g <- colData(faahko_sub)$sample_group
test_that("plotMiss works.", {
p1 <- plotMiss(faahko_sub, i = "raw")
expect_s3_class(p1, "patchwork")
p2 <- plotMiss(assay(faahko_sub, i = "raw"), group = g)
expect_s3_class(p2, "patchwork")
})
test_that("plotBox works.", {
p1 <- plotBox(faahko_sub, i = "raw")
expect_s3_class(p1, "ggplot")
p2 <- plotBox(assay(faahko_sub, i = "raw"), group = g)
expect_s3_class(p2, "ggplot")
})
test_that("plotReduced works.", {
out_pca <- reduceFeatures(faahko_sub, i = "knn_vsn", method = "pca")
out_tsne <- reduceFeatures(faahko_sub, i = "knn_vsn", method = "tsne",
perplexity = 1)
out_plsda <- reduceFeatures(faahko_sub, i = "knn_vsn", method = "plsda",
y = factor(g))
p1 <- plotReduced(out_pca, group = g)
expect_s3_class(p1, "ggplot")
p2 <- plotReduced(out_tsne, group = g)
expect_s3_class(p2, "ggplot")
p3 <- plotReduced(out_plsda, biplot = TRUE)
expect_s3_class(p3, "ggplot")
})
test_that("plotRTgroup works.", {
se <- clusterFeatures(faahko_sub, i = "knn_vsn", rtime_var = "rtmed")
expect_null(plotRTgroup(se, i = "knn_vsn", group = "FG.01", type = "graph"))
expect_null(plotRTgroup(se, i = "knn_vsn", group = "FG.01", type = "pairs"))
})
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