tests/testthat/test.ClusterSet_class.R
In dputhier/scigenex: The scigenex package (Single-Cell Informative GENe Explorer)
library(testthat)
testthat::test_that("Test the indexing operator of the ClusterSet", {
clusters <- 1:5
cluster_size <- c(12,10,8,6,4)
m <- matrix(rnorm(20000), nc=500, nr=40)
colnames(m) <- paste0("S_", 1:500)
gn <- paste0("G_", 1:40)
cls <- unlist(mapply(rep, clusters, cluster_size))
gene_cluster <- split(gn, cls)
rownames(m) <- paste0("G_", 1:40)
cls <- unlist(mapply(rep, clusters, cluster_size))
gene_clusters_metadata <- list()
gene_clusters_metadata$cluster_id <- as.numeric(names(gene_cluster))
gene_clusters_metadata$number <- length(clusters)
gene_clusters_metadata$size <- cluster_size
names(gene_clusters_metadata$size) <- clusters
gene_cluster_annotations <- list()
top_genes <- lapply(gene_cluster, "[", 1:3)
dbf_output <- list()
dbf_output$dknn <- runif(1000)
dbf_output$simulated_dknn <- runif(1000)
dbf_output$critical_distance <- 0.5
dbf_output$fdr <- 0.05
dbf_output$center <- do.call(rbind,
lapply(split.data.frame(as.data.frame(m),
as.factor(cls)),
apply, 2, mean))
colnames(dbf_output$center) <- colnames(m)
rownames(dbf_output$center) <- names(gene_cluster)
res <- new("ClusterSet",
data = m,
gene_clusters = split(gn, cls),
top_genes = top_genes,
gene_clusters_metadata = gene_clusters_metadata,
gene_cluster_annotations = gene_cluster_annotations,
cells_metadata = data.frame(cells_barcode=colnames(m),
row.names = colnames(m)),
dbf_output = dbf_output,
parameters = list(filename="oP0H7t6Sc0", distance_method="pearson",
k=50, inflation=2, noise_level=0.3, fdr=0.05,
min_nb_supporting_cell=0, min_pct_gene_expressed=40,
min_cluster_size=10, row_sum=-Inf, seed=123)
)
testthat::expect_equal(dim(res[1:3,4:5]), c(30, 2))
testthat::expect_equal(dim(res[c(2,4),1:5]), c(16, 5))
testthat::expect_equal(length(res[c(2,4),1:5]@gene_clusters), 2)
testthat::expect_equal(length(res[c(2,4),1:5]@gene_clusters), 2)
testthat::expect_equal(length(res[c(1,2,4),]@gene_clusters), 3)
testthat::expect_equal(dim(res[logical(), logical()]), c(0,0))
testthat::expect_equal(dim(res[c("1", "2"), ]), c(22, 500))
testthat::expect_equal(res[c("1", "2"), ]@gene_clusters_metadata$number, 2)
testthat::expect_equal(res[2:4, ]@gene_clusters_metadata$number, 3)
testthat::expect_equal(res[c("1", "2", "3"), ]@gene_clusters_metadata$number, 3)
testthat::expect_equal(res[logical(), ]@gene_clusters_metadata$number, 0)
testthat::expect_equal(dim(res[, ]), c(40, 500))
testthat::expect_equal(dim(res[, 10:20]), c(40, 11))
testthat::expect_equal(dim(res[1:3, 10:20]@cells_metadata), c(11, 1))
testthat::expect_equal(dim(res[1:3, 10:20]@cells_metadata), c(11, 1))
testthat::expect_equal(dim(res[1, 1]@cells_metadata), c(1, 1))
testthat::expect_equal(dim(res[1, 1]), c(12, 1))
testthat::expect_equal(length(res[1:2, 1]@top_genes), 2)
testthat::expect_equal(length(res[1:2, c()]@top_genes), 2)
testthat::expect_identical(res[c(1, 3), ], res[c(1, 3), seq_len(ncol(res))])
testthat::expect_identical(res[, c("S_408", "S_409")], res[, c(408, 409)])
testthat::expect_identical(res[c(1, 3), c("S_3", "S_4")], res[c(1, 3), 3:4])
testthat::expect_identical(res[-c(1, 2), ], res[c(3:nclust(res)), ])
testthat::expect_identical(res[as.character(2:5), c("S_3", "S_4")], res[2:5, 3:4])
testthat::expect_identical(res[as.character(2:5), ], res[2:5, ])
testthat::expect_identical(res[,paste0("S_",2:5)], res[,2:5])
testthat::expect_identical(res[c("2", "4"), ]@gene_clusters, res[c(2, 4), ]@gene_clusters)
testthat::expect_identical(res[c("1", "3"), ]@gene_clusters_metadata$number, res[c(1, 3), ]@gene_clusters_metadata$number)
testthat::expect_identical(res[3, ]@gene_clusters_metadata, res["3", ]@gene_clusters_metadata)
testthat::expect_error(res["a", "b"])
})
test_that("Test messages when looking at ClusterSet object", {
obj <- new("ClusterSet")
msg_clusterset <- capture.output(obj)
expect_equal(msg_clusterset[1], "\t\tAn object of class ClusterSet")
expect_equal(msg_clusterset[2], "\t\tName: ")
expect_equal(msg_clusterset[3], "\t\tMemory used: 2520 ")
expect_equal(msg_clusterset[4], "\t\tNumber of cells: 0 ")
expect_equal(msg_clusterset[5], "\t\tNumber of informative genes: 0 ")
expect_equal(msg_clusterset[6], "\t\tNumber of gene clusters: ")
expect_equal(msg_clusterset[7], "\t\tThis object contains the following informations:")
expect_equal(msg_clusterset[8], "\t\t\t - data ")
expect_equal(msg_clusterset[9], "\t\t\t - gene_clusters ")
expect_equal(msg_clusterset[10], "\t\t\t - top_genes ")
expect_equal(msg_clusterset[11], "\t\t\t - gene_clusters_metadata ")
expect_equal(msg_clusterset[12], "\t\t\t - gene_cluster_annotations ")
expect_equal(msg_clusterset[13], "\t\t\t - cells_metadata ")
expect_equal(msg_clusterset[14], "\t\t\t - dbf_output ")
expect_equal(msg_clusterset[15], "\t\t\t - parameters ")
})
set_verbosity(0)
load_example_dataset("7871581/files/pbmc3k_medium_clusters")
test_that("Check clust_names() is working.", {
a <- unique(unname(gene_cluster(pbmc3k_medium_clusters)))
b <- clust_names(pbmc3k_medium_clusters)
expect_true(all(as.character(a)==b))
})
test_that("Check clust_names() is working.", {
a <- show_methods()
expect_true(all(c("[", "clust_names", "clust_size", "cluster_stats", "col_names",
"dim", "enrich_go", "gene_cluster", "nclust", "rename_clust",
"row_names", "show", "top_genes", "viz_enrich", "which_clust") %in% a))
})# Set verbosity to 0
set_verbosity(0)
library(Seurat)
load_example_dataset("7871581/files/pbmc3k_medium_clusters")
load_example_dataset("7871581/files/pbmc3k_medium")
