Nothing
tests/testthat/test-GC_chart.R
In geneviewer: Gene Cluster Visualizations
# 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$direction, "row")
})
#GC_scale
test_that("GC_scale updates scale settings for specified clusters correctly", {
# Load ophA_clusters data
data("ophA_clusters", package = "geneviewer")
# Generate a GC chart
chart <- GC_chart(ophA_clusters, cluster = "cluster", group = "class", height = "400px")
# Update scale settings for specific clusters
updated_chart <- GC_scale(
GC_chart = chart,
cluster = c("ophA", "dbophA"),
start = c(2500, 18000),
end = c(22000, 44000),
padding = 5,
hidden = FALSE,
reverse = c(FALSE, TRUE),
axis_position = "top",
scale_breaks = TRUE,
scale_break_threshold = 30,
ticksCount = 8,
ticksFormat = ",.2f",
tickStyle = list(stroke = "blue", strokeWidth = 2),
textStyle = list(fill = "red", fontSize = "12px"),
lineStyle = list(stroke = "black", strokeWidth = 2)
)
# Assertions
expect_s3_class(updated_chart, "htmlwidget")
# Check if scale settings are applied to the specified clusters
expect_true("scale" %in% names(updated_chart$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$strokeWidth, 2)
})
# GC_scaleBar
test_that("GC_scaleBar updates scale bar settings for specified clusters correctly", {
# Load ophA_clusters data
data("ophA_clusters", package = "geneviewer")
# Generate a GC chart
chart <- GC_chart(ophA_clusters, cluster = "cluster", group = "class", height = "400px")
# Update scale bar settings for specific clusters
updated_chart <- GC_scaleBar(
GC_chart = chart,
show = TRUE,
cluster = c("ophA", "dbophA"),
scaleBarLineStyle = list(stroke = "black", strokeWidth = 1),
scaleBarTickStyle = list(stroke = "grey", strokeWidth = 2),
labelStyle = list(
labelPosition = "left",
fontSize = "12px",
fontFamily = "Arial",
fill = "blue"
),
title = c("1 kb", "2 kb"),
scaleBarUnit = c(1000, 2000)
)
# Assertions
expect_s3_class(updated_chart, "htmlwidget")
# Check if scale bar settings are applied to the specified clusters
expect_true("scaleBar" %in% names(updated_chart$x$series$ophA))
expect_true("scaleBar" %in% names(updated_chart$x$series$dbophA))
# Verify scale bar settings for `ophA` cluster
ophA_scaleBar <- updated_chart$x$series$ophA$scaleBar
expect_true(ophA_scaleBar$show)
expect_equal(ophA_scaleBar$scaleBarLineStyle$stroke, "black")
expect_equal(ophA_scaleBar$scaleBarLineStyle$strokeWidth, 1)
expect_equal(ophA_scaleBar$scaleBarTickStyle$stroke, "grey")
expect_equal(ophA_scaleBar$scaleBarTickStyle$strokeWidth, 2)
expect_equal(ophA_scaleBar$labelStyle$labelPosition, "left")
expect_equal(ophA_scaleBar$labelStyle$fontSize, "12px")
expect_equal(ophA_scaleBar$labelStyle$fontFamily, "Arial")
expect_equal(ophA_scaleBar$labelStyle$fill, "blue")
expect_equal(ophA_scaleBar$title, "1 kb")
expect_equal(ophA_scaleBar$scaleBarUnit, 1000)
# Verify scale bar settings for `dbophA` cluster
dbophA_scaleBar <- updated_chart$x$series$dbophA$scaleBar
expect_true(dbophA_scaleBar$show)
expect_equal(dbophA_scaleBar$scaleBarLineStyle$stroke, "black")
expect_equal(dbophA_scaleBar$scaleBarLineStyle$strokeWidth, 1)
expect_equal(dbophA_scaleBar$scaleBarTickStyle$stroke, "grey")
expect_equal(dbophA_scaleBar$scaleBarTickStyle$strokeWidth, 2)
expect_equal(dbophA_scaleBar$labelStyle$labelPosition, "left")
expect_equal(dbophA_scaleBar$labelStyle$fontSize, "12px")
expect_equal(dbophA_scaleBar$labelStyle$fontFamily, "Arial")
expect_equal(dbophA_scaleBar$labelStyle$fill, "blue")
expect_equal(dbophA_scaleBar$title, "2 kb")
expect_equal(dbophA_scaleBar$scaleBarUnit, 2000)
})
# GC_clusterLabel
test_that("GC_clusterLabel updates cluster labels for specified clusters correctly", {
# Load ophA_clusters data
data("ophA_clusters", package = "geneviewer")
# Generate a GC chart
chart <- GC_chart(ophA_clusters, cluster = "cluster", group = "class", height = "400px")
# Update cluster labels for specific clusters
updated_chart <- GC_clusterLabel(
GC_chart = chart,
title = c("Cluster A", "Cluster B"),
cluster = c("ophA", "dbophA"),
position = c("left", "right"),
width = "150px",
wrapLabel = TRUE,
wrapOptions = list(
dyAdjust = 0,
lineHeightEms = 1.1,
splitOnHyphen = TRUE
),
fontSize = "14px",
fontStyle = "italic",
fontWeight = "bold",
fontFamily = "Arial",
cursor = "pointer"
)
# Assertions
expect_s3_class(updated_chart, "htmlwidget")
# Check if cluster label settings are applied to the specified clusters
expect_true("clusterLabel" %in% names(updated_chart$x$series$ophA))
expect_true("clusterLabel" %in% names(updated_chart$x$series$dbophA))
# Verify cluster label settings for `ophA` cluster
ophA_label <- updated_chart$x$series$ophA$clusterLabel
expect_equal(ophA_label$title, "Cluster A")
expect_true(ophA_label$show)
expect_equal(ophA_label$position, "left")
expect_true(ophA_label$wrapLabel)
expect_equal(ophA_label$wrapOptions$dyAdjust, 0)
expect_equal(ophA_label$wrapOptions$lineHeightEms, 1.1)
expect_true(ophA_label$wrapOptions$splitOnHyphen)
expect_equal(ophA_label$fontSize, "14px")
expect_equal(ophA_label$fontStyle, "italic")
expect_equal(ophA_label$fontWeight, "bold")
expect_equal(ophA_label$fontFamily, "Arial")
expect_equal(ophA_label$cursor, "pointer")
# Verify cluster label settings for `dbophA` cluster
dbophA_label <- updated_chart$x$series$dbophA$clusterLabel
expect_equal(dbophA_label$title, "Cluster B")
expect_true(dbophA_label$show)
expect_equal(dbophA_label$position, "right")
expect_true(dbophA_label$wrapLabel)
expect_equal(dbophA_label$wrapOptions$dyAdjust, 0)
expect_equal(dbophA_label$wrapOptions$lineHeightEms, 1.1)
expect_true(dbophA_label$wrapOptions$splitOnHyphen)
expect_equal(dbophA_label$fontSize, "14px")
expect_equal(dbophA_label$fontStyle, "italic")
expect_equal(dbophA_label$fontWeight, "bold")
expect_equal(dbophA_label$fontFamily, "Arial")
expect_equal(dbophA_label$cursor, "pointer")
# Verify grid settings for label width
expect_equal(updated_chart$x$series$ophA$container$margin$left, "150px")
expect_equal(updated_chart$x$series$dbophA$container$margin$right, "150px")
})
# GC_clusterFooter
test_that("GC_clusterFooter updates footers with all options correctly", {
# Load ophA_clusters data
data("ophA_clusters", package = "geneviewer")
# Generate a GC chart
chart <- GC_chart(ophA_clusters, cluster = "cluster", group = "class")
# Update footers with all options
updated_chart <- GC_clusterFooter(
GC_chart = chart,
title = c("Footer for ophA", "Footer for dbophA"),
