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test_filehandling.R: Added code to normalize test seurat object so th…
…at it has a data slot that can be retrieved for building/testing.
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| #---------------testing get_choices_from_sce()-----------------# | ||
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| # create a model SingleCellExperiment object | ||
| gene_list <- c( | ||
| "gene1", "gene2", "gene3", "gene4", "gene5", | ||
| "gene6", "gene7", "gene8", "gene9", "gene10" | ||
| ) | ||
| counts <- matrix(rpois(100, lambda = 10), ncol = 10, nrow = 10, dimnames = list(gene_list, LETTERS[1:10])) | ||
| sce <- SingleCellExperiment::SingleCellExperiment(list(logcounts = counts), mainExpName = "TEST") | ||
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| sum_exp1 <- SummarizedExperiment::SummarizedExperiment(matrix(rpois(100, lambda = 5), ncol = 10, nrow = 10, dimnames = list(gene_list, LETTERS[1:10]))) | ||
| # SingleCellExperiment::rowData(sum_exp1)$foo <- sample(LETTERS, nrow(sum_exp1), replace = FALSE) | ||
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| test1_reduc <- matrix(rpois(20, lambda = 2), ncol = 2, nrow = 10) | ||
| SingleCellExperiment::reducedDim(sce, "pca") <- test1_reduc | ||
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| SingleCellExperiment::altExp(sce, "test1") <- sum_exp1 | ||
| SingleCellExperiment::colLabels(sce) <- sample(letters, ncol(sce), replace = TRUE) | ||
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| # tests | ||
| test_that(desc = "get_choices_from_sce retrieves the correct choices", { | ||
| test_choices_assays_sce <- get_choices_from_sce(category = "assays", sce_object = sce) | ||
| test_choices_metadata_sce <- get_choices_from_sce(category = "metadata", sce_object = sce) | ||
| test_choices_reduction_sce <- get_choices_from_sce(category = "reductions", sce_object = sce) | ||
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| expect_equal(test_choices_metadata_sce, "label") | ||
| expect_equal(test_choices_reduction_sce, "pca") | ||
| expect_equal(test_choices_assays_sce, c("TEST", "test1")) | ||
| }) | ||
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| #---------------testing get_data_from_sce()-----------------# | ||
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| # tests | ||
| test_that(desc = "get_data_from_sce retrieves the correct data", { | ||
| test_data_assays_sce <- get_data_from_sce( | ||
| category = "assays", | ||
| sce_object = sce, assay_name = "TEST", | ||
| assay_data_to_get = c("gene4", "gene6") | ||
| ) | ||
| test_data_metadata_sce <- get_data_from_sce(category = "metadata", sce_object = sce) | ||
| test_data_reduction_sce <- get_data_from_sce( | ||
| category = "reductions", | ||
| sce_object = sce, reduction_name = "pca" | ||
| ) | ||
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| expect_equal(names(test_data_metadata_sce), "label") | ||
| expect_equal(dim(test_data_metadata_sce), c(10, 1)) | ||
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| expect_equal(names(test_data_reduction_sce), c("V1", "V2")) | ||
| expect_equal(dim(test_data_reduction_sce), c(10, 2)) | ||
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| expect_equal(rownames(test_data_assays_sce), LETTERS[1:10]) | ||
| expect_equal(colnames(test_data_assays_sce), c("gene4", "gene6")) | ||
| }) | ||
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| #---------------testing get_choices_from_seurat()-----------------# | ||
| # create fake data | ||
| gene_list <- c("gene1", "gene2", "gene3") | ||
| adt_list <- c("adt1", "adt2", "adt3") | ||
| counts <- matrix(rpois(30, lambda = 20), | ||
| nrow = 3, ncol = 10, | ||
| dimnames = list(gene_list, LETTERS[1:10]) | ||
| ) | ||
| test_so <- Seurat::CreateSeuratObject(counts = counts, assay = "RNA") | ||
| test_adt <- Seurat::CreateAssayObject(counts = matrix(rpois(30, lambda = 20), | ||
| nrow = 3, ncol = 10, | ||
| dimnames = list(adt_list, LETTERS[1:10]) | ||
| )) | ||
| test_so[["ADT"]] <- test_adt | ||
| test_so[["pca"]] <- Seurat::CreateDimReducObject( | ||
| embeddings = matrix(rpois(20, lambda = 5), | ||
| ncol = 2, nrow = 10, | ||
| dimnames = list(LETTERS[1:10], c("pca_1", "pca_2")) | ||
| ), | ||
| key = "pca_", | ||
| assay = "RNA" | ||
| ) | ||
| test_so[["umap"]] <- Seurat::CreateDimReducObject( | ||