gn <- pbmc3k_medium_clusters
test_that("Check 'rename' is working.", {
expect_true(nclust(rename_clust(gn, 1:nclust(gn))) == nclust(gn))
expect_true(all(names(rename_clust(gn, nclust(gn):1)@gene_clusters) == 15:1))
rn <- rename_clust(gn, letters[1:nclust(gn)])
expect_true(ggplot2::is.ggplot(plot_profiles(rn, ident = Seurat::Idents(pbmc3k_medium))))
})
set_verbosity(0)
library(Seurat)
load_example_dataset("7871581/files/pbmc3k_medium_clusters")
res <- pbmc3k_medium_clusters
test_that("Check 'which_clust' is working.", {
expect_true(all(which_clust(res, c('APOBEC3A', 'RPL11', 'PF4')) == c(3,1,2)))
expect_true(all(is.na(which_clust(res, c('APOBEC3A', 'RPL11', 'bla'))) == c(F,F,T)))
})
set_verbosity(0)
load_example_dataset("7871581/files/pbmc3k_medium_clusters")
test_that("Check clust_names() is working.", {
a <- unique(unname(gene_cluster(pbmc3k_medium_clusters)))
b <- clust_names(pbmc3k_medium_clusters)
expect_true(all(as.character(a)==b))
})
# Set verbosity to 0
set_verbosity(0)
load_example_dataset("7871581/files/pbmc3k_medium_clusters")
res <- pbmc3k_medium_clusters
test_that("Checking ncol()", {
expect_equal(ncol(res), 361)
})
test_that("Checking nrow()", {
expect_equal(nrow(res), 291)
})
test_that("Checking dim()", {
expect_equal(dim(res), c(291, 361))
})
test_that("Checking colnames()", {
expect_equal(col_names(res)[1:10], c("GATCTACTGGTGAG-1", "ACAGTGACTCACCC-1", "AGACGTACAGAGGC-1",
"GACGTAACCTGTGA-1", "TATACAGATCCAGA-1", "CGGATAACAGCTCA-1", "TTACCATGGTTGAC-1",
"TCCCACGATCATTC-1", "ATAGCGTGCAGATC-1", "TGTAGGTGTGCTGA-1"))
expect_equal(tail(col_names(res)), c("GGCATATGGGGAGT-1", "TTACGTACGTTCAG-1", "GGAACACTTCAGAC-1",
"ATCATCTGACACCA-1", "ACGAACTGGCTATG-1", "TAACACCTTGTTTC-1"))
})
test_that("Checking rownames()", {
expect_equal(row_names(res), c("MALAT1", "RPL9", "RPL23A", "RPL21", "RPS25", "RPS19", "RPS3",
"RPS12", "RPL18A", "RPL11", "RPL32", "RPLP2", "RPS18", "RPL3",
"RPL29", "RPL14", "RPS3A", "RPS15A", "RPS23", "RPL27A", "RPS16",
"RPL12", "EEF1A1", "RPL31", "RPS4X", "RPS8", "RPL28", "RPS29",
"RPS10", "RPS13", "RPS11", "RPS26", "RPL35A", "TPT1", "BTG1",
"RPL15", "RPL18", "RPS20", "RPS28", "RPL36", "RPL5", "EEF1B2",
"RPL7A", "RPL17", "NACA", "RPL27", "RPL26", "RPS9", "RPLP1",
"RPSAP58", "RPL6", "PTCRA", "ACRBP", "SDPR", "GNG11", "PF4",
"HIST1H2AC", "TMEM40", "TUBB1", "SPARC", "PPBP", "GP9", "MMD",
"AP001189.4", "CLU", "RGS18", "MPP1", "CA2", "F13A1", "TPM1",
"MYL9", "TREML1", "NGFRAP1", "PTGS1", "GAS2L1", "GRAP2", "ODC1",
"SNCA", "TPM4", "CTSA", "ILK", "PDLIM1", "ACTN1", "FERMT3", "PLA2G12A",
"HIST1H2BK", "SNN", "APP", "YWHAH", "ASAH1", "RAP1B", "MFSD1",
"GSN", "MARCH2", "H2AFJ", "TPTEP1", "PARVB", "MYL12A", "CD151",
"PVALB", "TYMP", "COTL1", "CTSS", "CFD", "S100A11", "LGALS2",
"GABARAP", "APOBEC3A", "TNFSF13B", "CPVL", "MNDA", "CD14", "IGSF6",
"CSTB", "MAFB", "AP2S1", "WARS", "IFI6", "LILRB2", "LILRB4",
"C1orf162", "SLC7A7", "IFNGR2", "SOD2", "TGFBI", "BLVRA", "CAPG",
"BID", "CTSZ", "NAAA", "FCGR2A", "CD300LF", "S100A10", "GAPDH",
"ALDH2", "EIF4EBP1", "GRINA", "NUP214", "CD302", "ATG3", "CAMK1",
"CYBB", "CNPY3", "GCA", "POU2F2", "CCL5", "GZMA", "CST7", "CTSW",
"HLA-C", "FGFBP2", "GZMB", "GNLY", "PRF1", "SPON2", "CCL4", "PTPRCAP",
"CLIC3", "IL2RB", "HOPX", "CD247", "AKR1C3", "IGFBP7", "KLRF1",
"CD99", "CD7", "XCL1", "EFHD2", "PLEK", "HEMGN", "EGFL7", "AC137932.6",
"hsa-mir-1199", "SEC14L5", "HEXIM2", "GATA2", "SH3BGRL2", "KIAA0513",
"PCP2", "PYGL", "DPY19L1", "RAB27B", "CLIC4", "LYL1", "FAM110A",
"RILP", "DAB2", "KIFC3", "BTK", "SPOCD1", "ARHGAP21", "ITGB3",
"ALOX12", "SCFD2", "ATP9A", "FAM212A", "ABCC3", "RP11-359I18.5",
"TGFB1I1", "CTNNAL1", "ENDOD1", "NEXN", "ABHD16A", "ARG2", "GLA",
"WIPI1", "PPP1R14A", "CLEC1B", "CMTM5", "GP1BA", "RP11-367G6.3",
"HIST1H2BD", "FNTB", "SENCR", "SEPT4", "MLH3", "SCGB1C1", "HIST2H2BE",
"C1orf198", "H1F0", "GLUL", "LGALSL", "SMOX", "SSX2IP", "AC147651.3",
"C19orf33", "FAM212B", "SERPINE2", "ZNF778", "TMCC2", "TRIM58",
"FN3K", "NFE2", "MGLL", "MOB3B", "HLA-DPA1", "HLA-DRB1", "HLA-DRA",
"HLA-DRB5", "HLA-DPB1", "CD74", "HLA-DQA1", "HLA-DQB1", "FAM26F",
"LY86", "HLA-DMB", "SLC25A6", "CD37", "RNASET2", "C2orf88", "CLDN5",
"HIST1H2BJ", "FAM63A", "SPHK1", "SLC40A1", "TUBA1C", "TMEM91",
"XPNPEP1", "PRKAR2B", "TJP2", "AC092295.7", "ENKUR", "LCN2",
"GFI1B", "ANKRD9", "PRUNE", "SMIM5", "PTPN18", "CD3D", "IL32",
"CD3E", "LDHB", "IL7R", "AES", "CD27", "HES4", "FCGR3A", "RHOC",
"IFITM2", "ABI3", "CLIC1", "RP11-879F14.2", "MEST", "ZHX1-C8ORF76",
"MTURN", "CAPZA2", "MS4A1", "LINC00926", "CD79B", "ISG20", "PKIG"
))
})
test_that("Checking clust_size()", {
expect_equal(clust_size(res), c(`1` = 51L, `2` = 49L, `3` = 45L, `4` = 24L, `5` = 20L, `6` = 18L,
`7` = 14L, `8` = 14L, `9` = 14L, `10` = 12L, `11` = 7L, `12` = 7L,
`13` = 6L, `14` = 5L, `15` = 5L))
})
test_that("Checking gene_cluster()", {
expect_equal(unname(gene_cluster(res)), c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L,
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L, 5L, 5L,
5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 6L, 6L,
6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L,
7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 8L, 8L,
8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 9L, 9L, 9L, 9L,
9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 10L, 10L, 10L, 10L, 10L,
10L, 10L, 10L, 10L, 10L, 10L, 10L, 11L, 11L, 11L, 11L, 11L, 11L,
11L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 13L, 13L, 13L, 13L, 13L,
13L, 14L, 14L, 14L, 14L, 14L, 15L, 15L, 15L, 15L, 15L))
})
# Set verbosity to 0
set_verbosity(0)