subtitle = c("Subtitle for ophA", "Subtitle for dbophA"),
spacing = c(15, 20),
show = TRUE,
cluster = c("ophA", "dbophA"),
x = c(6, 8),
y = c(-20, -25),
align = c("center", "right"),
titleFont = list(
fontSize = "12px",
fontWeight = "bold",
fontFamily = "sans-serif",
fill = "black",
cursor = "default"
),
subtitleFont = list(
fill = "grey",
fontSize = "10px",
fontStyle = "normal",
fontFamily = "sans-serif",
cursor = "default"
)
)
# Assertions
expect_s3_class(updated_chart, "htmlwidget")
# Verify footer settings for cluster ophA
ophA_footer <- updated_chart$x$series$ophA$footer
expect_equal(ophA_footer$title, "Footer for ophA")
expect_equal(ophA_footer$subtitle, "Subtitle for ophA")
expect_true(ophA_footer$show)
expect_equal(ophA_footer$titleFont$fontSize, "12px")
expect_equal(ophA_footer$titleFont$fontWeight, "bold")
expect_equal(ophA_footer$titleFont$fontFamily, "sans-serif")
expect_equal(ophA_footer$titleFont$fill, "black")
expect_equal(ophA_footer$titleFont$cursor, "default")
expect_equal(ophA_footer$subtitleFont$fontSize, "10px")
expect_equal(ophA_footer$subtitleFont$fontStyle, "normal")
expect_equal(ophA_footer$subtitleFont$fontFamily, "sans-serif")
expect_equal(ophA_footer$subtitleFont$fill, "grey")
expect_equal(ophA_footer$subtitleFont$cursor, "default")
expect_equal(ophA_footer$x, 6)
expect_equal(ophA_footer$y, -20)
# Verify footer settings for cluster dbophA
dbophA_footer <- updated_chart$x$series$dbophA$footer
expect_equal(dbophA_footer$title, "Footer for dbophA")
expect_equal(dbophA_footer$subtitle, "Subtitle for dbophA")
expect_true(dbophA_footer$show)
expect_equal(dbophA_footer$titleFont$fontSize, "12px")
expect_equal(dbophA_footer$titleFont$fontWeight, "bold")
expect_equal(dbophA_footer$titleFont$fontFamily, "sans-serif")
expect_equal(dbophA_footer$titleFont$fill, "black")
expect_equal(dbophA_footer$titleFont$cursor, "default")
expect_equal(dbophA_footer$subtitleFont$fontSize, "10px")
expect_equal(dbophA_footer$subtitleFont$fontStyle, "normal")
expect_equal(dbophA_footer$subtitleFont$fontFamily, "sans-serif")
expect_equal(dbophA_footer$subtitleFont$fill, "grey")
expect_equal(dbophA_footer$subtitleFont$cursor, "default")
expect_equal(dbophA_footer$x, 8)
expect_equal(dbophA_footer$y, -25)
})
# GC_labels
test_that("GC_labels updates labels with all options correctly", {
# Load ophA_clusters data
data("ophA_clusters", package = "geneviewer")
# Generate a GC chart
chart <- GC_chart(ophA_clusters, cluster = "cluster", group = "class")
# Update labels with all options
updated_chart <- GC_labels(
GC_chart = chart,
label = "name",
show = TRUE,
cluster = c("ophA", "dbophA"),
itemStyle = list(
list(index = 0, fill = "red", fontSize = "14px", fontWeight = "bold"),
list(index = 1, fill = "blue", fontSize = "12px", fontWeight = "normal")
),
x = 10,
y = -5,
adjustLabels = TRUE,
fontSize = "12px",
fontStyle = "italic",
fill = "black",
fontFamily = "sans-serif",
textAnchor = "middle",
cursor = "default"
)
# Assertions
expect_s3_class(updated_chart, "htmlwidget")
# Verify label settings for cluster ophA
ophA_label <- updated_chart$x$series$ophA$labels
expect_equal(ophA_label$label, "name")
expect_true(ophA_label$show)
expect_equal(ophA_label$itemStyle[[1]]$fill, "red")
expect_equal(ophA_label$itemStyle[[1]]$fontSize, "14px")
expect_equal(ophA_label$itemStyle[[1]]$fontWeight, "bold")
expect_equal(ophA_label$x, 10)
expect_equal(ophA_label$y, -5)
# Verify label settings for cluster dbophA
dbophA_label <- updated_chart$x$series$dbophA$labels
expect_equal(dbophA_label$label, "name")
expect_true(dbophA_label$show)
expect_equal(dbophA_label$itemStyle[[2]]$fill, "blue")
expect_equal(dbophA_label$itemStyle[[2]]$fontSize, "12px")
expect_equal(dbophA_label$itemStyle[[2]]$fontWeight, "normal")
expect_equal(dbophA_label$x, 10)
expect_equal(dbophA_label$y, -5)
})
# GC_coordinates
test_that("GC_coordinates updates coordinates with all options correctly", {
# Load ophA_clusters data
data("ophA_clusters", package = "geneviewer")
# Generate a GC chart
chart <- GC_chart(ophA_clusters, cluster = "cluster", group = "class")
# Update coordinates with all options
updated_chart <- GC_coordinates(
GC_chart = chart,
show = TRUE,
tickValuesTop = c(2522, 5286, 9536),
tickValuesBottom = c(4276, 4718, 10904),
ticksFormat = ",.0f",
tickStyle = list(
fontSize = "10px",
fontWeight = "normal",
fontFamily = "sans-serif",
fill = "grey",
cursor = "default"
),
textStyle = list(
fontSize = "12px",
fontStyle = "italic",
fontFamily = "sans-serif",
fill = "black",
textAnchor = "middle",
cursor = "default"
),
cluster = c("ophA"),
x = c(10, 15),
y = c(-5, -10)
)
# Assertions
expect_s3_class(updated_chart, "htmlwidget")
# Verify coordinate settings for cluster ophA
ophA_coordinates <- updated_chart$x$series$ophA$coordinates
expect_true(ophA_coordinates$show)
expect_equal(ophA_coordinates$tickValuesTop, c(2522, 5286, 9536))
expect_equal(ophA_coordinates$tickValuesBottom, c(4276, 4718, 10904))
expect_equal(ophA_coordinates$ticksFormat, ",.0f")
expect_equal(ophA_coordinates$tickStyle$fontSize, "10px")
expect_equal(ophA_coordinates$tickStyle$fill, "grey")
expect_equal(ophA_coordinates$textStyle$fontSize, "12px")
expect_equal(ophA_coordinates$textStyle$fill, "black")
expect_equal(ophA_coordinates$x, 10)
expect_equal(ophA_coordinates$y, -5)
})
# GC_genes test
test_that("GC_genes updates gene characteristics with all options correctly", {
# Load ophA_clusters data
data("ophA_clusters", package = "geneviewer")
# Generate a GC chart
chart <- GC_chart(ophA_clusters, cluster = "cluster", group = "class")
# Update genes with all options
updated_chart <- GC_genes(
GC_chart = chart,
group = "class",
show = TRUE,
marker = "arrow",
marker_size = "medium",
colorScheme = "schemeCategory10",
customColors = c("red", "blue", "green"),
cluster = c("ophA", "dbophA"),
itemStyle = list(
list(index = 0, fill = "red", stroke = "black"),
list(index = 1, fill = "blue", stroke = "grey")
),
x = c(10, 15),
y = c(-5, -10),
stroke = "black",
strokeWidth = 1,
arrowheadWidth = NULL,
arrowheadHeight = NULL,
arrowHeight = NULL,
markerHeight = NULL
)
# Assertions
expect_s3_class(updated_chart, "htmlwidget")
# Verify gene settings for cluster ophA
ophA_genes <- updated_chart$x$series$ophA$genes
expect_equal(ophA_genes$group, "class")
expect_true(ophA_genes$show)
expect_equal(ophA_genes$marker, "arrow")
expect_equal(ophA_genes$markerSize, "medium")
expect_equal(ophA_genes$colorScheme, "schemeCategory10")
