names(updated_chart$x))
+  expect_equal(updated_chart$x$title$title, "OphA Cluster Analysis")
+  expect_equal(updated_chart$x$title$subtitle, "Key Functional Clusters")
+  expect_equal(updated_chart$x$title$show, TRUE)
+  expect_equal(updated_chart$x$title$height, "50px")
+
+  # Check styles
+  expect_equal(updated_chart$x$title$style$backgroundColor, "#e0f7fa")
+
+  # Check title font
+  expect_equal(updated_chart$x$title$titleFont$fontSize, "18px")
+  expect_equal(updated_chart$x$title$titleFont$fontWeight, "bold")
+  expect_equal(updated_chart$x$title$titleFont$fill, "#004d40")
+
+  # Check subtitle font
+  expect_equal(updated_chart$x$title$subtitleFont$fontSize, "14px")
+  expect_equal(updated_chart$x$title$subtitleFont$fontStyle, "italic")
+  expect_equal(updated_chart$x$title$subtitleFont$fill, "#00796b")
+
+  # Ensure original chart is unmodified if no title or subtitle is provided
+  no_title_chart <- GC_title(chart, show = TRUE)
+  expect_equal(no_title_chart, chart)
+})
+
+#GC_title
+test_that("GC_clusterTitle updates the title and subtitle of specified clusters correctly", {
+  data("ophA_clusters", package = "geneviewer")
+
+  chart <- GC_chart(ophA_clusters, cluster = "cluster", group = "class", height = "400px")
+
+  # Update titles and subtitles for specific clusters
+  updated_chart <- GC_clusterTitle(
+    GC_chart = chart,
+    title = c("OphA Cluster", "dbOphA Cluster"),
+    subtitle = c("Cluster 1 Details", "Cluster 2 Details"),
+    cluster = c("ophA", "dbophA"),
+    height = c("40px", "50px")
+  )
+
+  # Assertions for the two clusters
+  expect_true("clusterTitle" %in% names(updated_chart$x$series$ophA))
+  expect_true("clusterTitle" %in% names(updated_chart$x$series$dbophA))
+
+  expect_equal(updated_chart$x$series$ophA$clusterTitle$title, "OphA Cluster")
+  expect_equal(updated_chart$x$series$ophA$clusterTitle$subtitle, "Cluster 1 Details")
+  expect_equal(updated_chart$x$series$dbophA$clusterTitle$title, "dbOphA Cluster")
+  expect_equal(updated_chart$x$series$dbophA$clusterTitle$subtitle, "Cluster 2 Details")
+})
+
+# GC_sequence
+test_that("GC_sequence updates sequence settings for specified clusters correctly", {
+  # Load ophA_clusters data
+  data("ophA_clusters", package = "geneviewer")
+
+  # Generate a GC chart
+  chart <- GC_chart(ophA_clusters, cluster = "cluster", group = "class", height = "400px")
+
+  # Update sequence settings for specific clusters
+  updated_chart <- GC_sequence(
+    GC_chart = chart,
+    show = TRUE,
+    cluster = c("ophA", "dbophA"),
+    y = c(60, 70),
+    sequenceStyle = list(stroke = "blue", strokeWidth = 2),
+    markerStyle = list(stroke = "red", strokeWidth = 1, gap = 5, tiltAmount = 10)
+  )
+
+  # Assertions
+  expect_s3_class(updated_chart, "htmlwidget")
+
+  # Check if sequence settings are applied to the specified clusters
+  expect_true("sequence" %in% names(updated_chart$x$series$ophA))
+  expect_true("sequence" %in% names(updated_chart$x$series$dbophA))
+
+  # Verify sequence settings for `ophA` cluster
+  ophA_sequence <- updated_chart$x$series$ophA$sequence
+  expect_true(ophA_sequence$show)
+  expect_equal(ophA_sequence$y, 60)
+  expect_equal(ophA_sequence$sequenceStyle$stroke, "blue")
+  expect_equal(ophA_sequence$sequenceStyle$strokeWidth, 2)
+  expect_equal(ophA_sequence$markerStyle$stroke, "red")
+  expect_equal(ophA_sequence$markerStyle$strokeWidth, 1)