load_example_dataset("7871581/files/pbmc3k_medium_clusters")
res <- pbmc3k_medium_clusters
test_that("Checking if get_genes stop if no slot top_genes in ClusterSet obj", {
expect_error(get_genes(res, cluster = "all", top = TRUE))
})
test_that("Checking get_genes is providing the right list of genes", {
# =======================================================
# Test gene list in all cluster
gene_names <- get_genes(res, cluster = "all")
gene_name_to_check <- c("MALAT1", "RPL9", "RPL23A", "RPL21", "RPS25", "RPS19", "RPS3",
"RPS12", "RPL18A", "RPL11", "RPL32", "RPLP2", "RPS18", "RPL3",
"RPL29", "RPL14", "RPS3A", "RPS15A", "RPS23", "RPL27A", "RPS16",
"RPL12", "EEF1A1", "RPL31", "RPS4X", "RPS8", "RPL28", "RPS29",
"RPS10", "RPS13", "RPS11", "RPS26", "RPL35A", "TPT1", "BTG1",
"RPL15", "RPL18", "RPS20", "RPS28", "RPL36", "RPL5", "EEF1B2",
"RPL7A", "RPL17", "NACA", "RPL27", "RPL26", "RPS9", "RPLP1",
"RPSAP58", "RPL6", "PTCRA", "ACRBP", "SDPR", "GNG11", "PF4",
"HIST1H2AC", "TMEM40", "TUBB1", "SPARC", "PPBP", "GP9", "MMD",
"AP001189.4", "CLU", "RGS18", "MPP1", "CA2", "F13A1", "TPM1",
"MYL9", "TREML1", "NGFRAP1", "PTGS1", "GAS2L1", "GRAP2", "ODC1",
"SNCA", "TPM4", "CTSA", "ILK", "PDLIM1", "ACTN1", "FERMT3", "PLA2G12A",
"HIST1H2BK", "SNN", "APP", "YWHAH", "ASAH1", "RAP1B", "MFSD1",
"GSN", "MARCH2", "H2AFJ", "TPTEP1", "PARVB", "MYL12A", "CD151",
"PVALB", "TYMP", "COTL1", "CTSS", "CFD", "S100A11", "LGALS2",
"GABARAP", "APOBEC3A", "TNFSF13B", "CPVL", "MNDA", "CD14", "IGSF6",
"CSTB", "MAFB", "AP2S1", "WARS", "IFI6", "LILRB2", "LILRB4",
"C1orf162", "SLC7A7", "IFNGR2", "SOD2", "TGFBI", "BLVRA", "CAPG",
"BID", "CTSZ", "NAAA", "FCGR2A", "CD300LF", "S100A10", "GAPDH",
"ALDH2", "EIF4EBP1", "GRINA", "NUP214", "CD302", "ATG3", "CAMK1",
"CYBB", "CNPY3", "GCA", "POU2F2", "CCL5", "GZMA", "CST7", "CTSW",
"HLA-C", "FGFBP2", "GZMB", "GNLY", "PRF1", "SPON2", "CCL4", "PTPRCAP",
"CLIC3", "IL2RB", "HOPX", "CD247", "AKR1C3", "IGFBP7", "KLRF1",
"CD99", "CD7", "XCL1", "EFHD2", "PLEK", "HEMGN", "EGFL7", "AC137932.6",
"hsa-mir-1199", "SEC14L5", "HEXIM2", "GATA2", "SH3BGRL2", "KIAA0513",
"PCP2", "PYGL", "DPY19L1", "RAB27B", "CLIC4", "LYL1", "FAM110A",
"RILP", "DAB2", "KIFC3", "BTK", "SPOCD1", "ARHGAP21", "ITGB3",
"ALOX12", "SCFD2", "ATP9A", "FAM212A", "ABCC3", "RP11-359I18.5",
"TGFB1I1", "CTNNAL1", "ENDOD1", "NEXN", "ABHD16A", "ARG2", "GLA",
"WIPI1", "PPP1R14A", "CLEC1B", "CMTM5", "GP1BA", "RP11-367G6.3",
"HIST1H2BD", "FNTB", "SENCR", "SEPT4", "MLH3", "SCGB1C1", "HIST2H2BE",
"C1orf198", "H1F0", "GLUL", "LGALSL", "SMOX", "SSX2IP", "AC147651.3",
"C19orf33", "FAM212B", "SERPINE2", "ZNF778", "TMCC2", "TRIM58",
"FN3K", "NFE2", "MGLL", "MOB3B", "HLA-DPA1", "HLA-DRB1", "HLA-DRA",
"HLA-DRB5", "HLA-DPB1", "CD74", "HLA-DQA1", "HLA-DQB1", "FAM26F",
"LY86", "HLA-DMB", "SLC25A6", "CD37", "RNASET2", "C2orf88", "CLDN5",
"HIST1H2BJ", "FAM63A", "SPHK1", "SLC40A1", "TUBA1C", "TMEM91",
"XPNPEP1", "PRKAR2B", "TJP2", "AC092295.7", "ENKUR", "LCN2",
"GFI1B", "ANKRD9", "PRUNE", "SMIM5", "PTPN18", "CD3D", "IL32",
"CD3E", "LDHB", "IL7R", "AES", "CD27", "HES4", "FCGR3A", "RHOC",
"IFITM2", "ABI3", "CLIC1", "RP11-879F14.2", "MEST", "ZHX1-C8ORF76",
"MTURN", "CAPZA2", "MS4A1", "LINC00926", "CD79B", "ISG20", "PKIG"
)
expect_equal(gene_names, gene_name_to_check)
expect_equal(gene_names, rownames(res@data))
expect_equal(gene_names, unlist(res@gene_clusters, use.names = FALSE))
# =======================================================
# Test gene list in cluster 1
gene_names <- get_genes(res, cluster = 1)
gene_name_to_check <- c("MALAT1", "RPL9", "RPL23A", "RPL21", "RPS25", "RPS19", "RPS3",
"RPS12", "RPL18A", "RPL11", "RPL32", "RPLP2", "RPS18", "RPL3",
"RPL29", "RPL14", "RPS3A", "RPS15A", "RPS23", "RPL27A", "RPS16",
"RPL12", "EEF1A1", "RPL31", "RPS4X", "RPS8", "RPL28", "RPS29",
"RPS10", "RPS13", "RPS11", "RPS26", "RPL35A", "TPT1", "BTG1",
"RPL15", "RPL18", "RPS20", "RPS28", "RPL36", "RPL5", "EEF1B2",
"RPL7A", "RPL17", "NACA", "RPL27", "RPL26", "RPS9", "RPLP1",
"RPSAP58", "RPL6")
expect_equal(gene_names, gene_name_to_check)
expect_equal(gene_names, res@gene_clusters$`1`)
# =======================================================
# Test gene list in cluster 2
gene_names <- get_genes(res, cluster = 2)
gene_name_to_check <- c("PTCRA", "ACRBP", "SDPR", "GNG11", "PF4", "HIST1H2AC", "TMEM40",
"TUBB1", "SPARC", "PPBP", "GP9", "MMD", "AP001189.4", "CLU",
"RGS18", "MPP1", "CA2", "F13A1", "TPM1", "MYL9", "TREML1", "NGFRAP1",
"PTGS1", "GAS2L1", "GRAP2", "ODC1", "SNCA", "TPM4", "CTSA", "ILK",
"PDLIM1", "ACTN1", "FERMT3", "PLA2G12A", "HIST1H2BK", "SNN",
"APP", "YWHAH", "ASAH1", "RAP1B", "MFSD1", "GSN", "MARCH2", "H2AFJ",
"TPTEP1", "PARVB", "MYL12A", "CD151", "PVALB")
expect_equal(gene_names, gene_name_to_check)
expect_equal(gene_names, res@gene_clusters$`2`)
# =======================================================
# Test gene list in cluster 3
gene_names <- get_genes(res, cluster = 3)
gene_name_to_check <- c("TYMP", "COTL1", "CTSS", "CFD", "S100A11", "LGALS2", "GABARAP",
"APOBEC3A", "TNFSF13B", "CPVL", "MNDA", "CD14", "IGSF6", "CSTB",
"MAFB", "AP2S1", "WARS", "IFI6", "LILRB2", "LILRB4", "C1orf162",
"SLC7A7", "IFNGR2", "SOD2", "TGFBI", "BLVRA", "CAPG", "BID",
"CTSZ", "NAAA", "FCGR2A", "CD300LF", "S100A10", "GAPDH", "ALDH2",
"EIF4EBP1", "GRINA", "NUP214", "CD302", "ATG3", "CAMK1", "CYBB",
"CNPY3", "GCA", "POU2F2")
expect_equal(gene_names, gene_name_to_check)
expect_equal(gene_names, res@gene_clusters$`3`)
})
test_that("Checking get_genes using top genes.", {
res <- top_genes(res, top = 20, cluster = "all")
