tests/testthat/test_list.R

In clustifyr: Classifier for Single-cell RNA-seq Using Cell Clusters

context("compare_list")

test_that("warning if matrix is not binarized", {
    pbmc_mm <- matrixize_markers(pbmc_markers)
    pbmc_avg <- average_clusters(pbmc_matrix_small,
        pbmc_meta,
        cluster_col = "classified"
    )
    pbmc_avgb <- binarize_expr(pbmc_avg)
    gene_list_methods <- c("hyper")
    expect_warning(results <- lapply(
        gene_list_methods,
        function(x) {
            compare_lists(pbmc_avg,
                pbmc_mm,
                metric = x
            )
        }
    ))
})


test_that("run all gene list functions", {
    pbmc_mm <- matrixize_markers(pbmc_markers)
    pbmc_avg <- average_clusters(pbmc_matrix_small,
        pbmc_meta,
        cluster_col = "classified"
    )
    pbmc_avgb <- binarize_expr(pbmc_avg)
    gene_list_methods <- c("spearman", "hyper", "jaccard", "gsea")
    results <- lapply(
        gene_list_methods,
        function(x) {
            compare_lists(pbmc_avgb,
                pbmc_mm,
                metric = x
            )
        }
    )

    expect_equal(4, length(results))
})

test_that("gene list function options", {
    pbmc_mm <- matrixize_markers(pbmc_markers)
    pbmc_avg <- average_clusters(pbmc_matrix_small,
        pbmc_meta,
        cluster_col = "classified"
    )
    pbmc_avgb <- binarize_expr(pbmc_avg)
    expect_error(suppressWarnings(
        res <- compare_lists(
            pbmc_avgb,
            pbmc_mm,
            metric = "hyper",
            output_high = FALSE,
            n = 5
        )
    ))
})

test_that("run all gene list functions in clustify_lists", {
    gene_list_methods <- c("spearman", "hyper", "jaccard", "gsea")
    results <- lapply(
        gene_list_methods,
        function(x) {
            clustify_lists(
                pbmc_matrix_small,
                per_cell = FALSE,
                metadata = pbmc_meta,
                cluster_col = "classified",
                marker = pbmc_markers,
                marker_inmatrix = FALSE,
                metric = x
            )
        }
    )

    expect_equal(4, length(results))
})

test_that("gsea outputs in cor matrix format", {
    res <- clustify_lists(
        pbmc_matrix_small,
        per_cell = FALSE,
        metadata = pbmc_meta,
        cluster_col = "classified",
        marker = pbmc_markers,
        marker_inmatrix = FALSE,
        metric = "gsea"
    )
    res2 <- cor_to_call(res)

    expect_equal(9, nrow(res2))
})

test_that("seurat object clustify_lists-ing", {
    res <- clustify_lists(
        s_small,
        per_cell = FALSE,
        marker = pbmc_markers,
        marker_inmatrix = FALSE,
        metric = "jaccard",
        cluster_col = "res.1",
        seurat_out = FALSE,
        dr = "tsne"
    )
    res <- clustify_lists(
        s_small,
        per_cell = FALSE,
        marker = pbmc_markers,
        marker_inmatrix = FALSE,
        metric = "jaccard",
        cluster_col = "res.1",
        seurat_out = FALSE,
        dr = "tsne"
    )
    g <- plot_best_call(
        res,
        seurat_meta(s_small,
            dr = "tsne"
        ),
        cluster_col = "res.1",
        plot_r = TRUE,
        x = "tSNE_1",
        y = "tSNE_2"
    )
    expect_true(ggplot2::is.ggplot(g[[1]]))
})

test_that("clustify_lists inserts seurat metadata correctly", {
    res <- clustify_lists(
        s_small,
        per_cell = FALSE,
        marker = pbmc_markers,
        marker_inmatrix = FALSE,
        metric = "jaccard",
        cluster_col = "res.1",
        seurat_out = TRUE,
        dr = "tsne"
    )
    res2 <- clustify_lists(
        s_small,
        per_cell = TRUE,
        marker = pbmc_markers,
        marker_inmatrix = FALSE,
        metric = "jaccard",
        cluster_col = "res.1",
        seurat_out = TRUE,
        dr = "tsne"
    )
    if ("Seurat" %in% loadedNamespaces()) {
        expect_true(class(res) %in% c("seurat"))
    } else {
        expect_true(is.matrix(res))
    }
})

