unittest update for ggplot2

phenomecentre · Feb 26, 2024 · f4c86d9 · f4c86d9
1 parent 6611151
commit f4c86d9
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: peakPantheR
 Title: Peak Picking and Annotation of High Resolution Experiments
-Version: 1.17.1
-Date: 2023-11-04
+Version: 1.17.2
+Date: 2024-02-26
 Authors@R: c(person("Arnaud", "Wolfer", email = "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-5856-3218")),
 	person("Goncalo", "Correia", email = "[email protected]", role = "aut", comment = c(ORCID = "0000-0001-8271-9294")),
 	person("Jake", "Pearce", email = "[email protected]", role = "ctb"),
@@ -14,7 +14,7 @@ Depends:
 Imports: 
 	foreach (>= 1.4.4),
 	doParallel (>= 1.0.11),
-	ggplot2 (>= 3.3.0),
+	ggplot2 (>= 3.5.0),
 	gridExtra (>= 2.3),
 	MSnbase (>= 2.4.0),
 	mzR (>= 2.12.0),
@@ -37,7 +37,7 @@ BugReports: https://github.com/phenomecentre/peakPantheR/issues/new
 URL: https://github.com/phenomecentre/peakPantheR
 Encoding: UTF-8
 LazyData: false
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Suggests: testthat,
     devtools,
 	faahKO,

diff --git a/inst/NEWS b/inst/NEWS
@@ -1,3 +1,5 @@
+Changes in version 1.17.2 (2024-02-26)
+- update unittest for `ggplot2` 3.5.0
 Changes in version 1.17.1 (2023-11-04)
 - `peakPantheR_quickEIC()` to plot EIC from raw files
 - SVG output option for AnnotationDiagnostic summary plot

diff --git a/man/peakPantheR.Rd b/man/peakPantheR.Rd
diff --git a/tests/testthat/test_peakPantheRAnnotation_retentionTimeCorrection-method.R b/tests/testthat/test_peakPantheRAnnotation_retentionTimeCorrection-method.R
@@ -174,7 +174,7 @@ test_that('rt correction plot (uROI)', {
   expect_equal(length(resultCorrected$result), 2)
   # plot values
   expect_equal(resultCorrected$result$plot[[1]], expected_plotFrame, tolerance=1e-6)
-  expect_equal(length(resultCorrected$result$plot), 9)
+  expect_equal(length(resultCorrected$result$plot), length(ggplot2::ggplot()))
   expect_equal(resultCorrected$result$plot$labels$x, 'Retention time')
   expect_equal(resultCorrected$result$plot$labels$y, 'Retention time deviation')
   expect_is(resultCorrected$result$plot$layers[[1]]$geom, 'GeomPoint')

diff --git a/tests/testthat/test_peakPantheR_plotEICFit.R b/tests/testthat/test_peakPantheR_plotEICFit.R
@@ -38,7 +38,7 @@ test_that('plot feature in 1 sample', {
   expect_true(ggplot2::is.ggplot(result_plot1SplNoCol))
   expect_equal(result_plot1SplNoCol$labels$x, "Retention Time (sec)")
   expect_equal(result_plot1SplNoCol$labels$y, "Intensity")
-  expect_equal(length(result_plot1SplNoCol), 9)
+  expect_equal(length(result_plot1SplNoCol), length(ggplot2::ggplot()))
 })
 
 test_that('plot feature in 1 sample, no curveFit with warning', {
@@ -59,7 +59,7 @@ test_that('plot feature in 1 sample, no curveFit with warning', {
   expect_true(ggplot2::is.ggplot(result_plot1SplNoFitNoCol$result))
   expect_equal(result_plot1SplNoFitNoCol$result$labels$x, "Retention Time (sec)")
   expect_equal(result_plot1SplNoFitNoCol$result$labels$y, "Intensity")
-  expect_equal(length(result_plot1SplNoFitNoCol$result), 9)
+  expect_equal(length(result_plot1SplNoFitNoCol$result), length(ggplot2::ggplot()))
 })
 
 test_that('plot feature in 2 samples, change colours and sampling', {
@@ -73,7 +73,7 @@ test_that('plot feature in 2 samples, change colours and sampling', {
   expect_true(ggplot2::is.ggplot(result_plot2SplWithCol))
   expect_equal(result_plot2SplWithCol$labels$x, "Retention Time (sec)")
   expect_equal(result_plot2SplWithCol$labels$y, "Intensity")
-  expect_equal(length(result_plot2SplWithCol), 9)
+  expect_equal(length(result_plot2SplWithCol), length(ggplot2::ggplot()))
 })
 