# =======================================================
# Test top gene list in all cluster
gene_names <- get_genes(res, cluster = "all", top = T)
gene_name_to_check <- c("RPL11", "RPL32", "RPS12", "RPL18A", "RPS18", "RPS23", "RPS16",
"RPL9", "RPL23A", "RPS3", "RPL12", "RPS15A", "RPLP2", "RPL28",
"RPS19", "RPS25", "EEF1A1", "RPS8", "RPS4X", "RPL29", "SDPR",
"GNG11", "PF4", "SPARC", "PPBP", "TUBB1", "HIST1H2AC", "GP9",
"CLU", "AP001189.4", "RGS18", "PTCRA", "TREML1", "F13A1", "CA2",
"TMEM40", "MMD", "MYL9", "PTGS1", "MPP1", "TYMP", "COTL1", "CTSS",
"S100A11", "CFD", "LGALS2", "GABARAP", "TNFSF13B", "APOBEC3A",
"AP2S1", "IGSF6", "CSTB", "CPVL", "MAFB", "IFI6", "SLC7A7", "TGFBI",
"C1orf162", "CAPG", "BLVRA", "GZMB", "PRF1", "GNLY", "FGFBP2",
"GZMA", "CST7", "CCL4", "SPON2", "CTSW", "CLIC3", "CD247", "IL2RB",
"HOPX", "HLA-C", "CD7", "AKR1C3", "KLRF1", "XCL1", "IGFBP7",
"CCL5", "AC137932.6", "HEMGN", "hsa-mir-1199", "EGFL7", "SEC14L5",
"GATA2", "DPY19L1", "HEXIM2", "PCP2", "KIFC3", "RAB27B", "SH3BGRL2",
"KIAA0513", "DAB2", "RILP", "CLIC4", "PYGL", "FAM110A", "BTK",
"LYL1", "ARHGAP21", "SPOCD1", "ATP9A", "FAM212A", "CTNNAL1",
"ABCC3", "SCFD2", "ARG2", "ITGB3", "ALOX12", "ENDOD1", "NEXN",
"RP11-359I18.5", "TGFB1I1", "ABHD16A", "GLA", "WIPI1", "PPP1R14A",
"CLEC1B", "GP1BA", "CMTM5", "SCGB1C1", "HIST1H2BD", "RP11-367G6.3",
"FNTB", "SEPT4", "SENCR", "C1orf198", "MLH3", "HIST2H2BE", "GLUL",
"H1F0", "LGALSL", "SMOX", "SSX2IP", "FAM212B", "AC147651.3",
"TMCC2", "ZNF778", "SERPINE2", "TRIM58", "MOB3B", "NFE2", "C19orf33",
"MGLL", "FN3K", "HLA-DRB1", "HLA-DRA", "HLA-DPA1", "HLA-DRB5",
"HLA-DPB1", "CD74", "HLA-DQA1", "HLA-DQB1", "LY86", "HLA-DMB",
"FAM26F", "CD37", "RNASET2", "SLC25A6", "HIST1H2BJ", "CLDN5",
"C2orf88", "FAM63A", "TUBA1C", "SLC40A1", "SPHK1", "TMEM91",
"PRKAR2B", "TJP2", "AC092295.7", "XPNPEP1", "ENKUR", "LCN2",
"GFI1B", "ANKRD9", "PRUNE", "SMIM5", "PTPN18", "CD3D", "IL32",
"LDHB", "CD3E", "IL7R", "CD27", "AES", "FCGR3A", "RHOC", "IFITM2",
"ABI3", "HES4", "CLIC1", "RP11-879F14.2", "ZHX1-C8ORF76", "MTURN",
"MEST", "CAPZA2", "LINC00926", "CD79B", "MS4A1", "ISG20", "PKIG"
)
expect_equal(gene_names, gene_name_to_check)
expect_equal(sort(gene_names), sort(unlist(res@top_genes, use.names = F)))
# =======================================================
# Test top gene list in cluster 1
gene_names <- get_genes(res, cluster = 1, top = T)
gene_name_to_check <- c("RPL11", "RPL32", "RPS12", "RPL18A", "RPS18", "RPS23", "RPS16",
"RPL9", "RPL23A", "RPS3", "RPL12", "RPS15A", "RPLP2", "RPL28",
"RPS19", "RPS25", "EEF1A1", "RPS8", "RPS4X", "RPL29")
expect_equal(gene_names, gene_name_to_check)
expect_equal(sort(gene_names), sort(res@top_genes$`1`))
# =======================================================
# Test top gene list in cluster 2 and 3
gene_names <- get_genes(res, cluster = 2:3, top = T)
gene_name_to_check <- c("SDPR", "GNG11", "PF4", "SPARC", "PPBP", "TUBB1", "HIST1H2AC",
"GP9", "CLU", "AP001189.4", "RGS18", "PTCRA", "TREML1", "F13A1",
"CA2", "TMEM40", "MMD", "MYL9", "PTGS1", "MPP1", "TYMP", "COTL1",
"CTSS", "S100A11", "CFD", "LGALS2", "GABARAP", "TNFSF13B", "APOBEC3A",
"AP2S1", "IGSF6", "CSTB", "CPVL", "MAFB", "IFI6", "SLC7A7", "TGFBI",
"C1orf162", "CAPG", "BLVRA")
expect_equal(gene_names, gene_name_to_check)
expect_equal(sort(gene_names), sort(c(
res@top_genes$`2`,
res@top_genes$`3`
)))
})
set_verbosity(0)
load_example_dataset('7871581/files/pbmc3k_medium_clusters')
set_verbosity(0)
load_example_dataset('7871581/files/pbmc3k_medium_clusters')
test_that("Check cluster_set_to_xls", {
tp_dir <- file.path(tempdir(), create_rand_str())
dir.create(tp_dir, showWarnings = F, recursive = TRUE)
f_path <- file.path(tp_dir, "test.xls")
unlink(f_path)
cluster_set_to_xls(pbmc3k_medium_clusters, f_path)
testthat::expect_true(file.exists(f_path))
testthat::expect_error(cluster_set_to_xls(pbmc3k_medium_clusters, f_path))
tp_dir <- file.path(tempdir(), create_rand_str())
dir.create(tp_dir, showWarnings = F, recursive = TRUE)
f_path <- file.path(tp_dir, "test.xls")
unlink(f_path)
cluster_set_to_xls(pbmc3k_medium_clusters, f_path)
testthat::expect_true(file.exists(f_path))
testthat::expect_error(cluster_set_to_xls(pbmc3k_medium_clusters, f_path))
})
test_that("Checking gene_cluster() is working...", {
# Set verbosity to 0
set_verbosity(0)
load_example_dataset("7871581/files/pbmc3k_medium_clusters")
res <- pbmc3k_medium_clusters
expect_equal(length(gene_cluster(res)), 291)
expect_equal(paste0(table(gene_cluster(res)), collapse = " "), "51 49 45 24 20 18 14 14 14 12 7 7 6 5 5")
expect_equal(as.vector(table(gene_cluster(res, cluster = 1))), 51)
expect_equal(as.vector(table(gene_cluster(res, cluster = 2))), 49)
expect_equal(as.vector(table(gene_cluster(res, cluster = 3))), 45)
expect_equal(as.vector(table(gene_cluster(res, cluster = 4))), 24)
expect_equal(as.vector(table(gene_cluster(res, cluster = c(1,4)))), c(51, 24))
expect_equal(as.vector(table(gene_cluster(res, cluster = c(4,4)))), 24)
expect_error(gene_cluster(res, cluster = c(-1,8)))
expect_error(gene_cluster(res, cluster = c(0,9)))
expect_error(gene_cluster(res, cluster = c(0:8)))
expect_error(gene_cluster(res, cluster = c(1,40)))
expect_equal(paste0(res@gene_clusters[[1]], collapse = " "),
paste0(names(gene_cluster(res, cluster = 1)), collapse = " "))
expect_equal(paste0(unlist(res@gene_clusters[1:2]), collapse = " "),
paste0(names(gene_cluster(res, cluster = 1:2)), collapse = " "))
expect_equal(paste0(unlist(res@gene_clusters[1:4]), collapse = " "),
paste0(names(gene_cluster(res, cluster = 1:4)), collapse = " "))
})
dputhier/scigenex documentation built on May 31, 2024, 8:59 a.m.