expect_equal(ophA_genes$customColors, c("red", "blue", "green"))
expect_equal(ophA_genes$itemStyle[[1]]$fill, "red")
expect_equal(ophA_genes$itemStyle[[1]]$stroke, "black")
expect_equal(ophA_genes$itemStyle[[2]]$fill, "blue")
expect_equal(ophA_genes$itemStyle[[2]]$stroke, "grey")
expect_equal(ophA_genes$x, c(10, 15))
expect_equal(ophA_genes$y, c(-5, -10))
expect_equal(ophA_genes$stroke, "black")
expect_equal(ophA_genes$strokeWidth, 1)
# Verify gene settings for cluster dbophA
dbophA_genes <- updated_chart$x$series$dbophA$genes
expect_equal(dbophA_genes$group, "class")
expect_true(dbophA_genes$show)
expect_equal(dbophA_genes$marker, "arrow")
expect_equal(dbophA_genes$markerSize, "medium")
expect_equal(dbophA_genes$colorScheme, "schemeCategory10")
expect_equal(dbophA_genes$customColors, c("red", "blue", "green"))
expect_equal(dbophA_genes$itemStyle[[1]]$fill, "red")
expect_equal(dbophA_genes$itemStyle[[1]]$stroke, "black")
expect_equal(dbophA_genes$itemStyle[[2]]$fill, "blue")
expect_equal(dbophA_genes$itemStyle[[2]]$stroke, "grey")
expect_equal(dbophA_genes$x, c(10, 15))
expect_equal(dbophA_genes$y, c(-5, -10))
expect_equal(dbophA_genes$stroke, "black")
expect_equal(dbophA_genes$strokeWidth, 1)
})
#GC_color
test_that("GC_color updates color scheme with all options correctly", {
# Load ophA_clusters data
data("ophA_clusters", package = "geneviewer")
# Generate a GC chart
chart <- GC_chart(ophA_clusters, cluster = "cluster", group = "class", height = "100px")
# Update color scheme with predefined scheme
updated_chart1 <- GC_color(
GC_chart = chart,
colorScheme = "schemeCategory10"
)
# Assertions for predefined color scheme
expect_s3_class(updated_chart1, "htmlwidget")
expect_equal(updated_chart1$x$legend$legendOptions$colorScheme, "schemeCategory10")
expect_null(updated_chart1$x$legend$legendOptions$customColors)
# Validate series colorScheme
clusters <- names(updated_chart1$x$series)
for (cluster_name in clusters) {
expect_equal(updated_chart1$x$series[[cluster_name]]$genes$colorScheme, "schemeCategory10")
expect_null(updated_chart1$x$series[[cluster_name]]$genes$customColors)
expect_equal(updated_chart1$x$series[[cluster_name]]$transcript$colorScheme, "schemeCategory10")
expect_null(updated_chart1$x$series[[cluster_name]]$transcript$customColors)
}
# Update color scheme with custom colors
updated_chart2 <- GC_color(
GC_chart = chart,
customColors = c("red", "orange", "green")
)
# Assertions for custom colors
expect_s3_class(updated_chart2, "htmlwidget")
expect_null(updated_chart2$x$legend$legendOptions$colorScheme)
expect_equal(updated_chart2$x$legend$legendOptions$customColors, c("red", "orange", "green"))
# Validate series customColors
for (cluster_name in clusters) {
expect_null(updated_chart2$x$series[[cluster_name]]$genes$colorScheme)
expect_equal(updated_chart2$x$series[[cluster_name]]$genes$customColors, c("red", "orange", "green"))
expect_null(updated_chart2$x$series[[cluster_name]]$transcript$colorScheme)
expect_equal(updated_chart2$x$series[[cluster_name]]$transcript$customColors, c("red", "orange", "green"))
}
# Update color scheme with named custom colors
updated_chart3 <- GC_color(
GC_chart = chart,
customColors = list(A = "yellow", B = "pink", C = "purple")
)
# Assertions for named custom colors
expect_s3_class(updated_chart3, "htmlwidget")
expect_null(updated_chart3$x$legend$legendOptions$colorScheme)
expect_equal(updated_chart3$x$legend$legendOptions$customColors, list(A = "yellow", B = "pink", C = "purple"))
# Validate series named customColors
for (cluster_name in clusters) {
expect_null(updated_chart3$x$series[[cluster_name]]$genes$colorScheme)
expect_equal(updated_chart3$x$series[[cluster_name]]$genes$customColors, list(A = "yellow", B = "pink", C = "purple"))
expect_null(updated_chart3$x$series[[cluster_name]]$transcript$colorScheme)
expect_equal(updated_chart3$x$series[[cluster_name]]$transcript$customColors, list(A = "yellow", B = "pink", C = "purple"))
}
})
test_that("GC_legend updates legend options with all options correctly", {
# Load ophA_clusters data
data("ophA_clusters", package = "geneviewer")
# Generate a GC chart
chart <- GC_chart(ophA_clusters, cluster = "cluster", group = "class", height = "200px")
# Update legend with all options
updated_chart <- GC_legend(
GC_chart = chart,
group = "class",
show = TRUE,
backgroundColor = "#0000",
order = rev(unique(ophA_clusters$class)),
position = "bottom",
orientation = "horizontal",
x = 0,
y = 0,
adjustHeight = TRUE,
style = list(
backgroundColor = "red"
),
legendOptions = list(
cursor = "pointer",
colorScheme = NULL,
customColors = NULL
),
legendTextOptions = list(
cursor = "pointer",
textAnchor = "start",
dy = ".35em",
fontSize = "14px",
fontFamily = "sans-serif",
fill = "blue"
)
)
# Assertions for all options
expect_s3_class(updated_chart, "htmlwidget")
# Verify legend settings
expect_equal(updated_chart$x$legend$group, "class")
expect_true(updated_chart$x$legend$show)
expect_equal(updated_chart$x$legend$backgroundColor, "#0000")
expect_equal(updated_chart$x$legend$order, rev(unique(ophA_clusters$class)))
expect_equal(updated_chart$x$legend$position, "bottom")
expect_equal(updated_chart$x$legend$orientation, "horizontal")
expect_equal(updated_chart$x$legend$x, 0)
expect_equal(updated_chart$x$legend$y, 0)
expect_true(updated_chart$x$legend$adjustHeight)
expect_equal(updated_chart$x$legend$style$backgroundColor, "red")
expect_equal(updated_chart$x$legend$legendOptions$cursor, "pointer")
expect_null(updated_chart$x$legend$legendOptions$colorScheme)
expect_null(updated_chart$x$legend$legendOptions$customColors)
expect_equal(updated_chart$x$legend$legendTextOptions$cursor, "pointer")
expect_equal(updated_chart$x$legend$legendTextOptions$textAnchor, "start")
expect_equal(updated_chart$x$legend$legendTextOptions$dy, ".35em")
expect_equal(updated_chart$x$legend$legendTextOptions$fontSize, "14px")
expect_equal(updated_chart$x$legend$legendTextOptions$fontFamily, "sans-serif")
expect_equal(updated_chart$x$legend$legendTextOptions$fill, "blue")
})
# GC_annotation
test_that("GC_annotation adds annotations to GC chart correctly", {
data("ophA_clusters", package = "geneviewer")
# Generate a GC chart
chart <- GC_chart(ophA_clusters, cluster = "cluster", group = "class", height = "220px")
# Add multiple annotations
updated_chart <- chart %>%
GC_annotation(type = "textMarker", cluster = 1, position = 24, text = "Gene 1", arrowSize = 8) %>%
