tests/testthat/test.top_genes.R
In dputhier/scigenex: The scigenex package (Single-Cell Informative GENe Explorer)
# Set verbosity to 0
set_verbosity(0)
library(Seurat)
load_example_dataset("7871581/files/pbmc3k_medium_clusters")
res <- pbmc3k_medium_clusters
test_that("Cheking top_gene()", {
# ========================================
# Top 20
res_20 <- top_genes(res, cluster = "all", top = 20)
# Test top genes list in all cluster
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(unlist(res_20@top_genes, use.names = FALSE), gene_name_to_check)
# Test top genes list in cluster 1
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(res_20@top_genes$`1`, gene_name_to_check)
expect_equal(length(res_20@top_genes$`1`), 20)
# Test top genes list in cluster 2 and 3
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(c(res_20@top_genes$`2`, res_20@top_genes$`3`),
gene_name_to_check)
expect_equal(length(c(res_20@top_genes$`2`, res_20@top_genes$`3`)), 40)
# ========================================
# Top 10
res_10 <- top_genes(res, cluster = "all", top = 10)
# Test top genes list in all cluster
gene_name_to_check <- c("RPL11", "RPL32", "RPS12", "RPL18A", "RPS18", "RPS23", "RPS16",
"RPL9", "RPL23A", "RPS3", "SDPR", "GNG11", "PF4", "SPARC", "PPBP",
"TUBB1", "HIST1H2AC", "GP9", "CLU", "AP001189.4", "TYMP", "COTL1",
"CTSS", "S100A11", "CFD", "LGALS2", "GABARAP", "TNFSF13B", "APOBEC3A",
"AP2S1", "GZMB", "PRF1", "GNLY", "FGFBP2", "GZMA", "CST7", "CCL4",
"SPON2", "CTSW", "CLIC3", "AC137932.6", "HEMGN", "hsa-mir-1199",
"EGFL7", "SEC14L5", "GATA2", "DPY19L1", "HEXIM2", "PCP2", "KIFC3",
"ARHGAP21", "SPOCD1", "ATP9A", "FAM212A", "CTNNAL1", "ABCC3",
"SCFD2", "ARG2", "ITGB3", "ALOX12", "CLEC1B", "GP1BA", "CMTM5",
"SCGB1C1", "HIST1H2BD", "RP11-367G6.3", "FNTB", "SEPT4", "SENCR",
"C1orf198", "LGALSL", "SMOX", "SSX2IP", "FAM212B", "AC147651.3",
"TMCC2", "ZNF778", "SERPINE2", "TRIM58", "MOB3B", "HLA-DRB1",
"HLA-DRA", "HLA-DPA1", "HLA-DRB5", "HLA-DPB1", "CD74", "HLA-DQA1",
"HLA-DQB1", "LY86", "HLA-DMB", "HIST1H2BJ", "CLDN5", "C2orf88",
"FAM63A", "TUBA1C", "SLC40A1", "SPHK1", "TMEM91", "PRKAR2B",
"TJP2", "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(unlist(res_10@top_genes, use.names = FALSE), gene_name_to_check)
expect_equal(length(unlist(res_10@top_genes, use.names = FALSE)), 130)
# Test top genes list in cluster 1
gene_name_to_check <- c("RPL11", "RPL32", "RPS12", "RPL18A", "RPS18", "RPS23", "RPS16",
"RPL9", "RPL23A", "RPS3")
expect_equal(res_10@top_genes$`1`, gene_name_to_check)
expect_equal(length(res_10@top_genes$`1`), 10)
# Test top genes list in cluster 2 and 3
gene_name_to_check <- c("SDPR", "GNG11", "PF4", "SPARC", "PPBP", "TUBB1", "HIST1H2AC",
"GP9", "CLU", "AP001189.4", "TYMP", "COTL1", "CTSS", "S100A11",
"CFD", "LGALS2", "GABARAP", "TNFSF13B", "APOBEC3A", "AP2S1")
expect_equal(
c(res_10@top_genes$`2`, res_10@top_genes$`3`),
gene_name_to_check
)
expect_equal(length(c(res_10@top_genes$`2`, res_10@top_genes$`3`)), 20)