 test_that('plot feature in 2 samples, rtMin and/or rtMax have a NA (cannot plot fit)', {
@@ -87,7 +87,7 @@ test_that('plot feature in 2 samples, rtMin and/or rtMax have a NA (cannot plot
   expect_true(ggplot2::is.ggplot(result_plot2SplRTNA))
   expect_equal(result_plot2SplRTNA$labels$x, "Retention Time (sec)")
   expect_equal(result_plot2SplRTNA$labels$y, "Intensity")
-  expect_equal(length(result_plot2SplRTNA), 9)
+  expect_equal(length(result_plot2SplRTNA), length(ggplot2::ggplot()))
 })
 
 test_that('no rtMin and/or rtMax, cannot plot fit warning', {
@@ -107,7 +107,7 @@ test_that('no rtMin and/or rtMax, cannot plot fit warning', {
   expect_true(ggplot2::is.ggplot(result_plotFitWarning$result))
   expect_equal(result_plotFitWarning$result$labels$x, "Retention Time (sec)")
   expect_equal(result_plotFitWarning$result$labels$y, "Intensity")
-  expect_equal(length(result_plotFitWarning$result), 9)
+  expect_equal(length(result_plotFitWarning$result), length(ggplot2::ggplot()))
 })
 
 test_that('sampleColour length warning', {
@@ -128,7 +128,7 @@ test_that('sampleColour length warning', {
   expect_true(ggplot2::is.ggplot(result_plotColourWarning$result))
   expect_equal(result_plotColourWarning$result$labels$x, "Retention Time (sec)")
   expect_equal(result_plotColourWarning$result$labels$y, "Intensity")
-  expect_equal(length(result_plotColourWarning$result), 9)
+  expect_equal(length(result_plotColourWarning$result), length(ggplot2::ggplot()))
 })
 
 test_that('raise errors', {

diff --git a/tests/testthat/test_peakPantheR_plotPeakwidth.R b/tests/testthat/test_peakPantheR_plotPeakwidth.R
@@ -22,7 +22,7 @@ test_that('plot 3 samples, no color', {
   expect_true(ggplot2::is.ggplot(result_3splNoColNoRot))
   expect_equal(result_3splNoColNoRot$labels$x, "x")
   expect_equal(result_3splNoColNoRot$labels$y, "Test variable")
-  expect_equal(length(result_3splNoColNoRot), 9)
+  expect_equal(length(result_3splNoColNoRot), length(ggplot2::ggplot()))
 })
 
 test_that('plot 3 samples, no color, acquisition time', {
@@ -35,7 +35,7 @@ test_that('plot 3 samples, no color, acquisition time', {
   expect_true(ggplot2::is.ggplot(result_3splNoColNoRotRunOrder))
   expect_equal(result_3splNoColNoRotRunOrder$labels$x, "Acquisition Time")
   expect_equal(result_3splNoColNoRotRunOrder$labels$y, "Test variable 2")
-  expect_equal(length(result_3splNoColNoRotRunOrder), 9)
+  expect_equal(length(result_3splNoColNoRotRunOrder), length(ggplot2::ggplot()))
 })
 
 test_that('plot 3 samples, no color, rotate axis', {
@@ -48,7 +48,7 @@ test_that('plot 3 samples, no color, rotate axis', {
   expect_true(ggplot2::is.ggplot(result_3splNoColRot))
   expect_equal(result_3splNoColRot$labels$x, "Test variable 3")
   expect_equal(result_3splNoColRot$labels$y, "x")
-  expect_equal(length(result_3splNoColRot), 9)
+  expect_equal(length(result_3splNoColRot), length(ggplot2::ggplot()))
 })
 
 test_that('plot 3 samples, no color, acquisition time, rotate axis', {
@@ -61,7 +61,7 @@ test_that('plot 3 samples, no color, acquisition time, rotate axis', {
   expect_true(ggplot2::is.ggplot(result_3splNoColRotRunOrder))
   expect_equal(result_3splNoColRotRunOrder$labels$x, "Test variable 4")
   expect_equal(result_3splNoColRotRunOrder$labels$y, "Acquisition Time")
-  expect_equal(length(result_3splNoColRotRunOrder), 9)
+  expect_equal(length(result_3splNoColRotRunOrder), length(ggplot2::ggplot()))
 })
 