R Package Documentation
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library(testthat)
testthat::test_that("Test the indexing operator of the ClusterSet", {
clusters <- 1:5
cluster_size <- c(12,10,8,6,4)
m <- matrix(rnorm(20000), nc=500, nr=40)
colnames(m) <- paste0("S_", 1:500)
gn <- paste0("G_", 1:40)
cls <- unlist(mapply(rep, clusters, cluster_size))
gene_cluster <- split(gn, cls)
rownames(m) <- paste0("G_", 1:40)
cls <- unlist(mapply(rep, clusters, cluster_size))
gene_clusters_metadata <- list()
gene_clusters_metadata$cluster_id <- as.numeric(names(gene_cluster))
gene_clusters_metadata$number <- length(clusters)
gene_clusters_metadata$size <- cluster_size
names(gene_clusters_metadata$size) <- clusters
gene_cluster_annotations <- list()
top_genes <- lapply(gene_cluster, "[", 1:3)
dbf_output <- list()
dbf_output$dknn <- runif(1000)
dbf_output$simulated_dknn <- runif(1000)
dbf_output$critical_distance <- 0.5
dbf_output$fdr <- 0.05
dbf_output$center <- do.call(rbind,
lapply(split.data.frame(as.data.frame(m),
as.factor(cls)),
apply, 2, mean))
colnames(dbf_output$center) <- colnames(m)
rownames(dbf_output$center) <- names(gene_cluster)
res <- new("ClusterSet",
data = m,
gene_clusters = split(gn, cls),
top_genes = top_genes,
gene_clusters_metadata = gene_clusters_metadata,
gene_cluster_annotations = gene_cluster_annotations,
cells_metadata = data.frame(cells_barcode=colnames(m),
row.names = colnames(m)),
dbf_output = dbf_output,
parameters = list(filename="oP0H7t6Sc0", distance_method="pearson",
k=50, inflation=2, noise_level=0.3, fdr=0.05,
min_nb_supporting_cell=0, min_pct_gene_expressed=40,
min_cluster_size=10, row_sum=-Inf, seed=123)
)
testthat::expect_equal(dim(res[1:3,4:5]), c(30, 2))
testthat::expect_equal(dim(res[c(2,4),1:5]), c(16, 5))
testthat::expect_equal(length(res[c(2,4),1:5]@gene_clusters), 2)
testthat::expect_equal(length(res[c(2,4),1:5]@gene_clusters), 2)
testthat::expect_equal(length(res[c(1,2,4),]@gene_clusters), 3)
testthat::expect_equal(dim(res[logical(), logical()]), c(0,0))
testthat::expect_equal(dim(res[c("1", "2"), ]), c(22, 500))
testthat::expect_equal(res[c("1", "2"), ]@gene_clusters_metadata$number, 2)
testthat::expect_equal(res[2:4, ]@gene_clusters_metadata$number, 3)
testthat::expect_equal(res[c("1", "2", "3"), ]@gene_clusters_metadata$number, 3)
testthat::expect_equal(res[logical(), ]@gene_clusters_metadata$number, 0)
testthat::expect_equal(dim(res[, ]), c(40, 500))
testthat::expect_equal(dim(res[, 10:20]), c(40, 11))
testthat::expect_equal(dim(res[1:3, 10:20]@cells_metadata), c(11, 1))
testthat::expect_equal(dim(res[1:3, 10:20]@cells_metadata), c(11, 1))
testthat::expect_equal(dim(res[1, 1]@cells_metadata), c(1, 1))
testthat::expect_equal(dim(res[1, 1]), c(12, 1))
testthat::expect_equal(length(res[1:2, 1]@top_genes), 2)
testthat::expect_equal(length(res[1:2, c()]@top_genes), 2)
testthat::expect_identical(res[c(1, 3), ], res[c(1, 3), seq_len(ncol(res))])
testthat::expect_identical(res[, c("S_408", "S_409")], res[, c(408, 409)])
testthat::expect_identical(res[c(1, 3), c("S_3", "S_4")], res[c(1, 3), 3:4])
testthat::expect_identical(res[-c(1, 2), ], res[c(3:nclust(res)), ])
testthat::expect_identical(res[as.character(2:5), c("S_3", "S_4")], res[2:5, 3:4])
testthat::expect_identical(res[as.character(2:5), ], res[2:5, ])
testthat::expect_identical(res[,paste0("S_",2:5)], res[,2:5])
testthat::expect_identical(res[c("2", "4"), ]@gene_clusters, res[c(2, 4), ]@gene_clusters)
testthat::expect_identical(res[c("1", "3"), ]@gene_clusters_metadata$number, res[c(1, 3), ]@gene_clusters_metadata$number)
testthat::expect_identical(res[3, ]@gene_clusters_metadata, res["3", ]@gene_clusters_metadata)
testthat::expect_error(res["a", "b"])
})
test_that("Test messages when looking at ClusterSet object", {
obj <- new("ClusterSet")
msg_clusterset <- capture.output(obj)
expect_equal(msg_clusterset[1], "\t\tAn object of class ClusterSet")
expect_equal(msg_clusterset[2], "\t\tName: ")
expect_equal(msg_clusterset[3], "\t\tMemory used: 2520 ")
expect_equal(msg_clusterset[4], "\t\tNumber of cells: 0 ")
expect_equal(msg_clusterset[5], "\t\tNumber of informative genes: 0 ")
expect_equal(msg_clusterset[6], "\t\tNumber of gene clusters: ")
expect_equal(msg_clusterset[7], "\t\tThis object contains the following informations:")
expect_equal(msg_clusterset[8], "\t\t\t - data ")
expect_equal(msg_clusterset[9], "\t\t\t - gene_clusters ")
expect_equal(msg_clusterset[10], "\t\t\t - top_genes ")
expect_equal(msg_clusterset[11], "\t\t\t - gene_clusters_metadata ")
expect_equal(msg_clusterset[12], "\t\t\t - gene_cluster_annotations ")
expect_equal(msg_clusterset[13], "\t\t\t - cells_metadata ")
expect_equal(msg_clusterset[14], "\t\t\t - dbf_output ")
expect_equal(msg_clusterset[15], "\t\t\t - parameters ")
})
set_verbosity(0)
load_example_dataset("7871581/files/pbmc3k_medium_clusters")
test_that("Check clust_names() is working.", {
a <- unique(unname(gene_cluster(pbmc3k_medium_clusters)))
b <- clust_names(pbmc3k_medium_clusters)
expect_true(all(as.character(a)==b))
})
test_that("Check clust_names() is working.", {
a <- show_methods()
expect_true(all(c("[", "clust_names", "clust_size", "cluster_stats", "col_names",
"dim", "enrich_go", "gene_cluster", "nclust", "rename_clust",
"row_names", "show", "top_genes", "viz_enrich", "which_clust") %in% a))
})# Set verbosity to 0
set_verbosity(0)
library(Seurat)
load_example_dataset("7871581/files/pbmc3k_medium_clusters")
load_example_dataset("7871581/files/pbmc3k_medium")
gn <- pbmc3k_medium_clusters