# ========================================
# Top 5
res_5 <- top_genes(res, cluster = "all", top = 5)
# Test top genes list in all cluster
gene_name_to_check <- c("RPL11", "RPL32", "RPS12", "RPL18A", "RPS18", "SDPR", "GNG11",
"PF4", "SPARC", "PPBP", "TYMP", "COTL1", "CTSS", "S100A11", "CFD",
"GZMB", "PRF1", "GNLY", "FGFBP2", "GZMA", "AC137932.6", "HEMGN",
"hsa-mir-1199", "EGFL7", "SEC14L5", "ARHGAP21", "SPOCD1", "ATP9A",
"FAM212A", "CTNNAL1", "CLEC1B", "GP1BA", "CMTM5", "SCGB1C1",
"HIST1H2BD", "LGALSL", "SMOX", "SSX2IP", "FAM212B", "AC147651.3",
"HLA-DRB1", "HLA-DRA", "HLA-DPA1", "HLA-DRB5", "HLA-DPB1", "HIST1H2BJ",
"CLDN5", "C2orf88", "FAM63A", "TUBA1C", "ENKUR", "LCN2", "GFI1B",
"ANKRD9", "PRUNE", "CD3D", "IL32", "LDHB", "CD3E", "IL7R", "FCGR3A",
"RHOC", "IFITM2", "ABI3", "HES4", "RP11-879F14.2", "ZHX1-C8ORF76",
"MTURN", "MEST", "CAPZA2", "LINC00926", "CD79B", "MS4A1", "ISG20",
"PKIG")
expect_equal(unlist(res_5@top_genes, use.names = FALSE), gene_name_to_check)
expect_equal(length(unlist(res_5@top_genes, use.names = FALSE)), 75)
# Test top genes list in cluster 1
gene_name_to_check <- c("RPL11", "RPL32", "RPS12", "RPL18A", "RPS18")
expect_equal(res_5@top_genes$`1`, gene_name_to_check)
# Test top genes list in cluster 2 and 3
gene_name_to_check <- c("SDPR", "GNG11", "PF4", "SPARC", "PPBP", "TYMP", "COTL1", "CTSS",
"S100A11", "CFD")
expect_equal(c(res_5@top_genes$`2`, res_5@top_genes$`3`), gene_name_to_check)
# ========================================
# Top 100
res_100 <- suppressWarnings(top_genes(res, cluster = "all", top = 100))
# Test top genes list in all cluster
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", "RPL27A",
"RPL18", "RPL14", "RPL3", "RPL35A", "RPL21", "RPLP1", "RPS28",
"RPL6", "RPS10", "RPL26", "RPL7A", "RPL5", "RPL27", "RPL15",
"RPS13", "RPL17", "RPL31", "RPS3A", "RPS29", "RPL36", "MALAT1",
"RPS20", "TPT1", "RPS26", "RPS9", "EEF1B2", "RPS11", "NACA",
"RPSAP58", "BTG1", "SDPR", "GNG11", "PF4", "SPARC", "PPBP", "TUBB1",
"HIST1H2AC", "GP9", "CLU", "AP001189.4", "RGS18", "PTCRA", "TREML1",
"F13A1", "CA2", "TMEM40", "MMD", "MYL9", "PTGS1", "MPP1", "ACTN1",
"ACRBP", "TPM4", "TPM1", "SNCA", "NGFRAP1", "GAS2L1", "GRAP2",
"CTSA", "ILK", "ODC1", "SNN", "PDLIM1", "FERMT3", "HIST1H2BK",
"MARCH2", "PARVB", "PLA2G12A", "MFSD1", "PVALB", "CD151", "TPTEP1",
"GSN", "YWHAH", "RAP1B", "ASAH1", "APP", "MYL12A", "H2AFJ", "TYMP",
"COTL1", "CTSS", "S100A11", "CFD", "LGALS2", "GABARAP", "TNFSF13B",
"APOBEC3A", "AP2S1", "IGSF6", "CSTB", "CPVL", "MAFB", "IFI6",
"SLC7A7", "TGFBI", "C1orf162", "CAPG", "BLVRA", "BID", "MNDA",
"LILRB2", "S100A10", "CD14", "WARS", "NAAA", "NUP214", "ATG3",
"CNPY3", "CYBB", "GAPDH", "IFNGR2", "ALDH2", "EIF4EBP1", "CD300LF",
"GCA", "GRINA", "LILRB4", "SOD2", "CTSZ", "CD302", "CAMK1", "POU2F2",
"FCGR2A", "GZMB", "PRF1", "GNLY", "FGFBP2", "GZMA", "CST7", "CCL4",
"SPON2", "CTSW", "CLIC3", "CD247", "IL2RB", "HOPX", "HLA-C",