 test_that('plot 4 samples with color', {
@@ -74,7 +74,7 @@ test_that('plot 4 samples with color', {
   expect_true(ggplot2::is.ggplot(result_4splWithColNoRot))
   expect_equal(result_4splWithColNoRot$labels$x, "x")
   expect_equal(result_4splWithColNoRot$labels$y, "Test variable 5")
-  expect_equal(length(result_4splWithColNoRot), 9)
+  expect_equal(length(result_4splWithColNoRot), length(ggplot2::ggplot()))
 })
 
 test_that('plot 4 samples with color, acquisition time', {
@@ -87,7 +87,7 @@ test_that('plot 4 samples with color, acquisition time', {
   expect_true(ggplot2::is.ggplot(result_4splWithColNoRotRunOrder))
   expect_equal(result_4splWithColNoRotRunOrder$labels$x, "Acquisition Time")
   expect_equal(result_4splWithColNoRotRunOrder$labels$y, "Test variable 6")
-  expect_equal(length(result_4splWithColNoRotRunOrder), 9)
+  expect_equal(length(result_4splWithColNoRotRunOrder), length(ggplot2::ggplot()))
 })
 
 test_that('plot 4 samples with color, rotate axis', {
@@ -100,7 +100,7 @@ test_that('plot 4 samples with color, rotate axis', {
   expect_true(ggplot2::is.ggplot(result_4splWithColRot))
   expect_equal(result_4splWithColRot$labels$x, "Test variable 7")
   expect_equal(result_4splWithColRot$labels$y, "x")
-  expect_equal(length(result_4splWithColRot), 9)
+  expect_equal(length(result_4splWithColRot), length(ggplot2::ggplot()))
 })
 
 test_that('plot 4 samples with color, acquisition time, rotate axis', {
@@ -113,7 +113,7 @@ test_that('plot 4 samples with color, acquisition time, rotate axis', {
   expect_true(ggplot2::is.ggplot(result_4splWithColRotRunOrder))
   expect_equal(result_4splWithColRotRunOrder$labels$x, "Acquisition Time")
   expect_equal(result_4splWithColRotRunOrder$labels$y, "Test variable 8")
-  expect_equal(length(result_4splWithColRotRunOrder), 9)
+  expect_equal(length(result_4splWithColRotRunOrder), length(ggplot2::ggplot()))
 })
 
 test_that('sampleColour length warning, peakwidth and rotate and input order message', {
@@ -132,7 +132,7 @@ test_that('sampleColour length warning, peakwidth and rotate and input order mes
   expect_true(ggplot2::is.ggplot(result_plotColourWarning$result))
   expect_equal(result_plotColourWarning$result$labels$x, "Test variable 9")
   expect_equal(result_plotColourWarning$result$labels$y, "x")
-  expect_equal(length(result_plotColourWarning$result), 9)
+  expect_equal(length(result_plotColourWarning$result), length(ggplot2::ggplot()))
 })
 
 test_that('sampleColour length warning, no peakwidth (missing widthMax) and no rotate and run order message', {
@@ -151,7 +151,7 @@ test_that('sampleColour length warning, no peakwidth (missing widthMax) and no r
   expect_true(ggplot2::is.ggplot(result_plotColourWarningRunOrder$result))
   expect_equal(result_plotColourWarningRunOrder$result$labels$x, "Acquisition Time")
   expect_equal(result_plotColourWarningRunOrder$result$labels$y, "Test variable 10")
-  expect_equal(length(result_plotColourWarningRunOrder$result), 9)
+  expect_equal(length(result_plotColourWarningRunOrder$result), length(ggplot2::ggplot()))
 })
 
 test_that('missing widthMin, no peakwidth plot', {
@@ -170,7 +170,7 @@ test_that('missing widthMin, no peakwidth plot', {
   expect_true(ggplot2::is.ggplot(result_plotNoWidthMin$result))
   expect_equal(result_plotNoWidthMin$result$labels$x, "x")
   expect_equal(result_plotNoWidthMin$result$labels$y, "Test variable 11")
-  expect_equal(length(result_plotNoWidthMin$result), 9)
+  expect_equal(length(result_plotNoWidthMin$result), length(ggplot2::ggplot()))
 })
 