test_that("Check 'rename' is working.", {
expect_true(nclust(rename_clust(gn, 1:nclust(gn))) == nclust(gn))
expect_true(all(names(rename_clust(gn, nclust(gn):1)@gene_clusters) == 15:1))
rn <- rename_clust(gn, letters[1:nclust(gn)])
expect_true(ggplot2::is.ggplot(plot_profiles(rn, ident = Seurat::Idents(pbmc3k_medium))))
})
set_verbosity(0)
library(Seurat)
load_example_dataset("7871581/files/pbmc3k_medium_clusters")
res <- pbmc3k_medium_clusters
test_that("Check 'which_clust' is working.", {
expect_true(all(which_clust(res, c('APOBEC3A', 'RPL11', 'PF4')) == c(3,1,2)))
expect_true(all(is.na(which_clust(res, c('APOBEC3A', 'RPL11', 'bla'))) == c(F,F,T)))
})
set_verbosity(0)
load_example_dataset("7871581/files/pbmc3k_medium_clusters")
test_that("Check clust_names() is working.", {
a <- unique(unname(gene_cluster(pbmc3k_medium_clusters)))
b <- clust_names(pbmc3k_medium_clusters)
expect_true(all(as.character(a)==b))
})
# Set verbosity to 0
set_verbosity(0)
load_example_dataset("7871581/files/pbmc3k_medium_clusters")
res <- pbmc3k_medium_clusters
test_that("Checking ncol()", {
expect_equal(ncol(res), 361)
})
test_that("Checking nrow()", {
expect_equal(nrow(res), 291)
})
test_that("Checking dim()", {
expect_equal(dim(res), c(291, 361))
})
test_that("Checking colnames()", {
expect_equal(col_names(res)[1:10], c("GATCTACTGGTGAG-1", "ACAGTGACTCACCC-1", "AGACGTACAGAGGC-1",
"GACGTAACCTGTGA-1", "TATACAGATCCAGA-1", "CGGATAACAGCTCA-1", "TTACCATGGTTGAC-1",
"TCCCACGATCATTC-1", "ATAGCGTGCAGATC-1", "TGTAGGTGTGCTGA-1"))
expect_equal(tail(col_names(res)), c("GGCATATGGGGAGT-1", "TTACGTACGTTCAG-1", "GGAACACTTCAGAC-1",
"ATCATCTGACACCA-1", "ACGAACTGGCTATG-1", "TAACACCTTGTTTC-1"))
})
test_that("Checking rownames()", {
expect_equal(row_names(res), c("MALAT1", "RPL9", "RPL23A", "RPL21", "RPS25", "RPS19", "RPS3",
"RPS12", "RPL18A", "RPL11", "RPL32", "RPLP2", "RPS18", "RPL3",
"RPL29", "RPL14", "RPS3A", "RPS15A", "RPS23", "RPL27A", "RPS16",
"RPL12", "EEF1A1", "RPL31", "RPS4X", "RPS8", "RPL28", "RPS29",
"RPS10", "RPS13", "RPS11", "RPS26", "RPL35A", "TPT1", "BTG1",
"RPL15", "RPL18", "RPS20", "RPS28", "RPL36", "RPL5", "EEF1B2",
"RPL7A", "RPL17", "NACA", "RPL27", "RPL26", "RPS9", "RPLP1",
"RPSAP58", "RPL6", "PTCRA", "ACRBP", "SDPR", "GNG11", "PF4",
"HIST1H2AC", "TMEM40", "TUBB1", "SPARC", "PPBP", "GP9", "MMD",
"AP001189.4", "CLU", "RGS18", "MPP1", "CA2", "F13A1", "TPM1",
"MYL9", "TREML1", "NGFRAP1", "PTGS1", "GAS2L1", "GRAP2", "ODC1",
"SNCA", "TPM4", "CTSA", "ILK", "PDLIM1", "ACTN1", "FERMT3", "PLA2G12A",
"HIST1H2BK", "SNN", "APP", "YWHAH", "ASAH1", "RAP1B", "MFSD1",
"GSN", "MARCH2", "H2AFJ", "TPTEP1", "PARVB", "MYL12A", "CD151",
"PVALB", "TYMP", "COTL1", "CTSS", "CFD", "S100A11", "LGALS2",
"GABARAP", "APOBEC3A", "TNFSF13B", "CPVL", "MNDA", "CD14", "IGSF6",
"CSTB", "MAFB", "AP2S1", "WARS", "IFI6", "LILRB2", "LILRB4",
"C1orf162", "SLC7A7", "IFNGR2", "SOD2", "TGFBI", "BLVRA", "CAPG",
"BID", "CTSZ", "NAAA", "FCGR2A", "CD300LF", "S100A10", "GAPDH",
"ALDH2", "EIF4EBP1", "GRINA", "NUP214", "CD302", "ATG3", "CAMK1",
"CYBB", "CNPY3", "GCA", "POU2F2", "CCL5", "GZMA", "CST7", "CTSW",
"HLA-C", "FGFBP2", "GZMB", "GNLY", "PRF1", "SPON2", "CCL4", "PTPRCAP",
"CLIC3", "IL2RB", "HOPX", "CD247", "AKR1C3", "IGFBP7", "KLRF1",
"CD99", "CD7", "XCL1", "EFHD2", "PLEK", "HEMGN", "EGFL7", "AC137932.6",
"hsa-mir-1199", "SEC14L5", "HEXIM2", "GATA2", "SH3BGRL2", "KIAA0513",
"PCP2", "PYGL", "DPY19L1", "RAB27B", "CLIC4", "LYL1", "FAM110A",
"RILP", "DAB2", "KIFC3", "BTK", "SPOCD1", "ARHGAP21", "ITGB3",
"ALOX12", "SCFD2", "ATP9A", "FAM212A", "ABCC3", "RP11-359I18.5",
"TGFB1I1", "CTNNAL1", "ENDOD1", "NEXN", "ABHD16A", "ARG2", "GLA",
"WIPI1", "PPP1R14A", "CLEC1B", "CMTM5", "GP1BA", "RP11-367G6.3",
"HIST1H2BD", "FNTB", "SENCR", "SEPT4", "MLH3", "SCGB1C1", "HIST2H2BE",
"C1orf198", "H1F0", "GLUL", "LGALSL", "SMOX", "SSX2IP", "AC147651.3",
"C19orf33", "FAM212B", "SERPINE2", "ZNF778", "TMCC2", "TRIM58",
"FN3K", "NFE2", "MGLL", "MOB3B", "HLA-DPA1", "HLA-DRB1", "HLA-DRA",
"HLA-DRB5", "HLA-DPB1", "CD74", "HLA-DQA1", "HLA-DQB1", "FAM26F",
"LY86", "HLA-DMB", "SLC25A6", "CD37", "RNASET2", "C2orf88", "CLDN5",
"HIST1H2BJ", "FAM63A", "SPHK1", "SLC40A1", "TUBA1C", "TMEM91",
"XPNPEP1", "PRKAR2B", "TJP2", "AC092295.7", "ENKUR", "LCN2",
"GFI1B", "ANKRD9", "PRUNE", "SMIM5", "PTPN18", "CD3D", "IL32",
"CD3E", "LDHB", "IL7R", "AES", "CD27", "HES4", "FCGR3A", "RHOC",
"IFITM2", "ABI3", "CLIC1", "RP11-879F14.2", "MEST", "ZHX1-C8ORF76",
"MTURN", "CAPZA2", "MS4A1", "LINC00926", "CD79B", "ISG20", "PKIG"
))
})
test_that("Checking clust_size()", {
expect_equal(clust_size(res), c(`1` = 51L, `2` = 49L, `3` = 45L, `4` = 24L, `5` = 20L, `6` = 18L,
`7` = 14L, `8` = 14L, `9` = 14L, `10` = 12L, `11` = 7L, `12` = 7L,
`13` = 6L, `14` = 5L, `15` = 5L))
})
test_that("Checking gene_cluster()", {
expect_equal(unname(gene_cluster(res)), c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L,
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L, 5L, 5L,
5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 6L, 6L,
6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L,
7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 8L, 8L,
8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 9L, 9L, 9L, 9L,
9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 10L, 10L, 10L, 10L, 10L,
10L, 10L, 10L, 10L, 10L, 10L, 10L, 11L, 11L, 11L, 11L, 11L, 11L,
11L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 13L, 13L, 13L, 13L, 13L,
13L, 14L, 14L, 14L, 14L, 14L, 15L, 15L, 15L, 15L, 15L))
})
# Set verbosity to 0
set_verbosity(0)
load_example_dataset("7871581/files/pbmc3k_medium_clusters")
