tests/testthat/test-plotAnansi.R

In thomazbastiaanssen/anansi: Annotation-Based Analysis of Specific Interactions

test_that("plotAnansi", {
    library(ggplot2)
    data(FMT_data)

    t1 <- t(FMT_metab)
    t2 <- t(FMT_KOs)
    web <- weaveWeb(
        formula = cpd ~ ko,
        tableY = t1,
        tableX = t2,
        link = kegg_link()
    )
    out <- anansi(
        web = web,
        formula = ~Legend,
        groups = "Legend",
        metadata = FMT_metadata,
        adjust.method = "BH",
    )
    # Check arguments
    expect_no_error(plotAnansi(out))
    expect_error(plotAnansi(out, association.type = "wrong"))
    expect_error(plotAnansi(out, model.var = "wrong"))
    expect_warning(
        plotAnansi(out, association.type = "full", model.var = "Legend"),
        "'model.var' is ignored when 'association type' is set to full"
    )
    expect_warning(
        plotAnansi(out, signif.threshold = 0.05),
        "'signif.threshold' is ignored when 'association type' is not defined"
    )
    expect_error(
        plotAnansi(out, association.type = "emergent"),
        "'model.var' must specify a variable of the anansi model when 'association type' is set to emergent",
        fixed = TRUE
    )
    expect_error(
        plotAnansi(
            out,
            association.type = "disjointed",
            model.var = "Legend",
            shape_by = "wrong"
        ),
        "'shape_by' must be a character string specifying the name of a 'groups' term used in the original anansi call",
        fixed = TRUE
    )
    expect_no_error(plotAnansi(
        out,
        association.type = "disjointed",
        model.var = "Legend",
        shape_by = "group"
    ))
    # Check output plot
    p <- plotAnansi(
        out,
        association.type = "emergent",
        model.var = "Legend",
        fill_by = "group"
    )
    expect_length(p$guides$guides, 2)
    expect_equal(dim(p$data), c(260, 8))
    expect_false(any(is.na(p$data[["fill"]])))
})