 test_that('missing widthMax, no peakwidth plot', {
@@ -189,7 +189,7 @@ test_that('missing widthMax, no peakwidth plot', {
   expect_true(ggplot2::is.ggplot(result_plotNoWidthMax$result))
   expect_equal(result_plotNoWidthMax$result$labels$x, "x")
   expect_equal(result_plotNoWidthMax$result$labels$y, "Test variable 11")
-  expect_equal(length(result_plotNoWidthMax$result), 9)
+  expect_equal(length(result_plotNoWidthMax$result), length(ggplot2::ggplot()))
 })
 
 test_that('NA in acquisition time, revert to input order plot', {
@@ -208,7 +208,7 @@ test_that('NA in acquisition time, revert to input order plot', {
   expect_true(ggplot2::is.ggplot(result_plotFallBackNAAcqu$result))
   expect_equal(result_plotFallBackNAAcqu$result$labels$x, "x")
   expect_equal(result_plotFallBackNAAcqu$result$labels$y, "Test variable 12")
-  expect_equal(length(result_plotFallBackNAAcqu$result), 9)
+  expect_equal(length(result_plotFallBackNAAcqu$result), length(ggplot2::ggplot()))
 })
 
 test_that('raise errors', {

diff --git a/tests/testthat/test_peakPantheR_quickEIC.R b/tests/testthat/test_peakPantheR_quickEIC.R
@@ -20,7 +20,7 @@ test_that('default plot EIC, subset rt and mz, verbose', {
   expect_true(ggplot2::is.ggplot(result_peakPantheR_quickEIC$result))
   expect_equal(result_peakPantheR_quickEIC$result$labels$x, "Retention Time (sec)")
   expect_equal(result_peakPantheR_quickEIC$result$labels$y, "Intensity")
-  expect_equal(length(result_peakPantheR_quickEIC$result), 9)
+  expect_equal(length(result_peakPantheR_quickEIC$result), length(ggplot2::ggplot()))
 
   # Check result messages (reading and timing)
   expect_equal(length(result_peakPantheR_quickEIC$messages), 3)
@@ -35,7 +35,7 @@ test_that('default plot EIC, no verbose', {
   expect_true(ggplot2::is.ggplot(result_peakPantheR_quickEIC$result))
   expect_equal(result_peakPantheR_quickEIC$result$labels$x, "Retention Time (sec)")
   expect_equal(result_peakPantheR_quickEIC$result$labels$y, "Intensity")
-  expect_equal(length(result_peakPantheR_quickEIC$result), 9)
+  expect_equal(length(result_peakPantheR_quickEIC$result), length(ggplot2::ggplot()))
 
   # Check result messages (None other than MSnbase)
   expect_equal(length(result_peakPantheR_quickEIC$messages), 1)

diff --git a/tests/testthat/test_plotHistogram.R b/tests/testthat/test_plotHistogram.R
@@ -32,7 +32,7 @@ test_that('histogram and density, with NA in input', {
   expect_equal(result_histoAndDensity$labels$x, "Test variable")
   expect_equal(result_histoAndDensity$labels$y, "density")
   expect_equal(result_histoAndDensity$data, expected_data)
-  expect_equal(length(result_histoAndDensity), 9)
+  expect_equal(length(result_histoAndDensity), length(ggplot2::ggplot()))
 
   # Check message (warning is caught as result and not warning!?!)
   expect_equal(result_message$messages, expected_message)
@@ -50,7 +50,7 @@ test_that('histogram without density', {
   expect_equal(result_histoNoDensity$labels$x, "Test variable 2")
   expect_equal(result_histoNoDensity$labels$y[1], "count")
   expect_equal(result_histoNoDensity$data, expected_data)
-  expect_equal(length(result_histoNoDensity), 9)
+  expect_equal(length(result_histoNoDensity), length(ggplot2::ggplot()))
 })
 
 test_that('histogram and density with modified ... (bins)', {
@@ -71,5 +71,5 @@ test_that('histogram and density with modified ... (bins)', {
   expect_equal(result_histoChangeBins$labels$x, "Test variable 3")
   expect_equal(result_histoChangeBins$labels$y, "density")
   expect_equal(result_histoChangeBins$data, expected_data)
-  expect_equal(length(result_histoChangeBins), 9)
+  expect_equal(length(result_histoChangeBins), length(ggplot2::ggplot()))
 })