tests/testthat/test.gene_clustering.R
In dputhier/dbfmcl: The scigenex package (Single-Cell Informative GENe Explorer)
# Set verbosity to 0
set_verbosity(0)
load_example_dataset("7871581/files/pbmc3k_medium")
pbmc3k_medium_clust <- select_genes(data = pbmc3k_medium,
distance_method = "pearson")
test_that("Checking output slots generated by gene_clustering() using keep_nn as FALSE", {
# Create output directory
tmp_dir <- tempdir()
dir.create(tmp_dir, recursive = TRUE, showWarnings = FALSE)
## A rather stringent version
res_no_keep_nn <- gene_clustering(object = pbmc3k_medium_clust,
inflation = 1.8,
keep_nn = FALSE,
s = 5,
threads = 6,
output_path = tmp_dir)
# =======================================================
# Test name of temporary files
expect_true(file.exists(file.path(res_no_keep_nn@parameters$output_path,
paste0(res_no_keep_nn@parameters$name,
".graph_input.txt"))))
expect_true(file.exists(file.path(res_no_keep_nn@parameters$output_path,
paste0(res_no_keep_nn@parameters$name,
".graph_out.txt"))))
expect_equal(length(res_no_keep_nn@parameters$name), 1)
expect_true(is.character(res_no_keep_nn@parameters$name))
# =======================================================
# Test matrix in res_no_keep_nn@data
expect_equal(round(sum(res_no_keep_nn@data), 0), 70172)
expect_equal(round(mean(res_no_keep_nn@data), 6), 0.639414)
expect_equal(round(median(res_no_keep_nn@data), 6), 0)
expect_equal(round(sd(res_no_keep_nn@data), 6), 1.329959)
expect_equal(round(sum(colMeans(res_no_keep_nn@data)), 1), 230.8)
expect_equal(round(sum(rowMeans(res_no_keep_nn@data)), 4), 194.382)
expect_equal(ncol(res_no_keep_nn@data), 361)
expect_equal(head(colnames(res_no_keep_nn@data)), c("GATCTACTGGTGAG-1", "ACAGTGACTCACCC-1", "AGACGTACAGAGGC-1",
"GACGTAACCTGTGA-1", "TATACAGATCCAGA-1", "CGGATAACAGCTCA-1"))
expect_equal(tail(colnames(res_no_keep_nn@data)), c("GGCATATGGGGAGT-1", "TTACGTACGTTCAG-1", "GGAACACTTCAGAC-1",
"ATCATCTGACACCA-1", "ACGAACTGGCTATG-1", "TAACACCTTGTTTC-1"))
expect_equal(nrow(res_no_keep_nn@data), 304)
expect_equal(nrow(res_no_keep_nn@data), length(get_genes(res_no_keep_nn)))
expect_equal(rownames(res_no_keep_nn@data), get_genes(res_no_keep_nn))
expect_equal(rownames(res_no_keep_nn@data), unlist(res_no_keep_nn@gene_clusters, use.names = F))
expect_equal(nrow(res_no_keep_nn@data), length(get_genes(res_no_keep_nn)))
expect_equal(nrow(res_no_keep_nn@data), length(unlist(res_no_keep_nn@gene_clusters)))
expect_equal(round(sum(res_no_keep_nn@data^2), 1), 238981.3)
expect_true(is.matrix(res_no_keep_nn@data))
expect_equal(length(res_no_keep_nn@data), 109744)
# =======================================================
# Test observed distances in res_no_keep_nn@dbf_output$dknn
expect_equal(round(sum(res_no_keep_nn@dbf_output$dknn), 3), 1324.35)
expect_equal(round(mean(res_no_keep_nn@dbf_output$dknn), 7), 0.8650231)
expect_equal(round(median(res_no_keep_nn@dbf_output$dknn), 7), 0.886363)
expect_equal(round(sd(res_no_keep_nn@dbf_output$dknn), 6), 0.069147)
expect_equal(length(res_no_keep_nn@dbf_output$dknn), 1531)
expect_equal(round(sum(res_no_keep_nn@dbf_output$dknn^2), 2), 1152.91)
# =======================================================
# Test simulated distances in res_no_keep_nn@dbf_output$simulated_dknn
expect_equal(round(sum(res_no_keep_nn@dbf_output$simulated_dknn), 3), 1335.374)
expect_equal(round(mean(res_no_keep_nn@dbf_output$simulated_dknn), 7), 0.8722235)
expect_equal(round(median(res_no_keep_nn@dbf_output$simulated_dknn), 7), 0.8722685)
expect_equal(round(sd(res_no_keep_nn@dbf_output$simulated_dknn), 6), 0.008386)
expect_equal(length(res_no_keep_nn@dbf_output$simulated_dknn), 1531)
expect_equal(round(sum(res_no_keep_nn@dbf_output$simulated_dknn^2), 2), 1164.85)
expect_true(is.numeric(res_no_keep_nn@dbf_output$simulated_dknn))