| embeddings = matrix(rpois(20, lambda = 11), | ||
| ncol = 2, nrow = 10, | ||
| dimnames = list(LETTERS[1:10], c("umap_1", "umap_2")) | ||
| ), | ||
| key = "umap_", | ||
| assay = "RNA" | ||
| ) | ||
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| # tests | ||
| test_that(desc = "get_choices_from_seurat retrieves the correct choices", { | ||
| test_choices_assays_so <- get_choices_from_seurat(category = "assays", seurat_object = test_so) | ||
| test_choices_metadata_so <- get_choices_from_seurat(category = "metadata", seurat_object = test_so) | ||
| test_choices_reduction_so <- get_choices_from_seurat(category = "reductions", seurat_object = test_so) | ||
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| expect_equal(test_choices_metadata_so, "orig.ident") | ||
| expect_equal(test_choices_reduction_so, c("pca", "umap")) | ||
| expect_equal(test_choices_assays_so, c("ADT", "RNA")) | ||
| }) | ||
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| #---------------testing get_data_from_seurat()-----------------# | ||
| # tests | ||
| test_that(desc = "get_data_from_seurat retrieves the correct data", { | ||
| test_data_assays_so <- get_data_from_seurat( | ||
| category = "assays", | ||
| seurat_object = test_so, assay_name = "RNA", | ||
| assay_data_to_get = c("gene1", "gene2") | ||
| ) | ||
| test_data_metadata_so <- get_data_from_seurat(category = "metadata", seurat_object = test_so) | ||
| test_data_reduction_so <- get_data_from_seurat( | ||
| category = "reductions", | ||
| seurat_object = test_so, | ||
| reduction_name = "pca" | ||
| ) | ||
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| expect_equal(names(test_data_metadata_so), c( | ||
| "orig.ident", "nCount_RNA", | ||
| "nFeature_RNA", "nCount_ADT", | ||
| "nFeature_ADT" | ||
| )) | ||
| expect_equal(dim(test_data_metadata_so), c(10, 5)) | ||
| expect_equal(names(test_data_reduction_so), c("pca_1", "pca_2")) | ||
| expect_equal(dim(test_data_reduction_so), c(10, 2)) | ||
| expect_equal(rownames(test_data_assays_so), LETTERS[1:10]) | ||
| expect_equal(colnames(test_data_assays_so), c("gene1", "gene2")) | ||
| }) | ||
| #---------------testing get_choices_from_sce()-----------------# | ||
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| # create a model SingleCellExperiment object | ||
| gene_list <- c( | ||
| "gene1", "gene2", "gene3", "gene4", "gene5", | ||
| "gene6", "gene7", "gene8", "gene9", "gene10" | ||
| ) | ||
| counts <- matrix(rpois(100, lambda = 10), ncol = 10, nrow = 10, dimnames = list(gene_list, LETTERS[1:10])) | ||
| sce <- SingleCellExperiment::SingleCellExperiment(list(logcounts = counts), mainExpName = "TEST") | ||
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| sum_exp1 <- SummarizedExperiment::SummarizedExperiment(matrix(rpois(100, lambda = 5), ncol = 10, nrow = 10, dimnames = list(gene_list, LETTERS[1:10]))) | ||
| # SingleCellExperiment::rowData(sum_exp1)$foo <- sample(LETTERS, nrow(sum_exp1), replace = FALSE) | ||
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| test1_reduc <- matrix(rpois(20, lambda = 2), ncol = 2, nrow = 10) | ||
| SingleCellExperiment::reducedDim(sce, "pca") <- test1_reduc | ||
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| SingleCellExperiment::altExp(sce, "test1") <- sum_exp1 | ||
| SingleCellExperiment::colLabels(sce) <- sample(letters, ncol(sce), replace = TRUE) | ||
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| # tests | ||
| test_that(desc = "get_choices_from_sce retrieves the correct choices", { | ||
| test_choices_assays_sce <- get_choices_from_sce(category = "assays", sce_object = sce) | ||
| test_choices_metadata_sce <- get_choices_from_sce(category = "metadata", sce_object = sce) | ||
| test_choices_reduction_sce <- get_choices_from_sce(category = "reductions", sce_object = sce) | ||
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| expect_equal(test_choices_metadata_sce, "label") | ||
| expect_equal(test_choices_reduction_sce, "pca") | ||
| expect_equal(test_choices_assays_sce, c("TEST", "test1")) | ||
| }) | ||
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| #---------------testing get_data_from_sce()-----------------# | ||
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| # tests | ||
| test_that(desc = "get_data_from_sce retrieves the correct data", { | ||
| test_data_assays_sce <- get_data_from_sce( | ||