res <- pbmc3k_medium_clusters
test_that("Checking if get_genes stop if no slot top_genes in ClusterSet obj", {
expect_error(get_genes(res, cluster = "all", top = TRUE))
})
test_that("Checking get_genes is providing the right list of genes", {
# =======================================================
# Test gene list in all cluster
gene_names <- get_genes(res, cluster = "all")
gene_name_to_check <- c("MALAT1", "RPL9", "RPL23A", "RPL21", "RPS25", "RPS19", "RPS3",
"RPS12", "RPL18A", "RPL11", "RPL32", "RPLP2", "RPS18", "RPL3",
"RPL29", "RPL14", "RPS3A", "RPS15A", "RPS23", "RPL27A", "RPS16",
"RPL12", "EEF1A1", "RPL31", "RPS4X", "RPS8", "RPL28", "RPS29",
"RPS10", "RPS13", "RPS11", "RPS26", "RPL35A", "TPT1", "BTG1",
"RPL15", "RPL18", "RPS20", "RPS28", "RPL36", "RPL5", "EEF1B2",
"RPL7A", "RPL17", "NACA", "RPL27", "RPL26", "RPS9", "RPLP1",
"RPSAP58", "RPL6", "PTCRA", "ACRBP", "SDPR", "GNG11", "PF4",
"HIST1H2AC", "TMEM40", "TUBB1", "SPARC", "PPBP", "GP9", "MMD",
"AP001189.4", "CLU", "RGS18", "MPP1", "CA2", "F13A1", "TPM1",
"MYL9", "TREML1", "NGFRAP1", "PTGS1", "GAS2L1", "GRAP2", "ODC1",
"SNCA", "TPM4", "CTSA", "ILK", "PDLIM1", "ACTN1", "FERMT3", "PLA2G12A",
"HIST1H2BK", "SNN", "APP", "YWHAH", "ASAH1", "RAP1B", "MFSD1",
"GSN", "MARCH2", "H2AFJ", "TPTEP1", "PARVB", "MYL12A", "CD151",
"PVALB", "TYMP", "COTL1", "CTSS", "CFD", "S100A11", "LGALS2",
"GABARAP", "APOBEC3A", "TNFSF13B", "CPVL", "MNDA", "CD14", "IGSF6",
"CSTB", "MAFB", "AP2S1", "WARS", "IFI6", "LILRB2", "LILRB4",
"C1orf162", "SLC7A7", "IFNGR2", "SOD2", "TGFBI", "BLVRA", "CAPG",
"BID", "CTSZ", "NAAA", "FCGR2A", "CD300LF", "S100A10", "GAPDH",
"ALDH2", "EIF4EBP1", "GRINA", "NUP214", "CD302", "ATG3", "CAMK1",
"CYBB", "CNPY3", "GCA", "POU2F2", "CCL5", "GZMA", "CST7", "CTSW",
"HLA-C", "FGFBP2", "GZMB", "GNLY", "PRF1", "SPON2", "CCL4", "PTPRCAP",
"CLIC3", "IL2RB", "HOPX", "CD247", "AKR1C3", "IGFBP7", "KLRF1",
"CD99", "CD7", "XCL1", "EFHD2", "PLEK", "HEMGN", "EGFL7", "AC137932.6",
"hsa-mir-1199", "SEC14L5", "HEXIM2", "GATA2", "SH3BGRL2", "KIAA0513",
"PCP2", "PYGL", "DPY19L1", "RAB27B", "CLIC4", "LYL1", "FAM110A",
"RILP", "DAB2", "KIFC3", "BTK", "SPOCD1", "ARHGAP21", "ITGB3",
"ALOX12", "SCFD2", "ATP9A", "FAM212A", "ABCC3", "RP11-359I18.5",
"TGFB1I1", "CTNNAL1", "ENDOD1", "NEXN", "ABHD16A", "ARG2", "GLA",
"WIPI1", "PPP1R14A", "CLEC1B", "CMTM5", "GP1BA", "RP11-367G6.3",
"HIST1H2BD", "FNTB", "SENCR", "SEPT4", "MLH3", "SCGB1C1", "HIST2H2BE",
"C1orf198", "H1F0", "GLUL", "LGALSL", "SMOX", "SSX2IP", "AC147651.3",
"C19orf33", "FAM212B", "SERPINE2", "ZNF778", "TMCC2", "TRIM58",
"FN3K", "NFE2", "MGLL", "MOB3B", "HLA-DPA1", "HLA-DRB1", "HLA-DRA",
"HLA-DRB5", "HLA-DPB1", "CD74", "HLA-DQA1", "HLA-DQB1", "FAM26F",
"LY86", "HLA-DMB", "SLC25A6", "CD37", "RNASET2", "C2orf88", "CLDN5",
"HIST1H2BJ", "FAM63A", "SPHK1", "SLC40A1", "TUBA1C", "TMEM91",
"XPNPEP1", "PRKAR2B", "TJP2", "AC092295.7", "ENKUR", "LCN2",
"GFI1B", "ANKRD9", "PRUNE", "SMIM5", "PTPN18", "CD3D", "IL32",
"CD3E", "LDHB", "IL7R", "AES", "CD27", "HES4", "FCGR3A", "RHOC",
"IFITM2", "ABI3", "CLIC1", "RP11-879F14.2", "MEST", "ZHX1-C8ORF76",
"MTURN", "CAPZA2", "MS4A1", "LINC00926", "CD79B", "ISG20", "PKIG"
)
expect_equal(gene_names, gene_name_to_check)
expect_equal(gene_names, rownames(res@data))
expect_equal(gene_names, unlist(res@gene_clusters, use.names = FALSE))
# =======================================================
# Test gene list in cluster 1
gene_names <- get_genes(res, cluster = 1)
gene_name_to_check <- c("MALAT1", "RPL9", "RPL23A", "RPL21", "RPS25", "RPS19", "RPS3",
"RPS12", "RPL18A", "RPL11", "RPL32", "RPLP2", "RPS18", "RPL3",
"RPL29", "RPL14", "RPS3A", "RPS15A", "RPS23", "RPL27A", "RPS16",
"RPL12", "EEF1A1", "RPL31", "RPS4X", "RPS8", "RPL28", "RPS29",
"RPS10", "RPS13", "RPS11", "RPS26", "RPL35A", "TPT1", "BTG1",
"RPL15", "RPL18", "RPS20", "RPS28", "RPL36", "RPL5", "EEF1B2",
"RPL7A", "RPL17", "NACA", "RPL27", "RPL26", "RPS9", "RPLP1",
"RPSAP58", "RPL6")
expect_equal(gene_names, gene_name_to_check)
expect_equal(gene_names, res@gene_clusters$`1`)
# =======================================================
# Test gene list in cluster 2
gene_names <- get_genes(res, cluster = 2)
gene_name_to_check <- c("PTCRA", "ACRBP", "SDPR", "GNG11", "PF4", "HIST1H2AC", "TMEM40",
"TUBB1", "SPARC", "PPBP", "GP9", "MMD", "AP001189.4", "CLU",
"RGS18", "MPP1", "CA2", "F13A1", "TPM1", "MYL9", "TREML1", "NGFRAP1",
"PTGS1", "GAS2L1", "GRAP2", "ODC1", "SNCA", "TPM4", "CTSA", "ILK",
"PDLIM1", "ACTN1", "FERMT3", "PLA2G12A", "HIST1H2BK", "SNN",
"APP", "YWHAH", "ASAH1", "RAP1B", "MFSD1", "GSN", "MARCH2", "H2AFJ",
"TPTEP1", "PARVB", "MYL12A", "CD151", "PVALB")
expect_equal(gene_names, gene_name_to_check)
expect_equal(gene_names, res@gene_clusters$`2`)
# =======================================================
# Test gene list in cluster 3
gene_names <- get_genes(res, cluster = 3)
gene_name_to_check <- c("TYMP", "COTL1", "CTSS", "CFD", "S100A11", "LGALS2", "GABARAP",
"APOBEC3A", "TNFSF13B", "CPVL", "MNDA", "CD14", "IGSF6", "CSTB",
"MAFB", "AP2S1", "WARS", "IFI6", "LILRB2", "LILRB4", "C1orf162",
"SLC7A7", "IFNGR2", "SOD2", "TGFBI", "BLVRA", "CAPG", "BID",
"CTSZ", "NAAA", "FCGR2A", "CD300LF", "S100A10", "GAPDH", "ALDH2",
"EIF4EBP1", "GRINA", "NUP214", "CD302", "ATG3", "CAMK1", "CYBB",
"CNPY3", "GCA", "POU2F2")
expect_equal(gene_names, gene_name_to_check)
expect_equal(gene_names, res@gene_clusters$`3`)
})
test_that("Checking get_genes using top genes.", {
res <- top_genes(res, top = 20, cluster = "all")
