fix unit tests checking plotting properly

tests/testthat/test-tune.block.plsda.R

@@ -42,6 +42,8 @@ test_that("tune.block.plsda works and is the same as perf alone and in tune wrap
   .expect_numerically_close(tune.res.3$error.rate.per.class$mrna$max.dist[3,2], 0.25)
 
   # check can plot outputs
+  pdf(NULL)
+  on.exit(dev.off())
   expect_silent(plot(tune.res.1))
   expect_silent(plot(tune.res.2))
   expect_silent(plot(tune.res.3))

tests/testthat/test-tune.block.splsda.R

@@ -159,6 +159,8 @@ test_that("tune.block.splsda works independently and in tune wrapper the same",
   expect_equal(tune11$choice.keepX, tune41$choice.keepX)
 
   # check can plot outputs
+  pdf(NULL)
+  on.exit(dev.off())
   expect_silent(plot(tune41))
   expect_silent(plot(tune11))
 

tests/testthat/test-tune.mint.plsda.R

@@ -36,6 +36,8 @@ test_that("tune.mint.plsda works and is the same perf alone and in tune wrapper"
   .expect_numerically_close(tune.res.3$global.error$BER[1,1], 0.3803556)
 
   # check can plot outputs
+  pdf(NULL)
+  on.exit(dev.off())
   expect_silent(plot(tune.res.1))
   expect_silent(plot(tune.res.2))
   expect_silent(plot(tune.res.3))

tests/testthat/test-tune.mint.splsda.R

@@ -21,7 +21,9 @@ test_that("tune.mint.splsda works", code = {
     expect_equal(out$choice.ncomp$ncomp, 1)
 
     # check can plot
-    expect_silent(plot(out))
+    pdf(NULL)
+    on.exit(dev.off())
+    expect_error(plot(out), NA) # makes note about not being able to plot SD bars
 
 })
 
@@ -47,7 +49,9 @@ test_that("tune.mint.splsda works with custom alpha", code = {
     expect_equal(out$choice.ncomp$ncomp, 1)
 
     # check can plot
-    expect_silent(plot(out))
+    pdf(NULL)
+    on.exit(dev.off())
+    expect_error(plot(out), NA) # makes note about not being able to plot SD bars
 
 })
 

tests/testthat/test-tune.pca.R

@@ -9,6 +9,8 @@ test_that("tune.pca and tune(method='pca') are equivalent", {
   expect_equal(object1$ncomp, object2$ncomp)
   expect_equal(object1$sdev[1], object2$sdev[1])
   # check can plot outputs without errors
+  pdf(NULL)
+  on.exit(dev.off())
   expect_silent(plot(object1))
   expect_silent(plot(object2))
 })

tests/testthat/test-tune.pls.R

@@ -31,6 +31,8 @@ test_that("tune.pls works and is the same as perf alone and in tune wrapper", co
   .expect_numerically_close(tune.res.3$measures$Q2$summary[1,3], -0.1304012)
 
   # check can plot outputs
+  pdf(NULL)
+  on.exit(dev.off())
   expect_silent(plot(tune.res.1))
   expect_silent(plot(tune.res.2))
   expect_silent(plot(tune.res.3))

tests/testthat/test-tune.plsda.R

@@ -43,6 +43,8 @@ test_that("tune.plsda works and is the same perf alone and in tune wrapper", cod
   .expect_numerically_close(tune.plsda.res.3$error.rate$overall[1,1], 0.5106383)
 
   # check can plot
+  pdf(NULL)
+  on.exit(dev.off())
   expect_silent(plot(tune.plsda.res.1))
   expect_silent(plot(tune.plsda.res.2))
   expect_silent(plot(tune.plsda.res.3))

tests/testthat/test-tune.rcc.R

@@ -16,6 +16,8 @@ test_that("tune.rcc works with Mfold method", code = {
   expect_equal(tune.rcc.res$grid1, c(0.00100, 0.25075, 0.50050, 0.75025, 1.00000))
 