GC_annotation(type = "text", text = "feature 1", x = 91, y = 71) %>%
GC_annotation(type = "symbol", symbol = "triangle", x = 95, y = 64, size = 10, rotation = 180) %>%
GC_annotation(type = "terminator", x = 81) %>%
GC_annotation(type = "promoter", x = 49)
# Assertions
expect_s3_class(updated_chart, "htmlwidget")
# Verify textMarker annotation
text_marker <- updated_chart$x$series[[1]]$annotations[[1]]
expect_equal(text_marker$type, "textMarker")
expect_equal(text_marker$position, 24)
expect_equal(text_marker$text, "Gene 1")
expect_equal(text_marker$arrowSize, 8)
# Verify text annotation
text_annotation <- updated_chart$x$series[[1]]$annotations[[2]]
expect_equal(text_annotation$type, "text")
expect_equal(text_annotation$text, "feature 1")
expect_equal(text_annotation$x, 91)
expect_equal(text_annotation$y, 71)
# Verify symbol annotation
symbol_annotation <- updated_chart$x$series[[1]]$annotations[[3]]
expect_equal(symbol_annotation$type, "symbol")
expect_equal(symbol_annotation$symbol, "triangle")
expect_equal(symbol_annotation$x, 95)
expect_equal(symbol_annotation$y, 64)
expect_equal(symbol_annotation$size, 10)
expect_equal(symbol_annotation$rotation, 180)
# Verify terminator annotation
terminator_annotation <- updated_chart$x$series[[1]]$annotations[[4]]
expect_equal(terminator_annotation$type, "terminator")
expect_equal(terminator_annotation$x, 81)
# Verify promoter annotation
promoter_annotation <- updated_chart$x$series[[1]]$annotations[[5]]
expect_equal(promoter_annotation$type, "promoter")
expect_equal(promoter_annotation$x, 49)
})
test_that("GC_trackMouse enables or disables mouse tracking correctly", {
data("ophA_clusters", package = "geneviewer")
# Generate a GC chart
chart <- GC_chart(ophA_clusters, cluster = "cluster", group = "class", height = "200px")
# Enable mouse tracking on all clusters
updated_chart <- GC_trackMouse(GC_chart = chart, show = TRUE)
# Assertions
expect_s3_class(updated_chart, "htmlwidget")
clusters <- names(updated_chart$x$series)
for (cluster_name in clusters) {
expect_true(updated_chart$x$series[[cluster_name]]$trackMouse$show)
}
# Disable mouse tracking on all clusters
updated_chart <- GC_trackMouse(GC_chart = chart, show = FALSE)
# Assertions
for (cluster_name in clusters) {
expect_false(updated_chart$x$series[[cluster_name]]$trackMouse$show)
}
})
# Test for GC_cluster function
test_that("GC_cluster applies prevent_gene_overlap and other options correctly", {
# Load or create the human_hox_genes dataset
data("human_hox_genes", package = "geneviewer")
# Create a basic GC_chart object
chart <- GC_chart(human_hox_genes, cluster = "cluster", group = "name", height = "600px")
# Apply GC_cluster function with specified options
updated_chart <- GC_cluster(
GC_chart = chart,
separate_strands = NULL,
prevent_gene_overlap = TRUE,
cluster = NULL,
strand_spacing = 5,
overlap_spacing = 10,
style = list(backgroundColor = "lightgrey"),
tooltip = TRUE
)
# Assertions
expect_s3_class(updated_chart, "htmlwidget")
# Check that 'prevent_gene_overlap' has been applied
clusters <- updated_chart$x$series
for (i in seq_along(clusters)) {
cluster_options <- clusters[[i]]$cluster
expect_true(cluster_options$subset_data)
expect_equal(cluster_options$overlapSpacing, 10)
}
# Check that 'strand_spacing' is set correctly if applicable
for (i in seq_along(clusters)) {
cluster_options <- clusters[[i]]$cluster
expect_equal(cluster_options$strandSpacing, 5)
}
# Verify style settings
for (i in seq_along(clusters)) {
container_style <- clusters[[i]]$container$style
expect_equal(container_style$backgroundColor, "lightgrey")
}
# Verify tooltip option
for (i in seq_along(clusters)) {
container_tooltip <- clusters[[i]]$container$tooltip
expect_true(container_tooltip) # Ensure tooltips are enabled
}
})
test_that("GC_transcript modifies transcript characteristics correctly", {
# Load or create the transcript dataset
transcript_data <- data.frame(
transcript = c("transcript1", "transcript1", "transcript1",
"transcript2", "transcript2", "transcript2"),
type = c("5_utr", "exon", "3_utr", "5_utr", "exon", "3_utr"),
start = c(1, 101, 301, 1, 101, 301),
end = c(50, 200, 350, 50, 200, 350),
strand = c("forward", "forward", "forward", "forward", "forward", "forward")
)
# Create a basic GC_chart object
chart <- GC_chart(
transcript_data,
start = "start",
end = "end",
height = "300px"
)
# Apply GC_transcript with various options
updated_chart <- GC_transcript(
GC_chart = chart,
transcript = "transcript",
type = "type",
strand = "strand",
group = "transcript",
selection = "transcript1",
show = TRUE,
colorScheme = "schemeCategory10",
customColors = list("red", "blue", "green"),
styleExons = list(marker = "box", fill = "yellow", strokeWidth = 2),
styleIntrons = list(marker = "intron", fill = "grey", strokeWidth = 1),
styleUTRs = list(fill = "lightblue", strokeWidth = 0.5),
itemStyleExons = list(list(index = 1, fill = "orange")),
labelOptions = list(fontSize = "12px", color = "black", xOffset = 2)
)
# Assertions
expect_s3_class(updated_chart, "htmlwidget") # Verify object type
# Check transcript settings for 'transcript1'
transcript1 <- updated_chart$x$series$transcript1$transcript
expect_equal(transcript1$group, "transcript") # Verify grouping column
expect_true(transcript1$show) # Ensure show option is TRUE
expect_equal(transcript1$colorScheme, "schemeCategory10") # Color scheme
expect_equal(transcript1$customColors, list("red", "blue", "green")) # Custom colors
# Verify exon styles
expect_equal(transcript1$styleExons$marker, "box")
expect_equal(transcript1$styleExons$fill, "yellow")
expect_equal(transcript1$styleExons$strokeWidth, 2)
# Verify intron styles
expect_equal(transcript1$styleIntrons$marker, "intron")
expect_equal(transcript1$styleIntrons$fill, "grey")
expect_equal(transcript1$styleIntrons$strokeWidth, 1)
# Verify UTR styles
expect_equal(transcript1$styleUTRs$fill, "lightblue")
expect_equal(transcript1$styleUTRs$strokeWidth, 0.5)
# Verify item style for specific exon
expect_equal(transcript1$itemStyleExons[[1]]$index, 1)
expect_equal(transcript1$itemStyleExons[[1]]$fill, "orange")
# Verify label options
expect_equal(transcript1$labelOptions$fontSize, "12px")
expect_equal(transcript1$labelOptions$color, "black")
expect_equal(transcript1$labelOptions$xOffset, 2)
# Verify strand information
expect_equal(updated_chart$x$params$strand, "strand")
})