# =======================================================
# Test top gene list in all cluster
gene_names <- get_genes(res, cluster = "all", top = T)
gene_name_to_check <- c("RPL11", "RPL32", "RPS12", "RPL18A", "RPS18", "RPS23", "RPS16",
"RPL9", "RPL23A", "RPS3", "RPL12", "RPS15A", "RPLP2", "RPL28",
"RPS19", "RPS25", "EEF1A1", "RPS8", "RPS4X", "RPL29", "SDPR",
"GNG11", "PF4", "SPARC", "PPBP", "TUBB1", "HIST1H2AC", "GP9",
"CLU", "AP001189.4", "RGS18", "PTCRA", "TREML1", "F13A1", "CA2",
"TMEM40", "MMD", "MYL9", "PTGS1", "MPP1", "TYMP", "COTL1", "CTSS",
"S100A11", "CFD", "LGALS2", "GABARAP", "TNFSF13B", "APOBEC3A",
"AP2S1", "IGSF6", "CSTB", "CPVL", "MAFB", "IFI6", "SLC7A7", "TGFBI",
"C1orf162", "CAPG", "BLVRA", "GZMB", "PRF1", "GNLY", "FGFBP2",
"GZMA", "CST7", "CCL4", "SPON2", "CTSW", "CLIC3", "CD247", "IL2RB",
"HOPX", "HLA-C", "CD7", "AKR1C3", "KLRF1", "XCL1", "IGFBP7",
"CCL5", "AC137932.6", "HEMGN", "hsa-mir-1199", "EGFL7", "SEC14L5",
"GATA2", "DPY19L1", "HEXIM2", "PCP2", "KIFC3", "RAB27B", "SH3BGRL2",
"KIAA0513", "DAB2", "RILP", "CLIC4", "PYGL", "FAM110A", "BTK",
"LYL1", "ARHGAP21", "SPOCD1", "ATP9A", "FAM212A", "CTNNAL1",
"ABCC3", "SCFD2", "ARG2", "ITGB3", "ALOX12", "ENDOD1", "NEXN",
"RP11-359I18.5", "TGFB1I1", "ABHD16A", "GLA", "WIPI1", "PPP1R14A",
"CLEC1B", "GP1BA", "CMTM5", "SCGB1C1", "HIST1H2BD", "RP11-367G6.3",
"FNTB", "SEPT4", "SENCR", "C1orf198", "MLH3", "HIST2H2BE", "GLUL",
"H1F0", "LGALSL", "SMOX", "SSX2IP", "FAM212B", "AC147651.3",
"TMCC2", "ZNF778", "SERPINE2", "TRIM58", "MOB3B", "NFE2", "C19orf33",
"MGLL", "FN3K", "HLA-DRB1", "HLA-DRA", "HLA-DPA1", "HLA-DRB5",
"HLA-DPB1", "CD74", "HLA-DQA1", "HLA-DQB1", "LY86", "HLA-DMB",
"FAM26F", "CD37", "RNASET2", "SLC25A6", "HIST1H2BJ", "CLDN5",
"C2orf88", "FAM63A", "TUBA1C", "SLC40A1", "SPHK1", "TMEM91",
"PRKAR2B", "TJP2", "AC092295.7", "XPNPEP1", "ENKUR", "LCN2",
"GFI1B", "ANKRD9", "PRUNE", "SMIM5", "PTPN18", "CD3D", "IL32",
"LDHB", "CD3E", "IL7R", "CD27", "AES", "FCGR3A", "RHOC", "IFITM2",
"ABI3", "HES4", "CLIC1", "RP11-879F14.2", "ZHX1-C8ORF76", "MTURN",
"MEST", "CAPZA2", "LINC00926", "CD79B", "MS4A1", "ISG20", "PKIG"
)
expect_equal(gene_names, gene_name_to_check)
expect_equal(sort(gene_names), sort(unlist(res@top_genes, use.names = F)))
# =======================================================
# Test top gene list in cluster 1
gene_names <- get_genes(res, cluster = 1, top = T)
gene_name_to_check <- c("RPL11", "RPL32", "RPS12", "RPL18A", "RPS18", "RPS23", "RPS16",
"RPL9", "RPL23A", "RPS3", "RPL12", "RPS15A", "RPLP2", "RPL28",
"RPS19", "RPS25", "EEF1A1", "RPS8", "RPS4X", "RPL29")
expect_equal(gene_names, gene_name_to_check)
expect_equal(sort(gene_names), sort(res@top_genes$`1`))
# =======================================================
# Test top gene list in cluster 2 and 3
gene_names <- get_genes(res, cluster = 2:3, top = T)
gene_name_to_check <- c("SDPR", "GNG11", "PF4", "SPARC", "PPBP", "TUBB1", "HIST1H2AC",
"GP9", "CLU", "AP001189.4", "RGS18", "PTCRA", "TREML1", "F13A1",
"CA2", "TMEM40", "MMD", "MYL9", "PTGS1", "MPP1", "TYMP", "COTL1",
"CTSS", "S100A11", "CFD", "LGALS2", "GABARAP", "TNFSF13B", "APOBEC3A",
"AP2S1", "IGSF6", "CSTB", "CPVL", "MAFB", "IFI6", "SLC7A7", "TGFBI",
"C1orf162", "CAPG", "BLVRA")
expect_equal(gene_names, gene_name_to_check)
expect_equal(sort(gene_names), sort(c(
res@top_genes$`2`,
res@top_genes$`3`
)))
})
set_verbosity(0)
load_example_dataset('7871581/files/pbmc3k_medium_clusters')
set_verbosity(0)
load_example_dataset('7871581/files/pbmc3k_medium_clusters')
test_that("Check cluster_set_to_xls", {
tp_dir <- file.path(tempdir(), create_rand_str())
dir.create(tp_dir, showWarnings = F, recursive = TRUE)
f_path <- file.path(tp_dir, "test.xls")
unlink(f_path)
cluster_set_to_xls(pbmc3k_medium_clusters, f_path)
testthat::expect_true(file.exists(f_path))
testthat::expect_error(cluster_set_to_xls(pbmc3k_medium_clusters, f_path))
tp_dir <- file.path(tempdir(), create_rand_str())
dir.create(tp_dir, showWarnings = F, recursive = TRUE)
f_path <- file.path(tp_dir, "test.xls")
unlink(f_path)
cluster_set_to_xls(pbmc3k_medium_clusters, f_path)
testthat::expect_true(file.exists(f_path))
testthat::expect_error(cluster_set_to_xls(pbmc3k_medium_clusters, f_path))
})
test_that("Checking gene_cluster() is working...", {
# Set verbosity to 0
set_verbosity(0)
load_example_dataset("7871581/files/pbmc3k_medium_clusters")
res <- pbmc3k_medium_clusters
expect_equal(length(gene_cluster(res)), 291)
expect_equal(paste0(table(gene_cluster(res)), collapse = " "), "51 49 45 24 20 18 14 14 14 12 7 7 6 5 5")
expect_equal(as.vector(table(gene_cluster(res, cluster = 1))), 51)
expect_equal(as.vector(table(gene_cluster(res, cluster = 2))), 49)
expect_equal(as.vector(table(gene_cluster(res, cluster = 3))), 45)
expect_equal(as.vector(table(gene_cluster(res, cluster = 4))), 24)
expect_equal(as.vector(table(gene_cluster(res, cluster = c(1,4)))), c(51, 24))
expect_equal(as.vector(table(gene_cluster(res, cluster = c(4,4)))), 24)
expect_error(gene_cluster(res, cluster = c(-1,8)))
expect_error(gene_cluster(res, cluster = c(0,9)))
expect_error(gene_cluster(res, cluster = c(0:8)))
expect_error(gene_cluster(res, cluster = c(1,40)))
expect_equal(paste0(res@gene_clusters[[1]], collapse = " "),
paste0(names(gene_cluster(res, cluster = 1)), collapse = " "))
expect_equal(paste0(unlist(res@gene_clusters[1:2]), collapse = " "),
paste0(names(gene_cluster(res, cluster = 1:2)), collapse = " "))
expect_equal(paste0(unlist(res@gene_clusters[1:4]), collapse = " "),
paste0(names(gene_cluster(res, cluster = 1:4)), collapse = " "))
})
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