"CD7", "AKR1C3", "KLRF1", "XCL1", "IGFBP7", "CCL5", "CD99", "PTPRCAP",
"PLEK", "EFHD2", "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(unlist(res_100@top_genes, use.names = FALSE), gene_name_to_check)
# Test top genes list in cluster 1
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", "RPL27A",
"RPL18", "RPL14", "RPL3", "RPL35A", "RPL21", "RPLP1", "RPS28",
"RPL6", "RPS10", "RPL26", "RPL7A", "RPL5", "RPL27", "RPL15",
"RPS13", "RPL17", "RPL31", "RPS3A", "RPS29", "RPL36", "MALAT1",
"RPS20", "TPT1", "RPS26", "RPS9", "EEF1B2", "RPS11", "NACA",
"RPSAP58", "BTG1")
expect_equal(res_100@top_genes$`1`, gene_name_to_check)
# Test top genes list in cluster 2 and 3
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", "ACTN1", "ACRBP",
"TPM4", "TPM1", "SNCA", "NGFRAP1", "GAS2L1", "GRAP2", "CTSA",
"ILK", "ODC1", "SNN", "PDLIM1", "FERMT3", "HIST1H2BK", "MARCH2",
"PARVB", "PLA2G12A", "MFSD1", "PVALB", "CD151", "TPTEP1", "GSN",
"YWHAH", "RAP1B", "ASAH1", "APP", "MYL12A", "H2AFJ", "TYMP",
"COTL1", "CTSS", "S100A11", "CFD", "LGALS2", "GABARAP", "TNFSF13B",
"APOBEC3A", "AP2S1", "IGSF6", "CSTB", "CPVL", "MAFB", "IFI6",
"SLC7A7", "TGFBI", "C1orf162", "CAPG", "BLVRA", "BID", "MNDA",
"LILRB2", "S100A10", "CD14", "WARS", "NAAA", "NUP214", "ATG3",
"CNPY3", "CYBB", "GAPDH", "IFNGR2", "ALDH2", "EIF4EBP1", "CD300LF",
"GCA", "GRINA", "LILRB4", "SOD2", "CTSZ", "CD302", "CAMK1", "POU2F2",
"FCGR2A")
expect_equal(
c(res_100@top_genes$`2`, res_100@top_genes$`3`),
gene_name_to_check
)
})
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# Set verbosity to 0
set_verbosity(0)
library(Seurat)
load_example_dataset("7871581/files/pbmc3k_medium_clusters")
res <- pbmc3k_medium_clusters
test_that("Cheking top_gene()", {
# ========================================
# Top 20
res_20 <- top_genes(res, cluster = "all", top = 20)
# Test top genes list in all cluster
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(unlist(res_20@top_genes, use.names = FALSE), gene_name_to_check)
# Test top genes list in cluster 1
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(res_20@top_genes$`1`, gene_name_to_check)
expect_equal(length(res_20@top_genes$`1`), 20)
# Test top genes list in cluster 2 and 3
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(c(res_20@top_genes$`2`, res_20@top_genes$`3`),
gene_name_to_check)
expect_equal(length(c(res_20@top_genes$`2`, res_20@top_genes$`3`)), 40)
# ========================================
# Top 10
res_10 <- top_genes(res, cluster = "all", top = 10)
# Test top genes list in all cluster
gene_name_to_check <- c("RPL11", "RPL32", "RPS12", "RPL18A", "RPS18", "RPS23", "RPS16",
"RPL9", "RPL23A", "RPS3", "SDPR", "GNG11", "PF4", "SPARC", "PPBP",
"TUBB1", "HIST1H2AC", "GP9", "CLU", "AP001189.4", "TYMP", "COTL1",
"CTSS", "S100A11", "CFD", "LGALS2", "GABARAP", "TNFSF13B", "APOBEC3A",
"AP2S1", "GZMB", "PRF1", "GNLY", "FGFBP2", "GZMA", "CST7", "CCL4",
"SPON2", "CTSW", "CLIC3", "AC137932.6", "HEMGN", "hsa-mir-1199",