| category = "assays", | ||
| sce_object = sce, assay_name = "TEST", | ||
| assay_data_to_get = c("gene4", "gene6") | ||
| ) | ||
| test_data_metadata_sce <- get_data_from_sce(category = "metadata", sce_object = sce) | ||
| test_data_reduction_sce <- get_data_from_sce( | ||
| category = "reductions", | ||
| sce_object = sce, reduction_name = "pca" | ||
| ) | ||
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| expect_equal(names(test_data_metadata_sce), "label") | ||
| expect_equal(dim(test_data_metadata_sce), c(10, 1)) | ||
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| expect_equal(names(test_data_reduction_sce), c("V1", "V2")) | ||
| expect_equal(dim(test_data_reduction_sce), c(10, 2)) | ||
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| expect_equal(rownames(test_data_assays_sce), LETTERS[1:10]) | ||
| expect_equal(colnames(test_data_assays_sce), c("gene4", "gene6")) | ||
| }) | ||
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| #---------------testing get_choices_from_seurat()-----------------# | ||
| # create fake data | ||
| gene_list <- c("gene1", "gene2", "gene3") | ||
| adt_list <- c("adt1", "adt2", "adt3") | ||
| counts <- matrix(rpois(30, lambda = 20), | ||
| nrow = 3, ncol = 10, | ||
| dimnames = list(gene_list, LETTERS[1:10]) | ||
| ) | ||
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| test_so <- Seurat::CreateSeuratObject(counts = counts, assay = "RNA") | ||
| test_adt <- Seurat::CreateAssayObject(counts = matrix(rpois(30, lambda = 20), | ||
| nrow = 3, ncol = 10, | ||
| dimnames = list(adt_list, LETTERS[1:10]) | ||
| )) | ||
| test_so[["ADT"]] <- test_adt | ||
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| # the simulated RNA assay needs a "data" slot, which is created when Seurat normalizes counts | ||
| Seurat::DefaultAssay(test_so) <- "RNA" | ||
| test_so <- Seurat::NormalizeData(test_so) | ||
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| test_so[["pca"]] <- Seurat::CreateDimReducObject( | ||
| embeddings = matrix(rpois(20, lambda = 5), | ||
| ncol = 2, nrow = 10, | ||
| dimnames = list(LETTERS[1:10], c("pca_1", "pca_2")) | ||
| ), | ||
| key = "pca_", | ||
| assay = "RNA" | ||
| ) | ||
| test_so[["umap"]] <- Seurat::CreateDimReducObject( | ||
| embeddings = matrix(rpois(20, lambda = 11), | ||
| ncol = 2, nrow = 10, | ||
| dimnames = list(LETTERS[1:10], c("umap_1", "umap_2")) | ||
| ), | ||
| key = "umap_", | ||
| assay = "RNA" | ||
| ) | ||
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| # tests | ||
| test_that(desc = "get_choices_from_seurat retrieves the correct choices", { | ||
| test_choices_assays_so <- get_choices_from_seurat(category = "assays", seurat_object = test_so) | ||
| test_choices_metadata_so <- get_choices_from_seurat(category = "metadata", seurat_object = test_so) | ||
| test_choices_reduction_so <- get_choices_from_seurat(category = "reductions", seurat_object = test_so) | ||
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| expect_equal(test_choices_metadata_so, "orig.ident") | ||
| expect_equal(test_choices_reduction_so, c("pca", "umap")) | ||
| expect_equal(test_choices_assays_so, c("ADT", "RNA")) | ||
| }) | ||
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| #---------------testing get_data_from_seurat()-----------------# | ||
| # tests | ||
| test_that(desc = "get_data_from_seurat retrieves the correct data", { | ||
| test_data_assays_so <- get_data_from_seurat( | ||
| category = "assays", | ||
| seurat_object = test_so, assay_name = "RNA", | ||
| assay_data_to_get = c("gene1", "gene2") | ||
| ) | ||
| test_data_metadata_so <- get_data_from_seurat(category = "metadata", seurat_object = test_so) | ||
| test_data_reduction_so <- get_data_from_seurat( | ||
| category = "reductions", | ||
| seurat_object = test_so, | ||
| reduction_name = "pca" | ||
| ) | ||
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| expect_equal(names(test_data_metadata_so), c( | ||
| "orig.ident", "nCount_RNA", | ||
| "nFeature_RNA", "nCount_ADT", | ||
| "nFeature_ADT" | ||
| )) | ||
| expect_equal(dim(test_data_metadata_so), c(10, 5)) | ||
| expect_equal(names(test_data_reduction_so), c("pca_1", "pca_2")) | ||
| expect_equal(dim(test_data_reduction_so), c(10, 2)) | ||
| expect_equal(rownames(test_data_assays_so), LETTERS[1:10]) | ||
| expect_equal(colnames(test_data_assays_so), c("gene1", "gene2")) | ||
| }) |