+  expect_equal(ophA_sequence$markerStyle$gap, 5)
+  expect_equal(ophA_sequence$markerStyle$tiltAmount, 10)
+
+  # Verify sequence settings for `dbophA` cluster
+  dbophA_sequence <- updated_chart$x$series$dbophA$sequence
+  expect_true(dbophA_sequence$show)
+  expect_equal(dbophA_sequence$y, 70)
+  expect_equal(dbophA_sequence$sequenceStyle$stroke, "blue")
+  expect_equal(dbophA_sequence$sequenceStyle$strokeWidth, 2)
+  expect_equal(dbophA_sequence$markerStyle$stroke, "red")
+  expect_equal(dbophA_sequence$markerStyle$strokeWidth, 1)
+  expect_equal(dbophA_sequence$markerStyle$gap, 5)
+  expect_equal(dbophA_sequence$markerStyle$tiltAmount, 10)
+
+})
+
+test_that("GC_grid updates grid settings for specified clusters correctly", {
+
+  # Load ophA_clusters data
+  data("ophA_clusters", package = "geneviewer")
+
+  # Generate a GC chart
+  chart <- GC_chart(ophA_clusters, cluster = "cluster", group = "class", height = "400px")
+
+  # Update grid settings for specific clusters
+  updated_chart <- GC_grid(
+    GC_chart = chart,
+    margin = list(left = "20px", right = "30px"),
+    width = c("50%", "50%"),
+    height = c("150px", "200px"),
+    direction = "row",
+    cluster = c("ophA", "dbophA")
+  )
+
+  # Assertions
+  expect_s3_class(updated_chart, "htmlwidget")
+
+  # Check if grid settings are applied to the specified clusters
+  expect_true("container" %in% names(updated_chart$x$series$ophA))
+  expect_true("container" %in% names(updated_chart$x$series$dbophA))
+
+  # Verify grid settings for `ophA` cluster
+  ophA_grid <- updated_chart$x$series$ophA$container
+  expect_equal(ophA_grid$margin$left, "20px")
+  expect_equal(ophA_grid$margin$right, "30px")
+  expect_equal(ophA_grid$style$width, "50%")
+  expect_equal(ophA_grid$height, 150)
+
+  # Verify grid settings for `dbophA` cluster
+  dbophA_grid <- updated_chart$x$series$dbophA$container
+  expect_equal(dbophA_grid$margin$left, "20px")
+  expect_equal(dbophA_grid$margin$right, "30px")
+  expect_equal(dbophA_grid$style$width, "50%")
+  expect_equal(dbophA_grid$height, 200)
+
+  # Check global settings
+  expect_equal(updated_chart$x$graphContainer$direction, "row")
+
+})
+
+test_that("GC_scale updates scale settings for specified clusters correctly", {
+
+  # Load ophA_clusters data
+  data("ophA_clusters", package = "geneviewer")
+
+  # Generate a GC chart
+  chart <- GC_chart(ophA_clusters, cluster = "cluster", group = "class", height = "400px")
+
+  # Update scale settings for specific clusters
+  updated_chart <- GC_scale(
+    GC_chart = chart,
+    cluster = c("ophA", "dbophA"),
+    start = c(2500, 18000),
+    end = c(22000, 44000),
+    padding = 5,
+    hidden = FALSE,
+    reverse = c(FALSE, TRUE),
+    axis_position = "top",
+    scale_breaks = TRUE,
+    scale_break_threshold = 30,
+    ticksCount = 8,
+    ticksFormat = ",.2f",
+    tickStyle = list(stroke = "blue", strokeWidth = 2),
+    textStyle = list(fill = "red", fontSize = "12px"),
+    lineStyle = list(stroke = "black", strokeWidth = 2)
+  )
+
+  # Assertions
+  expect_s3_class(updated_chart, "htmlwidget")
+
+  # Check if scale settings are applied to the specified clusters
+  expect_true("scale" %in% names(updated_chart$x$series$ophA))
+  expect_true("scale" %in% names(updated_chart$x$series$dbophA))
+
+  # Verify scale settings for `ophA` cluster