"EGFL7", "SEC14L5", "GATA2", "DPY19L1", "HEXIM2", "PCP2", "KIFC3",
"ARHGAP21", "SPOCD1", "ATP9A", "FAM212A", "CTNNAL1", "ABCC3",
"SCFD2", "ARG2", "ITGB3", "ALOX12", "CLEC1B", "GP1BA", "CMTM5",
"SCGB1C1", "HIST1H2BD", "RP11-367G6.3", "FNTB", "SEPT4", "SENCR",
"C1orf198", "LGALSL", "SMOX", "SSX2IP", "FAM212B", "AC147651.3",
"TMCC2", "ZNF778", "SERPINE2", "TRIM58", "MOB3B", "HLA-DRB1",
"HLA-DRA", "HLA-DPA1", "HLA-DRB5", "HLA-DPB1", "CD74", "HLA-DQA1",
"HLA-DQB1", "LY86", "HLA-DMB", "HIST1H2BJ", "CLDN5", "C2orf88",
"FAM63A", "TUBA1C", "SLC40A1", "SPHK1", "TMEM91", "PRKAR2B",
"TJP2", "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(unlist(res_10@top_genes, use.names = FALSE), gene_name_to_check)
expect_equal(length(unlist(res_10@top_genes, use.names = FALSE)), 130)
# Test top genes list in cluster 1
gene_name_to_check <- c("RPL11", "RPL32", "RPS12", "RPL18A", "RPS18", "RPS23", "RPS16",
"RPL9", "RPL23A", "RPS3")
expect_equal(res_10@top_genes$`1`, gene_name_to_check)
expect_equal(length(res_10@top_genes$`1`), 10)
# Test top genes list in cluster 2 and 3
gene_name_to_check <- c("SDPR", "GNG11", "PF4", "SPARC", "PPBP", "TUBB1", "HIST1H2AC",
"GP9", "CLU", "AP001189.4", "TYMP", "COTL1", "CTSS", "S100A11",
"CFD", "LGALS2", "GABARAP", "TNFSF13B", "APOBEC3A", "AP2S1")
expect_equal(
c(res_10@top_genes$`2`, res_10@top_genes$`3`),
gene_name_to_check
)
expect_equal(length(c(res_10@top_genes$`2`, res_10@top_genes$`3`)), 20)
# ========================================
# Top 5
res_5 <- top_genes(res, cluster = "all", top = 5)
# Test top genes list in all cluster
gene_name_to_check <- c("RPL11", "RPL32", "RPS12", "RPL18A", "RPS18", "SDPR", "GNG11",
"PF4", "SPARC", "PPBP", "TYMP", "COTL1", "CTSS", "S100A11", "CFD",
"GZMB", "PRF1", "GNLY", "FGFBP2", "GZMA", "AC137932.6", "HEMGN",
"hsa-mir-1199", "EGFL7", "SEC14L5", "ARHGAP21", "SPOCD1", "ATP9A",
"FAM212A", "CTNNAL1", "CLEC1B", "GP1BA", "CMTM5", "SCGB1C1",
"HIST1H2BD", "LGALSL", "SMOX", "SSX2IP", "FAM212B", "AC147651.3",
"HLA-DRB1", "HLA-DRA", "HLA-DPA1", "HLA-DRB5", "HLA-DPB1", "HIST1H2BJ",
"CLDN5", "C2orf88", "FAM63A", "TUBA1C", "ENKUR", "LCN2", "GFI1B",
"ANKRD9", "PRUNE", "CD3D", "IL32", "LDHB", "CD3E", "IL7R", "FCGR3A",
"RHOC", "IFITM2", "ABI3", "HES4", "RP11-879F14.2", "ZHX1-C8ORF76",
"MTURN", "MEST", "CAPZA2", "LINC00926", "CD79B", "MS4A1", "ISG20",
"PKIG")
expect_equal(unlist(res_5@top_genes, use.names = FALSE), gene_name_to_check)
expect_equal(length(unlist(res_5@top_genes, use.names = FALSE)), 75)
# Test top genes list in cluster 1
gene_name_to_check <- c("RPL11", "RPL32", "RPS12", "RPL18A", "RPS18")
expect_equal(res_5@top_genes$`1`, gene_name_to_check)
# Test top genes list in cluster 2 and 3
gene_name_to_check <- c("SDPR", "GNG11", "PF4", "SPARC", "PPBP", "TYMP", "COTL1", "CTSS",
"S100A11", "CFD")
expect_equal(c(res_5@top_genes$`2`, res_5@top_genes$`3`), gene_name_to_check)
# ========================================
# Top 100
res_100 <- suppressWarnings(top_genes(res, cluster = "all", top = 100))