   # check can plot
+  pdf(NULL)
+  on.exit(dev.off())
   expect_silent(plot(tune.rcc.res))
 })
 
@@ -34,6 +36,8 @@ test_that("tune.rcc works with loo method", code = {
   expect_equal(tune.rcc.res$grid1, c(0.00100, 0.25075, 0.50050, 0.75025, 1.00000))
 
   # check can plot
+  pdf(NULL)
+  on.exit(dev.off())
   expect_silent(plot(tune.rcc.res))
 })
 
@@ -56,6 +60,8 @@ test_that("tune.rcc works in parallel same as in series", code = {
   expect_equal(tune.rcc.res$grid2, tune.rcc.res.parallel$grid2)
 
   # check can plot
+  pdf(NULL)
+  on.exit(dev.off())
   expect_silent(plot(tune.rcc.res))
   expect_silent(plot(tune.rcc.res.parallel))
 })
@@ -86,6 +92,8 @@ test_that("tune.rcc and tune(method='rcc') are equivalent", {
   expect_equal(tune.rcc.res.1$grid2, tune.rcc.res.2$grid2)
 
   # check can plot
+  pdf(NULL)
+  on.exit(dev.off())
   expect_silent(plot(tune.rcc.res.1))
   expect_silent(plot(tune.rcc.res.2))
 

tests/testthat/test-tune.spca.R

@@ -20,6 +20,8 @@ test_that("tune.spca works in serial and parallel", {
   expect_equal(object_parallel$choice.keepX[[2]], 5)
   .expect_numerically_close(object_parallel$cor.comp$comp1[1,2], 0.3994544)
   # test can plot outputs
+  pdf(NULL)
+  on.exit(dev.off())
   expect_silent(plot(object_serial))
   expect_silent(plot(object_parallel))
 })
@@ -81,6 +83,8 @@ test_that("tune.spca and tune(method='spca') are equivalent", {
   expect_equal(object1$choice.keepX[[2]], object2$choice.keepX[[2]])
   .expect_numerically_close(object1$cor.comp$comp1[3,3], object2$cor.comp$comp1[3,3])
   # test can plot outputs
+  pdf(NULL)
+  on.exit(dev.off())
   expect_silent(plot(object1))
   expect_silent(plot(object2))
 })

tests/testthat/test-tune.splsda.R

@@ -31,11 +31,13 @@ test_that("tune.splsda works and is the same in parallel and when run in tune wr
                          method = "splsda")
 
 
-  # check outputs
+  # check outputs format
   expect_equal(class(tune.splsda.res.1), "tune.splsda")
   expect_equal(class(tune.splsda.res.2), "tune.splsda")
   expect_equal(class(tune.splsda.res.3), "tune.splsda")
   expect_equal(class(tune.splsda.res.4), "tune.splsda")
+
+  # check output values
   expect_equal(unname(tune.splsda.res.1$choice.keepX), c(10,15))
   expect_equal(unname(tune.splsda.res.2$choice.keepX), c(10,15))
   expect_equal(unname(tune.splsda.res.3$choice.keepX), c(10,15))
@@ -46,10 +48,10 @@ test_that("tune.splsda works and is the same in parallel and when run in tune wr
   .expect_numerically_close(tune.splsda.res.4$error.rate[1,1], 0.3111111)
 
   # check can plot outputs
-  expect_silent(plot(tune.splsda.res.1))
-  expect_silent(plot(tune.splsda.res.2))
-  expect_silent(plot(tune.splsda.res.3))
-  expect_silent(plot(tune.splsda.res.4))
+  expect_is(plot(tune.splsda.res.1), "ggplot")
+  expect_is(plot(tune.splsda.res.2), "ggplot")
+  expect_is(plot(tune.splsda.res.3), "ggplot")
+  expect_is(plot(tune.splsda.res.4), "ggplot")
 
 })