tests/testthat/test_simple.R

In clatworthylab/bowerbird: A single-cell package for Functional Annotation + Gene Module Summarization.

test_that("simple running mode", {
	expect_error(bower())
	expect_s4_class(bower(list()), "BOWER")

	gmt_file <- system.file("extdata", "h.all.v7.4.symbols.gmt", package = "bowerbird")
	bwr <- bower(gmt_file)
	bwr <- snn_graph(bwr)
	bwr <- find_clusters(bwr)
	bwr <- summarize_clusters(bwr)

	print(bwr)
	
	bwr2 <- summarize_clusters(bwr, disconnect_graph = TRUE)
	expect_error(expect_equal(bwr2, bwr))

	p <- plot_graph(bwr, colorby = 'cluster', node.size = 'geneset_size')
	p <- plot_graph(bwr@graph, colorby = 'cluster', node.size = 'geneset_size')
	expect_s4_class(bwr, "BOWER")

	new_clusters <- rev(bwr@clusters)
	bwr <- set_clusters(bwr, new_clusters)
	bwr <- summarize_clusters(bwr)
	l <- snn_graph(bwr@coregenes)
	expect_type(l, "list")
	expect_s4_class(bwr, "BOWER")

	graph <- summarize_clusters(bwr@graph)
	graph <- summarize_clusters(bwr@graph, disconnect_graph = TRUE)
})