# Test top genes list in all cluster
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", "RPL27A",
"RPL18", "RPL14", "RPL3", "RPL35A", "RPL21", "RPLP1", "RPS28",
"RPL6", "RPS10", "RPL26", "RPL7A", "RPL5", "RPL27", "RPL15",
"RPS13", "RPL17", "RPL31", "RPS3A", "RPS29", "RPL36", "MALAT1",
"RPS20", "TPT1", "RPS26", "RPS9", "EEF1B2", "RPS11", "NACA",
"RPSAP58", "BTG1", "SDPR", "GNG11", "PF4", "SPARC", "PPBP", "TUBB1",
"HIST1H2AC", "GP9", "CLU", "AP001189.4", "RGS18", "PTCRA", "TREML1",
"F13A1", "CA2", "TMEM40", "MMD", "MYL9", "PTGS1", "MPP1", "ACTN1",
"ACRBP", "TPM4", "TPM1", "SNCA", "NGFRAP1", "GAS2L1", "GRAP2",
"CTSA", "ILK", "ODC1", "SNN", "PDLIM1", "FERMT3", "HIST1H2BK",
"MARCH2", "PARVB", "PLA2G12A", "MFSD1", "PVALB", "CD151", "TPTEP1",
"GSN", "YWHAH", "RAP1B", "ASAH1", "APP", "MYL12A", "H2AFJ", "TYMP",
"COTL1", "CTSS", "S100A11", "CFD", "LGALS2", "GABARAP", "TNFSF13B",
"APOBEC3A", "AP2S1", "IGSF6", "CSTB", "CPVL", "MAFB", "IFI6",
"SLC7A7", "TGFBI", "C1orf162", "CAPG", "BLVRA", "BID", "MNDA",
"LILRB2", "S100A10", "CD14", "WARS", "NAAA", "NUP214", "ATG3",
"CNPY3", "CYBB", "GAPDH", "IFNGR2", "ALDH2", "EIF4EBP1", "CD300LF",
"GCA", "GRINA", "LILRB4", "SOD2", "CTSZ", "CD302", "CAMK1", "POU2F2",
"FCGR2A", "GZMB", "PRF1", "GNLY", "FGFBP2", "GZMA", "CST7", "CCL4",
"SPON2", "CTSW", "CLIC3", "CD247", "IL2RB", "HOPX", "HLA-C",
"CD7", "AKR1C3", "KLRF1", "XCL1", "IGFBP7", "CCL5", "CD99", "PTPRCAP",
"PLEK", "EFHD2", "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(unlist(res_100@top_genes, use.names = FALSE), gene_name_to_check)
# Test top genes list in cluster 1
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", "RPL27A",
"RPL18", "RPL14", "RPL3", "RPL35A", "RPL21", "RPLP1", "RPS28",
"RPL6", "RPS10", "RPL26", "RPL7A", "RPL5", "RPL27", "RPL15",
"RPS13", "RPL17", "RPL31", "RPS3A", "RPS29", "RPL36", "MALAT1",
"RPS20", "TPT1", "RPS26", "RPS9", "EEF1B2", "RPS11", "NACA",
"RPSAP58", "BTG1")
expect_equal(res_100@top_genes$`1`, gene_name_to_check)
# Test top genes list in cluster 2 and 3
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", "ACTN1", "ACRBP",
"TPM4", "TPM1", "SNCA", "NGFRAP1", "GAS2L1", "GRAP2", "CTSA",
"ILK", "ODC1", "SNN", "PDLIM1", "FERMT3", "HIST1H2BK", "MARCH2",
"PARVB", "PLA2G12A", "MFSD1", "PVALB", "CD151", "TPTEP1", "GSN",
"YWHAH", "RAP1B", "ASAH1", "APP", "MYL12A", "H2AFJ", "TYMP",
"COTL1", "CTSS", "S100A11", "CFD", "LGALS2", "GABARAP", "TNFSF13B",
"APOBEC3A", "AP2S1", "IGSF6", "CSTB", "CPVL", "MAFB", "IFI6",
"SLC7A7", "TGFBI", "C1orf162", "CAPG", "BLVRA", "BID", "MNDA",
"LILRB2", "S100A10", "CD14", "WARS", "NAAA", "NUP214", "ATG3",
"CNPY3", "CYBB", "GAPDH", "IFNGR2", "ALDH2", "EIF4EBP1", "CD300LF",
"GCA", "GRINA", "LILRB4", "SOD2", "CTSZ", "CD302", "CAMK1", "POU2F2",
"FCGR2A")
expect_equal(
c(res_100@top_genes$`2`, res_100@top_genes$`3`),
gene_name_to_check
)
})
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