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# 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$direction, "row")
})
#GC_scale
test_that("GC_scale updates scale settings for specified clusters correctly", {
# Load ophA_clusters data
data("ophA_clusters", package = "geneviewer")
# Generate a GC chart
chart <- GC_chart(ophA_clusters, cluster = "cluster", group = "class", height = "400px")
# Update scale settings for specific clusters
updated_chart <- GC_scale(
GC_chart = chart,
cluster = c("ophA", "dbophA"),
start = c(2500, 18000),
end = c(22000, 44000),
padding = 5,
hidden = FALSE,
reverse = c(FALSE, TRUE),
axis_position = "top",
scale_breaks = TRUE,
scale_break_threshold = 30,
ticksCount = 8,
ticksFormat = ",.2f",
tickStyle = list(stroke = "blue", strokeWidth = 2),
textStyle = list(fill = "red", fontSize = "12px"),
lineStyle = list(stroke = "black", strokeWidth = 2)
)
# Assertions
expect_s3_class(updated_chart, "htmlwidget")
# Check if scale settings are applied to the specified clusters
expect_true("scale" %in% names(updated_chart$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$strokeWidth, 2)
})
# GC_scaleBar
test_that("GC_scaleBar updates scale bar settings for specified clusters correctly", {
# Load ophA_clusters data
data("ophA_clusters", package = "geneviewer")
# Generate a GC chart
chart <- GC_chart(ophA_clusters, cluster = "cluster", group = "class", height = "400px")
# Update scale bar settings for specific clusters
updated_chart <- GC_scaleBar(
GC_chart = chart,
show = TRUE,
cluster = c("ophA", "dbophA"),
scaleBarLineStyle = list(stroke = "black", strokeWidth = 1),
scaleBarTickStyle = list(stroke = "grey", strokeWidth = 2),
labelStyle = list(
labelPosition = "left",
fontSize = "12px",
fontFamily = "Arial",
fill = "blue"
),
title = c("1 kb", "2 kb"),
scaleBarUnit = c(1000, 2000)
)
# Assertions
expect_s3_class(updated_chart, "htmlwidget")
# Check if scale bar settings are applied to the specified clusters
expect_true("scaleBar" %in% names(updated_chart$x$series$ophA))
expect_true("scaleBar" %in% names(updated_chart$x$series$dbophA))
# Verify scale bar settings for `ophA` cluster
ophA_scaleBar <- updated_chart$x$series$ophA$scaleBar
expect_true(ophA_scaleBar$show)
expect_equal(ophA_scaleBar$scaleBarLineStyle$stroke, "black")
expect_equal(ophA_scaleBar$scaleBarLineStyle$strokeWidth, 1)
expect_equal(ophA_scaleBar$scaleBarTickStyle$stroke, "grey")
expect_equal(ophA_scaleBar$scaleBarTickStyle$strokeWidth, 2)
expect_equal(ophA_scaleBar$labelStyle$labelPosition, "left")
expect_equal(ophA_scaleBar$labelStyle$fontSize, "12px")
expect_equal(ophA_scaleBar$labelStyle$fontFamily, "Arial")
expect_equal(ophA_scaleBar$labelStyle$fill, "blue")
expect_equal(ophA_scaleBar$title, "1 kb")
expect_equal(ophA_scaleBar$scaleBarUnit, 1000)
# Verify scale bar settings for `dbophA` cluster
dbophA_scaleBar <- updated_chart$x$series$dbophA$scaleBar
expect_true(dbophA_scaleBar$show)
expect_equal(dbophA_scaleBar$scaleBarLineStyle$stroke, "black")
expect_equal(dbophA_scaleBar$scaleBarLineStyle$strokeWidth, 1)
expect_equal(dbophA_scaleBar$scaleBarTickStyle$stroke, "grey")
expect_equal(dbophA_scaleBar$scaleBarTickStyle$strokeWidth, 2)
expect_equal(dbophA_scaleBar$labelStyle$labelPosition, "left")
expect_equal(dbophA_scaleBar$labelStyle$fontSize, "12px")
expect_equal(dbophA_scaleBar$labelStyle$fontFamily, "Arial")
expect_equal(dbophA_scaleBar$labelStyle$fill, "blue")
expect_equal(dbophA_scaleBar$title, "2 kb")
expect_equal(dbophA_scaleBar$scaleBarUnit, 2000)
})
# GC_clusterLabel
test_that("GC_clusterLabel updates cluster labels for specified clusters correctly", {
# Load ophA_clusters data
data("ophA_clusters", package = "geneviewer")
# Generate a GC chart
chart <- GC_chart(ophA_clusters, cluster = "cluster", group = "class", height = "400px")
# Update cluster labels for specific clusters
updated_chart <- GC_clusterLabel(
GC_chart = chart,
title = c("Cluster A", "Cluster B"),
cluster = c("ophA", "dbophA"),
position = c("left", "right"),
width = "150px",
wrapLabel = TRUE,
wrapOptions = list(
dyAdjust = 0,
lineHeightEms = 1.1,
splitOnHyphen = TRUE
),
fontSize = "14px",
fontStyle = "italic",
fontWeight = "bold",
fontFamily = "Arial",
cursor = "pointer"
)
# Assertions
expect_s3_class(updated_chart, "htmlwidget")
# Check if cluster label settings are applied to the specified clusters
expect_true("clusterLabel" %in% names(updated_chart$x$series$ophA))
expect_true("clusterLabel" %in% names(updated_chart$x$series$dbophA))
# Verify cluster label settings for `ophA` cluster
ophA_label <- updated_chart$x$series$ophA$clusterLabel
expect_equal(ophA_label$title, "Cluster A")
expect_true(ophA_label$show)
expect_equal(ophA_label$position, "left")
expect_true(ophA_label$wrapLabel)
expect_equal(ophA_label$wrapOptions$dyAdjust, 0)
expect_equal(ophA_label$wrapOptions$lineHeightEms, 1.1)
expect_true(ophA_label$wrapOptions$splitOnHyphen)
expect_equal(ophA_label$fontSize, "14px")
expect_equal(ophA_label$fontStyle, "italic")
expect_equal(ophA_label$fontWeight, "bold")
expect_equal(ophA_label$fontFamily, "Arial")
expect_equal(ophA_label$cursor, "pointer")
# Verify cluster label settings for `dbophA` cluster
dbophA_label <- updated_chart$x$series$dbophA$clusterLabel
expect_equal(dbophA_label$title, "Cluster B")
expect_true(dbophA_label$show)
expect_equal(dbophA_label$position, "right")
expect_true(dbophA_label$wrapLabel)
expect_equal(dbophA_label$wrapOptions$dyAdjust, 0)
expect_equal(dbophA_label$wrapOptions$lineHeightEms, 1.1)
expect_true(dbophA_label$wrapOptions$splitOnHyphen)
expect_equal(dbophA_label$fontSize, "14px")
expect_equal(dbophA_label$fontStyle, "italic")
expect_equal(dbophA_label$fontWeight, "bold")
expect_equal(dbophA_label$fontFamily, "Arial")
expect_equal(dbophA_label$cursor, "pointer")
# Verify grid settings for label width
expect_equal(updated_chart$x$series$ophA$container$margin$left, "150px")
expect_equal(updated_chart$x$series$dbophA$container$margin$right, "150px")
})
# GC_clusterFooter
test_that("GC_clusterFooter updates footers with all options correctly", {
# Load ophA_clusters data
data("ophA_clusters", package = "geneviewer")
# Generate a GC chart
chart <- GC_chart(ophA_clusters, cluster = "cluster", group = "class")
# Update footers with all options
updated_chart <- GC_clusterFooter(
GC_chart = chart,
title = c("Footer for ophA", "Footer for dbophA"),
subtitle = c("Subtitle for ophA", "Subtitle for dbophA"),