+  ophA_scale <- updated_chart$x$series$ophA$scale
+  expect_equal(ophA_scale$start, 2500)
+  expect_equal(ophA_scale$end, 22000)
+  expect_equal(ophA_scale$padding, 5)
+  expect_false(ophA_scale$hidden)
+  expect_false(ophA_scale$reverse)
+  expect_equal(ophA_scale$axisPosition, "top")
+  expect_true(ophA_scale$scale_breaks)
+  expect_equal(ophA_scale$scale_break_threshold, 30)
+  expect_equal(ophA_scale$ticksCount, 8)
+  expect_equal(ophA_scale$ticksFormat, ",.2f")
+  expect_equal(ophA_scale$tickStyle$stroke, "blue")
+  expect_equal(ophA_scale$tickStyle$strokeWidth, 2)
+  expect_equal(ophA_scale$textStyle$fill, "red")
+  expect_equal(ophA_scale$textStyle$fontSize, "12px")
+  expect_equal(ophA_scale$lineStyle$stroke, "black")
+  expect_equal(ophA_scale$lineStyle$strokeWidth, 2)
+
+  # Verify scale settings for `dbophA` cluster
+  dbophA_scale <- updated_chart$x$series$dbophA$scale
+  expect_equal(dbophA_scale$start, 18000)
+  expect_equal(dbophA_scale$end, 44000)
+  expect_equal(dbophA_scale$padding, 5)
+  expect_false(dbophA_scale$hidden)
+  expect_true(dbophA_scale$reverse)
+  expect_equal(dbophA_scale$axisPosition, "top")
+  expect_true(dbophA_scale$scale_breaks)
+  expect_equal(dbophA_scale$scale_break_threshold, 30)
+  expect_equal(dbophA_scale$ticksCount, 8)
+  expect_equal(dbophA_scale$ticksFormat, ",.2f")
+  expect_equal(dbophA_scale$tickStyle$stroke, "blue")
+  expect_equal(dbophA_scale$tickStyle$strokeWidth, 2)
+  expect_equal(dbophA_scale$textStyle$fill, "red")
+  expect_equal(dbophA_scale$textStyle$fontSize, "12px")
+  expect_equal(dbophA_scale$lineStyle$stroke, "black")
+  expect_equal(dbophA_scale$lineStyle$strokeWidth, 2)
+
+})
+
+
+
+

tests/testthat/test-load_data.R

@@ -0,0 +1,49 @@
+test_that("Read .gbk file from file path", {
+  # Use the actual GBK file
+  gbk_file <- system.file("extdata", "BGC0000001.gbk", package = "geneviewer")
+
+  # Run the GC_chart function
+  chart <- GC_chart(gbk_file)
+
+  # Assertions
+  expect_s3_class(chart, "htmlwidget")
+  expect_true("strand" %in% names(chart$x$data))
+  expect_true("cluster" %in% names(chart$x$data))
+})
+
+test_that("Read FASTA from file path", {
+
+  # Use the actual FASTA file
+  file_path <- system.file("extdata", "BGC0000108.fasta", package = "geneviewer")
+  fasta_df <- geneviewer::read_fasta(file_path, sequence = FALSE)
+
+  # Run the GC_chart function
+  chart <- GC_chart(fasta_df)
+
+  # Assertions
+  expect_s3_class(chart, "htmlwidget")
+  expect_true("strand" %in% names(chart$x$data))
+  expect_true("cluster" %in% names(chart$x$data))
+})
+
+test_that("Read .gff3 from file path", {
+  # Use the actual .gff3 file
+  file_path <- system.file("extdata", "HQ113105.1.gff3", package = "geneviewer")
+
+  # Read the .gff3 file with all specified fields
+  gff_df <- geneviewer::read_gff(
+    file_path,
+    fields = c("source", "type", "start", "end", "strand", "Name")
+  )
+
+  # Run the GC_chart function
+  chart <- GC_chart(gff_df)
+
+  # Assertions for the chart object
+  expect_s3_class(chart, "htmlwidget")
+
+  # Assertions for all required fields in the processed data
+  expected_fields <- c("source", "type", "start", "end", "strand", "Name", "rowID")
+  missing_fields <- setdiff(expected_fields, names(chart$x$data))
+  expect_equal(length(missing_fields), 0, info = paste("Missing fields:", paste(missing_fields, collapse = ", ")))
+})