tests/testthat/test.enrichment_analysis.R

In dputhier/scigenex: The scigenex package (Single-Cell Informative GENe Explorer)

# library(testthat)
# library(org.Hs.eg.db)
# 
# # Set verbosit  y to 0
# set_verbosity(0)
# 
# # Load seurat object
# data(pbmc_small, package = "SeuratObject")
# 
# ## Select informative genes
# res <- select_genes(data=pbmc_small,
#                     distance_method="pearson",
#                     k=10,
#                     row_sum=-Inf,
#                     noise_level=0.95,
#                     fdr = 1e-6)
# 
# ## Cluster genes
# res <- gene_clustering(object = res,
#                        inflation = 1.2,
#                        keep_nn = FALSE,
#                        s = 5,
#                        threads = 1)
# set_verbosity(2)
# 
# 
# test_that("Check if enrich_go stops when species argument is invalid", {
#   expect_error(enrich_go(res, species = "Not working"))
# })
# 
# res_enrich <- enrich_go(res[1,])
# test_that("Check enrich_go results with all ontologies", {
#   set_verbosity(0)
#   
#   # Check results from gene cluster 1
#   expect_equal(length(res_enrich@gene_cluster_annotations), 1)
#   expect_equal(res_enrich@gene_cluster_annotations$`1`@pvalueCutoff, 0.05)
#   expect_equal(res_enrich@gene_cluster_annotations$`1`@pAdjustMethod, "BH")
#   expect_equal(res_enrich@gene_cluster_annotations$`1`@qvalueCutoff, 0.2)
#   expect_equal(res_enrich@gene_cluster_annotations$`1`@organism, "Homo sapiens")
#   expect_equal(res_enrich@gene_cluster_annotations$`1`@ontology, "GOALL")
#   
#   
#   expect_equal(res_enrich@gene_cluster_annotations$`1`@keytype, "ENTREZID")
#   expect_true(length(res_enrich@gene_cluster_annotations$`1`@geneSets) > 1000)
#   expect_true(res_enrich@gene_cluster_annotations$`1`@readable)
#   
#   
#   
#   expect_true("MHC class II protein complex assembly" %in% res_enrich@gene_cluster_annotations$`1`@result$Description[1:10])
#   expect_true(all(c("BP", "CC") %in% res_enrich@gene_cluster_annotations$`1`@result$ONTOLOGY))
#   expect_true(length(grep("CST3", res_enrich@gene_cluster_annotations$`1`@result$geneID)) > 0)
#   expect_true(length(grep("HLA-DMB", res_enrich@gene_cluster_annotations$`1`@result$geneID)) > 0)
#   
#   
#   # #########################
#   # Test viz_enrich()
#   # #########################
#   plot_res_enrich <- viz_enrich(res_enrich)
#   
#   expect_equal(length(plot_res_enrich), 2)
#   expect_equal(class(plot_res_enrich[[1]]), c("gg", "ggplot"))
#   expect_equal(class(plot_res_enrich[[2]]), c("gg", "ggplot"))
#   
#   # Barplot
#   expect_equal(plot_res_enrich[[1]]$labels$title, "Gene cluster 1")
#   expect_equal(plot_res_enrich[[1]]$labels$fill, "p.adjust")
#   expect_equal(unique(plot_res_enrich[[1]]$data$ONTOLOGY), c("BP", "CC", "MF"))
# 
#   expect_equal(plot_res_enrich[[1]]$labels$title, "Gene cluster 1")
#   expect_equal(plot_res_enrich[[1]]$labels$fill, "p.adjust")
#   expect_equal(unique(plot_res_enrich[[1]]$data$ONTOLOGY), c("BP", "CC", "MF"))
#   
#   expect_equal(plot_res_enrich[[1]]$data$ONTOLOGY, c(rep("BP", 20),
#                                                      rep("CC", 20),
#                                                      rep("MF", 20)))
#   expect_equal(plot_res_enrich[[1]]$data$ID[1:20],
#                res_enrich@gene_cluster_annotations$`1`@result$ID[1:20])
#   expect_equal(as.vector(plot_res_enrich[[1]]$data$Description[1:20]),
#                res_enrich@gene_cluster_annotations$`1`@result$Description[1:20])
#   expect_equal(plot_res_enrich[[1]]$data$pvalue[1:20],
#                res_enrich@gene_cluster_annotations$`1`@result$pvalue[1:20])
#   expect_equal(plot_res_enrich[[1]]$data$p.adjust[1:20],
#                res_enrich@gene_cluster_annotations$`1`@result$p.adjust[1:20])
#   expect_equal(plot_res_enrich[[1]]$data$qvalue[1:20],
#                res_enrich@gene_cluster_annotations$`1`@result$qvalue[1:20])
#   expect_equal(plot_res_enrich[[1]]$data$geneID[1:20],
#                res_enrich@gene_cluster_annotations$`1`@result$geneID[1:20])
#   expect_equal(plot_res_enrich[[1]]$data$Count[1:20],
#                res_enrich@gene_cluster_annotations$`1`@result$Count[1:20])
#   
#  
# })