spacing = c(15, 20),
show = TRUE,
cluster = c("ophA", "dbophA"),
x = c(6, 8),
y = c(-20, -25),
align = c("center", "right"),
titleFont = list(
fontSize = "12px",
fontWeight = "bold",
fontFamily = "sans-serif",
fill = "black",
cursor = "default"
),
subtitleFont = list(
fill = "grey",
fontSize = "10px",
fontStyle = "normal",
fontFamily = "sans-serif",
cursor = "default"
)
)
# Assertions
expect_s3_class(updated_chart, "htmlwidget")
# Verify footer settings for cluster ophA
ophA_footer <- updated_chart$x$series$ophA$footer
expect_equal(ophA_footer$title, "Footer for ophA")
expect_equal(ophA_footer$subtitle, "Subtitle for ophA")
expect_true(ophA_footer$show)
expect_equal(ophA_footer$titleFont$fontSize, "12px")
expect_equal(ophA_footer$titleFont$fontWeight, "bold")
expect_equal(ophA_footer$titleFont$fontFamily, "sans-serif")
expect_equal(ophA_footer$titleFont$fill, "black")
expect_equal(ophA_footer$titleFont$cursor, "default")
expect_equal(ophA_footer$subtitleFont$fontSize, "10px")
expect_equal(ophA_footer$subtitleFont$fontStyle, "normal")
expect_equal(ophA_footer$subtitleFont$fontFamily, "sans-serif")
expect_equal(ophA_footer$subtitleFont$fill, "grey")
expect_equal(ophA_footer$subtitleFont$cursor, "default")
expect_equal(ophA_footer$x, 6)
expect_equal(ophA_footer$y, -20)
# Verify footer settings for cluster dbophA
dbophA_footer <- updated_chart$x$series$dbophA$footer
expect_equal(dbophA_footer$title, "Footer for dbophA")
expect_equal(dbophA_footer$subtitle, "Subtitle for dbophA")
expect_true(dbophA_footer$show)
expect_equal(dbophA_footer$titleFont$fontSize, "12px")
expect_equal(dbophA_footer$titleFont$fontWeight, "bold")
expect_equal(dbophA_footer$titleFont$fontFamily, "sans-serif")
expect_equal(dbophA_footer$titleFont$fill, "black")
expect_equal(dbophA_footer$titleFont$cursor, "default")
expect_equal(dbophA_footer$subtitleFont$fontSize, "10px")
expect_equal(dbophA_footer$subtitleFont$fontStyle, "normal")
expect_equal(dbophA_footer$subtitleFont$fontFamily, "sans-serif")
expect_equal(dbophA_footer$subtitleFont$fill, "grey")
expect_equal(dbophA_footer$subtitleFont$cursor, "default")
expect_equal(dbophA_footer$x, 8)
expect_equal(dbophA_footer$y, -25)
})
# GC_labels
test_that("GC_labels updates labels with all options correctly", {
# Load ophA_clusters data
data("ophA_clusters", package = "geneviewer")
# Generate a GC chart
chart <- GC_chart(ophA_clusters, cluster = "cluster", group = "class")
# Update labels with all options
updated_chart <- GC_labels(
GC_chart = chart,
label = "name",
show = TRUE,
cluster = c("ophA", "dbophA"),
itemStyle = list(
list(index = 0, fill = "red", fontSize = "14px", fontWeight = "bold"),
list(index = 1, fill = "blue", fontSize = "12px", fontWeight = "normal")
),
x = 10,
y = -5,
adjustLabels = TRUE,
fontSize = "12px",
fontStyle = "italic",
fill = "black",
fontFamily = "sans-serif",
textAnchor = "middle",
cursor = "default"
)
# Assertions
expect_s3_class(updated_chart, "htmlwidget")
# Verify label settings for cluster ophA
ophA_label <- updated_chart$x$series$ophA$labels
expect_equal(ophA_label$label, "name")
expect_true(ophA_label$show)
expect_equal(ophA_label$itemStyle[[1]]$fill, "red")
expect_equal(ophA_label$itemStyle[[1]]$fontSize, "14px")
expect_equal(ophA_label$itemStyle[[1]]$fontWeight, "bold")
expect_equal(ophA_label$x, 10)
expect_equal(ophA_label$y, -5)
# Verify label settings for cluster dbophA
dbophA_label <- updated_chart$x$series$dbophA$labels
expect_equal(dbophA_label$label, "name")
expect_true(dbophA_label$show)
expect_equal(dbophA_label$itemStyle[[2]]$fill, "blue")
expect_equal(dbophA_label$itemStyle[[2]]$fontSize, "12px")
expect_equal(dbophA_label$itemStyle[[2]]$fontWeight, "normal")
expect_equal(dbophA_label$x, 10)
expect_equal(dbophA_label$y, -5)
})
# GC_coordinates
test_that("GC_coordinates updates coordinates with all options correctly", {
# Load ophA_clusters data
data("ophA_clusters", package = "geneviewer")
# Generate a GC chart
chart <- GC_chart(ophA_clusters, cluster = "cluster", group = "class")
# Update coordinates with all options
updated_chart <- GC_coordinates(
GC_chart = chart,
show = TRUE,
tickValuesTop = c(2522, 5286, 9536),
tickValuesBottom = c(4276, 4718, 10904),
ticksFormat = ",.0f",
tickStyle = list(
fontSize = "10px",
fontWeight = "normal",
fontFamily = "sans-serif",
fill = "grey",
cursor = "default"
),
textStyle = list(
fontSize = "12px",
fontStyle = "italic",
fontFamily = "sans-serif",
fill = "black",
textAnchor = "middle",
cursor = "default"
),
cluster = c("ophA"),
x = c(10, 15),
y = c(-5, -10)
)
# Assertions
expect_s3_class(updated_chart, "htmlwidget")
# Verify coordinate settings for cluster ophA
ophA_coordinates <- updated_chart$x$series$ophA$coordinates
expect_true(ophA_coordinates$show)
expect_equal(ophA_coordinates$tickValuesTop, c(2522, 5286, 9536))
expect_equal(ophA_coordinates$tickValuesBottom, c(4276, 4718, 10904))
expect_equal(ophA_coordinates$ticksFormat, ",.0f")
expect_equal(ophA_coordinates$tickStyle$fontSize, "10px")
expect_equal(ophA_coordinates$tickStyle$fill, "grey")
expect_equal(ophA_coordinates$textStyle$fontSize, "12px")
expect_equal(ophA_coordinates$textStyle$fill, "black")
expect_equal(ophA_coordinates$x, 10)
expect_equal(ophA_coordinates$y, -5)
})
# GC_genes test
test_that("GC_genes updates gene characteristics with all options correctly", {
# Load ophA_clusters data
data("ophA_clusters", package = "geneviewer")
# Generate a GC chart
chart <- GC_chart(ophA_clusters, cluster = "cluster", group = "class")
# Update genes with all options
updated_chart <- GC_genes(
GC_chart = chart,
group = "class",
show = TRUE,
marker = "arrow",
marker_size = "medium",
colorScheme = "schemeCategory10",
customColors = c("red", "blue", "green"),
cluster = c("ophA", "dbophA"),
itemStyle = list(
list(index = 0, fill = "red", stroke = "black"),
list(index = 1, fill = "blue", stroke = "grey")
),
x = c(10, 15),
y = c(-5, -10),
stroke = "black",
strokeWidth = 1,
arrowheadWidth = NULL,
arrowheadHeight = NULL,
arrowHeight = NULL,
markerHeight = NULL
)
# Assertions
expect_s3_class(updated_chart, "htmlwidget")
# Verify gene settings for cluster ophA
ophA_genes <- updated_chart$x$series$ophA$genes
expect_equal(ophA_genes$group, "class")
expect_true(ophA_genes$show)
expect_equal(ophA_genes$marker, "arrow")
expect_equal(ophA_genes$markerSize, "medium")
expect_equal(ophA_genes$colorScheme, "schemeCategory10")