test_that("seurat3 object clustify_lists-ing", {
    res <- clustify_lists(
        s_small3,
        per_cell = FALSE,
        marker = pbmc_markers,
        marker_inmatrix = FALSE,
        metric = "jaccard",
        cluster_col = "RNA_snn_res.1",
        seurat_out = TRUE,
        dr = "tsne"
    )
    res <- clustify_lists(
        s_small3,
        per_cell = FALSE,
        marker = pbmc_markers,
        marker_inmatrix = FALSE,
        metric = "jaccard",
        cluster_col = "RNA_snn_res.1",
        seurat_out = FALSE,
        dr = "tsne"
    )
    g <- plot_best_call(
        res,
        seurat_meta(s_small3,
            dr = "tsne"
        ),
        cluster_col = "RNA_snn_res.1",
        plot_r = TRUE,
        x = "tSNE_1",
        y = "tSNE_2"
    )
    expect_true(ggplot2::is.ggplot(g[[1]]))
})

test_that("clustify_lists inserts seurat3 metadata correctly", {
    res <- clustify_lists(
        s_small3,
        per_cell = FALSE,
        marker = pbmc_markers,
        marker_inmatrix = FALSE,
        metric = "jaccard",
        cluster_col = "RNA_snn_res.1",
        seurat_out = TRUE,
        dr = "tsne"
    )
    res2 <- clustify_lists(
        s_small3,
        per_cell = TRUE,
        marker = pbmc_markers,
        marker_inmatrix = FALSE,
        metric = "jaccard",
        cluster_col = "RNA_snn_res.1",
        seurat_out = TRUE,
        dr = "tsne"
    )
    if ("Seurat" %in% loadedNamespaces()) {
        expect_true(class(res) %in% c("Seurat"))
    } else {
        expect_true(is.matrix(res))
    }
})

test_that("run all gene list functions and then use consensus_call", {
    pbmc_mm <- matrixize_markers(pbmc_markers)
    pbmc_avg <- average_clusters(pbmc_matrix_small,
        pbmc_meta,
        cluster_col = "classified"
    )
    pbmc_avgb <- binarize_expr(pbmc_avg)
    gene_list_methods <- c("spearman", "hyper", "jaccard", "gsea")
    results <- lapply(
        gene_list_methods,
        function(x) {
            compare_lists(pbmc_avgb,
                pbmc_mm,
                metric = x
            )
        }
    )
    call_list <- lapply(
        results,
        cor_to_call_rank
    )
    calls <- call_consensus(call_list)
    expect_equal(4, length(results))
})

test_that("run all gene list functions in clustify_lists", {
    res <- clustify_lists(
        pbmc_matrix_small,
        cbmc_m,
        metadata = pbmc_meta,
        cluster_col = "classified",
        metric = "consensus"
    )
    expect_equal(9, nrow(res))
})

test_that("run all gene list functions in clustify_lists and seurat object", {
    res <- clustify_lists(
        s_small3,
        marker = cbmc_m,
        dr = "tsne",
        cluster_col = "RNA_snn_res.1",
        metric = "consensus",
        seurat_out = TRUE
    )
    expect_true(is.data.frame(res) | "Seurat" %in% class(res))
})

test_that("run all gene list functions in clustify_lists and seurat object", {
    res <- clustify_lists(
        s_small,
        marker = cbmc_m,
        dr = "tsne",
        cluster_col = "res.1",
        metric = "consensus",
        seurat_out = TRUE
    )
    expect_true(is.data.frame(res) | "seurat" %in% class(res))
})

test_that("lists of genes will work with posneg", {
    lst_of_markers <- split(pbmc_markers$gene, pbmc_markers$cluster)
    res <- clustify_lists(
        input = pbmc_matrix_small,
        per_cell = FALSE,
        cluster_col = "classified",
        metadata = pbmc_meta,
        marker = lst_of_markers,
        marker_inmatrix = TRUE,
        metric = "posneg",
        seurat_out = FALSE
    )
    expect_true(ncol(res) == length(lst_of_markers))
})