tests/testthat/test.convert.R

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

library(testthat)
library(Seurat)
library(SeuratObject)

set_verbosity(0)

 

test_that("Checking cluster_set_from_matrix() #1", {
  
  m <- create_3_rnd_clust()[1:300,] 
  rownames(m) <- paste0("gene", 1:300)
  m_sub <- m[1:200, ]
  
  marker_sub <- list(a=paste0("gene", 1:100), 
                     b=paste0("gene", 101:200))
  
  markers <- list(a=paste0("gene", 1:100), 
                  b=paste0("gene", 101:200),
                  c=paste0("gene", 201:300))
  
  marker_fake <- list(a=letters[1:10])
  
  x <- cluster_set_from_matrix(m, marker_sub)
  testthat::expect_true(all(dim(x) == c(200, 20))) 
  
  x <- cluster_set_from_matrix(m_sub, markers)
  testthat::expect_true(all(dim(x) == c(200, 20))) 
  
  x <- cluster_set_from_matrix(m_sub, marker_fake)
  testthat::expect_true(all(dim(x) == c(0, 0))) 

})


test_that("Check cluster_set_from_seurat is working.", {
  data("pbmc_small", package="SeuratObject")
  markers <- Seurat::FindAllMarkers(pbmc_small)
  cs <- cluster_set_from_seurat(pbmc_small, markers)
   expect_true(all(cs@gene_clusters[[1]] == markers$gene[markers$cluster == "0"]))
   expect_true(all(cs@gene_clusters[[2]] == markers$gene[markers$cluster == "1"]))
   expect_true(all(cs@gene_clusters[[3]] == markers$gene[markers$cluster == "2"]))
   expect_true(nrow(cs[1,]@data) == nrow(pbmc_small@assays$RNA[markers$gene[markers$cluster == "0"],]))
   expect_true(nrow(cs["0",]@data) == nrow(pbmc_small@assays$RNA[markers$gene[markers$cluster == "0"],]))
   expect_true(sum(cs[1,]@data) == sum(pbmc_small@assays$RNA[markers$gene[markers$cluster == "0"],]))
   expect_true(nrow(cs[2,]@data) == nrow(pbmc_small@assays$RNA[markers$gene[markers$cluster == "1"],]))
   expect_true(nrow(cs["1",]@data) == nrow(pbmc_small@assays$RNA[markers$gene[markers$cluster == "1"],]))
   expect_true(sum(cs[2,]@data) == sum(pbmc_small@assays$RNA[markers$gene[markers$cluster == "1"],]))
   expect_true(nrow(cs[3,]@data) == nrow(pbmc_small@assays$RNA[markers$gene[markers$cluster == "2"],]))
   expect_true(sum(cs[3,]@data) == sum(pbmc_small@assays$RNA[markers$gene[markers$cluster == "2"],]))
   expect_true(cs@gene_clusters_metadata$number == 3)
   expect_true(all(cs@gene_clusters_metadata$cluster_id == setNames(c("0","1","2"), c("0","1","2"))))
   expect_true(all(cs@gene_clusters_metadata$cluster_id == setNames(c("0","1","2"), c("0","1","2"))))
   p <- plot_heatmap(cs[1,])
   testthat::expect_error(print(p), NA)
   p <- plot_heatmap(cs, cell_clusters = Idents(pbmc_small))
   testthat::expect_error(print(p), NA)
   p <- plot_profiles(cs, ident = Idents(pbmc_small))
   testthat::expect_error(print(p), NA) 
})