expect_equal(ophA_genes$customColors, c("red", "blue", "green"))
expect_equal(ophA_genes$itemStyle[[1]]$fill, "red")
expect_equal(ophA_genes$itemStyle[[1]]$stroke, "black")
expect_equal(ophA_genes$itemStyle[[2]]$fill, "blue")
expect_equal(ophA_genes$itemStyle[[2]]$stroke, "grey")
expect_equal(ophA_genes$x, c(10, 15))
expect_equal(ophA_genes$y, c(-5, -10))
expect_equal(ophA_genes$stroke, "black")
expect_equal(ophA_genes$strokeWidth, 1)
# Verify gene settings for cluster dbophA
dbophA_genes <- updated_chart$x$series$dbophA$genes
expect_equal(dbophA_genes$group, "class")
expect_true(dbophA_genes$show)
expect_equal(dbophA_genes$marker, "arrow")
expect_equal(dbophA_genes$markerSize, "medium")
expect_equal(dbophA_genes$colorScheme, "schemeCategory10")
expect_equal(dbophA_genes$customColors, c("red", "blue", "green"))
expect_equal(dbophA_genes$itemStyle[[1]]$fill, "red")
expect_equal(dbophA_genes$itemStyle[[1]]$stroke, "black")
expect_equal(dbophA_genes$itemStyle[[2]]$fill, "blue")
expect_equal(dbophA_genes$itemStyle[[2]]$stroke, "grey")
expect_equal(dbophA_genes$x, c(10, 15))
expect_equal(dbophA_genes$y, c(-5, -10))
expect_equal(dbophA_genes$stroke, "black")
expect_equal(dbophA_genes$strokeWidth, 1)
})
#GC_color
test_that("GC_color updates color scheme with all options correctly", {
# Load ophA_clusters data
data("ophA_clusters", package = "geneviewer")
# Generate a GC chart
chart <- GC_chart(ophA_clusters, cluster = "cluster", group = "class", height = "100px")
# Update color scheme with predefined scheme
updated_chart1 <- GC_color(
GC_chart = chart,
colorScheme = "schemeCategory10"
)
# Assertions for predefined color scheme
expect_s3_class(updated_chart1, "htmlwidget")
expect_equal(updated_chart1$x$legend$legendOptions$colorScheme, "schemeCategory10")
expect_null(updated_chart1$x$legend$legendOptions$customColors)
# Validate series colorScheme
clusters <- names(updated_chart1$x$series)
for (cluster_name in clusters) {
expect_equal(updated_chart1$x$series[[cluster_name]]$genes$colorScheme, "schemeCategory10")
expect_null(updated_chart1$x$series[[cluster_name]]$genes$customColors)
expect_equal(updated_chart1$x$series[[cluster_name]]$transcript$colorScheme, "schemeCategory10")
expect_null(updated_chart1$x$series[[cluster_name]]$transcript$customColors)
}
# Update color scheme with custom colors
updated_chart2 <- GC_color(
GC_chart = chart,
customColors = c("red", "orange", "green")
)
# Assertions for custom colors
expect_s3_class(updated_chart2, "htmlwidget")
expect_null(updated_chart2$x$legend$legendOptions$colorScheme)
expect_equal(updated_chart2$x$legend$legendOptions$customColors, c("red", "orange", "green"))
# Validate series customColors
for (cluster_name in clusters) {
expect_null(updated_chart2$x$series[[cluster_name]]$genes$colorScheme)
expect_equal(updated_chart2$x$series[[cluster_name]]$genes$customColors, c("red", "orange", "green"))
expect_null(updated_chart2$x$series[[cluster_name]]$transcript$colorScheme)
expect_equal(updated_chart2$x$series[[cluster_name]]$transcript$customColors, c("red", "orange", "green"))
}
# Update color scheme with named custom colors
updated_chart3 <- GC_color(
GC_chart = chart,
customColors = list(A = "yellow", B = "pink", C = "purple")
)
# Assertions for named custom colors
expect_s3_class(updated_chart3, "htmlwidget")
expect_null(updated_chart3$x$legend$legendOptions$colorScheme)
expect_equal(updated_chart3$x$legend$legendOptions$customColors, list(A = "yellow", B = "pink", C = "purple"))
# Validate series named customColors
for (cluster_name in clusters) {
expect_null(updated_chart3$x$series[[cluster_name]]$genes$colorScheme)
expect_equal(updated_chart3$x$series[[cluster_name]]$genes$customColors, list(A = "yellow", B = "pink", C = "purple"))
expect_null(updated_chart3$x$series[[cluster_name]]$transcript$colorScheme)
expect_equal(updated_chart3$x$series[[cluster_name]]$transcript$customColors, list(A = "yellow", B = "pink", C = "purple"))
}
})
test_that("GC_legend updates legend options with all options correctly", {
# Load ophA_clusters data
data("ophA_clusters", package = "geneviewer")
# Generate a GC chart
chart <- GC_chart(ophA_clusters, cluster = "cluster", group = "class", height = "200px")
# Update legend with all options
updated_chart <- GC_legend(
GC_chart = chart,
group = "class",
show = TRUE,
backgroundColor = "#0000",
order = rev(unique(ophA_clusters$class)),
position = "bottom",
orientation = "horizontal",
x = 0,
y = 0,
adjustHeight = TRUE,
style = list(
backgroundColor = "red"
),
legendOptions = list(
cursor = "pointer",
colorScheme = NULL,
customColors = NULL
),
legendTextOptions = list(
cursor = "pointer",
textAnchor = "start",
dy = ".35em",
fontSize = "14px",
fontFamily = "sans-serif",
fill = "blue"
)
)
# Assertions for all options
expect_s3_class(updated_chart, "htmlwidget")
# Verify legend settings
expect_equal(updated_chart$x$legend$group, "class")
expect_true(updated_chart$x$legend$show)
expect_equal(updated_chart$x$legend$backgroundColor, "#0000")
expect_equal(updated_chart$x$legend$order, rev(unique(ophA_clusters$class)))
expect_equal(updated_chart$x$legend$position, "bottom")
expect_equal(updated_chart$x$legend$orientation, "horizontal")
expect_equal(updated_chart$x$legend$x, 0)
expect_equal(updated_chart$x$legend$y, 0)
expect_true(updated_chart$x$legend$adjustHeight)
expect_equal(updated_chart$x$legend$style$backgroundColor, "red")
expect_equal(updated_chart$x$legend$legendOptions$cursor, "pointer")
expect_null(updated_chart$x$legend$legendOptions$colorScheme)
expect_null(updated_chart$x$legend$legendOptions$customColors)
expect_equal(updated_chart$x$legend$legendTextOptions$cursor, "pointer")
expect_equal(updated_chart$x$legend$legendTextOptions$textAnchor, "start")
expect_equal(updated_chart$x$legend$legendTextOptions$dy, ".35em")
expect_equal(updated_chart$x$legend$legendTextOptions$fontSize, "14px")
expect_equal(updated_chart$x$legend$legendTextOptions$fontFamily, "sans-serif")
expect_equal(updated_chart$x$legend$legendTextOptions$fill, "blue")
})
# GC_annotation
test_that("GC_annotation adds annotations to GC chart correctly", {
data("ophA_clusters", package = "geneviewer")
# Generate a GC chart
chart <- GC_chart(ophA_clusters, cluster = "cluster", group = "class", height = "220px")
# Add multiple annotations
updated_chart <- chart %>%
GC_annotation(type = "textMarker", cluster = 1, position = 24, text = "Gene 1", arrowSize = 8) %>%
GC_annotation(type = "text", text = "feature 1", x = 91, y = 71) %>%
GC_annotation(type = "symbol", symbol = "triangle", x = 95, y = 64, size = 10, rotation = 180) %>%
GC_annotation(type = "terminator", x = 81) %>%
GC_annotation(type = "promoter", x = 49)
# Assertions
expect_s3_class(updated_chart, "htmlwidget")
# Verify textMarker annotation
text_marker <- updated_chart$x$series[[1]]$annotations[[1]]
expect_equal(text_marker$type, "textMarker")
expect_equal(text_marker$position, 24)
expect_equal(text_marker$text, "Gene 1")
expect_equal(text_marker$arrowSize, 8)
# Verify text annotation
text_annotation <- updated_chart$x$series[[1]]$annotations[[2]]
expect_equal(text_annotation$type, "text")
expect_equal(text_annotation$text, "feature 1")
expect_equal(text_annotation$x, 91)
expect_equal(text_annotation$y, 71)
# Verify symbol annotation
symbol_annotation <- updated_chart$x$series[[1]]$annotations[[3]]
expect_equal(symbol_annotation$type, "symbol")
expect_equal(symbol_annotation$symbol, "triangle")
expect_equal(symbol_annotation$x, 95)
expect_equal(symbol_annotation$y, 64)
expect_equal(symbol_annotation$size, 10)
expect_equal(symbol_annotation$rotation, 180)
# Verify terminator annotation
terminator_annotation <- updated_chart$x$series[[1]]$annotations[[4]]
expect_equal(terminator_annotation$type, "terminator")
expect_equal(terminator_annotation$x, 81)
# Verify promoter annotation
promoter_annotation <- updated_chart$x$series[[1]]$annotations[[5]]
expect_equal(promoter_annotation$type, "promoter")
expect_equal(promoter_annotation$x, 49)
})
test_that("GC_trackMouse enables or disables mouse tracking correctly", {
data("ophA_clusters", package = "geneviewer")
# Generate a GC chart
chart <- GC_chart(ophA_clusters, cluster = "cluster", group = "class", height = "200px")
# Enable mouse tracking on all clusters
updated_chart <- GC_trackMouse(GC_chart = chart, show = TRUE)
# Assertions
expect_s3_class(updated_chart, "htmlwidget")
clusters <- names(updated_chart$x$series)
for (cluster_name in clusters) {
expect_true(updated_chart$x$series[[cluster_name]]$trackMouse$show)
}
# Disable mouse tracking on all clusters
updated_chart <- GC_trackMouse(GC_chart = chart, show = FALSE)
# Assertions
for (cluster_name in clusters) {
expect_false(updated_chart$x$series[[cluster_name]]$trackMouse$show)
}
})
# Test for GC_cluster function
test_that("GC_cluster applies prevent_gene_overlap and other options correctly", {
# Load or create the human_hox_genes dataset
data("human_hox_genes", package = "geneviewer")
# Create a basic GC_chart object
chart <- GC_chart(human_hox_genes, cluster = "cluster", group = "name", height = "600px")
# Apply GC_cluster function with specified options
updated_chart <- GC_cluster(
GC_chart = chart,
separate_strands = NULL,
prevent_gene_overlap = TRUE,
cluster = NULL,
strand_spacing = 5,
overlap_spacing = 10,
style = list(backgroundColor = "lightgrey"),
tooltip = TRUE
)
# Assertions
expect_s3_class(updated_chart, "htmlwidget")
# Check that 'prevent_gene_overlap' has been applied
clusters <- updated_chart$x$series
for (i in seq_along(clusters)) {
cluster_options <- clusters[[i]]$cluster
expect_true(cluster_options$subset_data)
expect_equal(cluster_options$overlapSpacing, 10)
}
# Check that 'strand_spacing' is set correctly if applicable
for (i in seq_along(clusters)) {
cluster_options <- clusters[[i]]$cluster
expect_equal(cluster_options$strandSpacing, 5)
}
# Verify style settings
for (i in seq_along(clusters)) {
container_style <- clusters[[i]]$container$style
expect_equal(container_style$backgroundColor, "lightgrey")
}
# Verify tooltip option
for (i in seq_along(clusters)) {
container_tooltip <- clusters[[i]]$container$tooltip
expect_true(container_tooltip) # Ensure tooltips are enabled
}
})
test_that("GC_transcript modifies transcript characteristics correctly", {
# Load or create the transcript dataset
transcript_data <- data.frame(
transcript = c("transcript1", "transcript1", "transcript1",
"transcript2", "transcript2", "transcript2"),
type = c("5_utr", "exon", "3_utr", "5_utr", "exon", "3_utr"),
start = c(1, 101, 301, 1, 101, 301),
end = c(50, 200, 350, 50, 200, 350),
strand = c("forward", "forward", "forward", "forward", "forward", "forward")
)
# Create a basic GC_chart object
chart <- GC_chart(
transcript_data,
start = "start",
end = "end",
height = "300px"
)
# Apply GC_transcript with various options
updated_chart <- GC_transcript(
GC_chart = chart,
transcript = "transcript",
type = "type",
strand = "strand",
group = "transcript",
selection = "transcript1",
show = TRUE,
colorScheme = "schemeCategory10",
customColors = list("red", "blue", "green"),
styleExons = list(marker = "box", fill = "yellow", strokeWidth = 2),
styleIntrons = list(marker = "intron", fill = "grey", strokeWidth = 1),
styleUTRs = list(fill = "lightblue", strokeWidth = 0.5),
itemStyleExons = list(list(index = 1, fill = "orange")),
labelOptions = list(fontSize = "12px", color = "black", xOffset = 2)
)
# Assertions
expect_s3_class(updated_chart, "htmlwidget") # Verify object type
# Check transcript settings for 'transcript1'
transcript1 <- updated_chart$x$series$transcript1$transcript
expect_equal(transcript1$group, "transcript") # Verify grouping column
expect_true(transcript1$show) # Ensure show option is TRUE
expect_equal(transcript1$colorScheme, "schemeCategory10") # Color scheme
expect_equal(transcript1$customColors, list("red", "blue", "green")) # Custom colors
# Verify exon styles
expect_equal(transcript1$styleExons$marker, "box")
expect_equal(transcript1$styleExons$fill, "yellow")
expect_equal(transcript1$styleExons$strokeWidth, 2)
# Verify intron styles
expect_equal(transcript1$styleIntrons$marker, "intron")
expect_equal(transcript1$styleIntrons$fill, "grey")
expect_equal(transcript1$styleIntrons$strokeWidth, 1)
# Verify UTR styles
expect_equal(transcript1$styleUTRs$fill, "lightblue")
expect_equal(transcript1$styleUTRs$strokeWidth, 0.5)
# Verify item style for specific exon
expect_equal(transcript1$itemStyleExons[[1]]$index, 1)
expect_equal(transcript1$itemStyleExons[[1]]$fill, "orange")
# Verify label options
expect_equal(transcript1$labelOptions$fontSize, "12px")
expect_equal(transcript1$labelOptions$color, "black")
expect_equal(transcript1$labelOptions$xOffset, 2)
# Verify strand information
expect_equal(updated_chart$x$params$strand, "strand")
})
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