# =======================================================
# Test critical distance in res_no_keep_nn@critical_distance
expect_equal(round(res_no_keep_nn@dbf_output$critical_distance, 7), 0.8369334)
expect_equal(length(res_no_keep_nn@dbf_output$critical_distance), 1)
# =======================================================
# Test gene clusters in res_no_keep_nn@gene_clusters
expect_equal(sum(as.numeric(names(res_no_keep_nn@gene_clusters))), 136)
expect_equal(names(res_no_keep_nn@gene_clusters), as.character(1:16))
expect_equal(length(unlist(res_no_keep_nn@gene_clusters)), 304)
expect_equal(length(unlist(res_no_keep_nn@gene_clusters$`1`)), 63)
expect_equal(length(unlist(res_no_keep_nn@gene_clusters$`2`)), 37)
expect_equal(length(unlist(res_no_keep_nn@gene_clusters$`3`)), 34)
expect_equal(length(unlist(res_no_keep_nn@gene_clusters$`4`)), 29)
expect_equal(length(unlist(res_no_keep_nn@gene_clusters$`10`)), 12)
expect_equal(unlist(res_no_keep_nn@gene_clusters, use.names = F), get_genes(res_no_keep_nn))
expect_equal(
unlist(res_no_keep_nn@gene_clusters$`1`, use.names = F),
get_genes(res_no_keep_nn, cluster = 1)
)
expect_equal(
unlist(res_no_keep_nn@gene_clusters$`2`, use.names = F),
get_genes(res_no_keep_nn, cluster = 2)
)
expect_equal(
unlist(res_no_keep_nn@gene_clusters$`3`, use.names = F),
get_genes(res_no_keep_nn, cluster = 3)
)
expect_equal(
unlist(res_no_keep_nn@gene_clusters$`4`, use.names = F),
get_genes(res_no_keep_nn, cluster = 4)
)
expect_equal(unlist(res_no_keep_nn@gene_clusters, use.names = F), rownames(res_no_keep_nn@data))
expect_true(is.list(res_no_keep_nn@gene_clusters))
expect_true(is.character(res_no_keep_nn@gene_clusters$`1`))
# =======================================================
# Test size of gene clusters in res_no_keep_nn@gene_clusters_metadata$size
expect_equal(res_no_keep_nn@gene_clusters_metadata$size, c(`1` = 63L, `2` = 37L, `3` = 34L, `4` = 29L, `5` = 26L, `6` = 24L,
`7` = 21L, `8` = 14L, `9` = 14L, `10` = 12L, `11` = 7L, `12` = 6L,
`13` = 5L, `14` = 5L, `15` = 4L, `16` = 3L))
expect_true(is.integer(res_no_keep_nn@gene_clusters_metadata$size))
expect_equal(
res_no_keep_nn@gene_clusters_metadata$size[1],
c("1" = length(res_no_keep_nn@gene_clusters$`1`))
)
expect_equal(
res_no_keep_nn@gene_clusters_metadata$size[2],
c("2" = length(res_no_keep_nn@gene_clusters$`2`))
)
expect_equal(
res_no_keep_nn@gene_clusters_metadata$size[3],
c("3" = length(res_no_keep_nn@gene_clusters$`3`))
)
expect_equal(
res_no_keep_nn@gene_clusters_metadata$size[4],
c("4" = length(res_no_keep_nn@gene_clusters$`4`))
)
expect_equal(
res_no_keep_nn@gene_clusters_metadata$size[1],
c("1" = length(get_genes(res_no_keep_nn, cluster = 1)))
)
expect_equal(
res_no_keep_nn@gene_clusters_metadata$size[2],
c("2" = length(get_genes(res_no_keep_nn, cluster = 2)))
)
expect_equal(
res_no_keep_nn@gene_clusters_metadata$size[3],
c("3" = length(get_genes(res_no_keep_nn, cluster = 3)))
)
expect_equal(
res_no_keep_nn@gene_clusters_metadata$size[4],
c("4" = length(get_genes(res_no_keep_nn, cluster = 4)))
)
# =======================================================
# Test parameters in res_no_keep_nn@parameters
expect_true(is.list(res_no_keep_nn@parameters))
expect_equal(length(res_no_keep_nn@parameters), 12)
expect_equal(names(res_no_keep_nn@parameters), c(
"distance_method",
"k",
"noise_level",
"fdr",
"row_sum",
"no_dknn_filter",
"seed",
"keep_nn",
"k_graph",
"output_path",
"name",
"inflation"
))
expect_equal(res_no_keep_nn@parameters$output_path, tmp_dir)
expect_true(is.character(res_no_keep_nn@parameters$output_path))
expect_equal(length(res_no_keep_nn@parameters$output_path), 1)
expect_true(is.character(res_no_keep_nn@parameters$name))
expect_equal(length(res_no_keep_nn@parameters$name), 1)
expect_equal(nchar(res_no_keep_nn@parameters$name), 10)
expect_true(grepl("[[:alnum:]]+", res_no_keep_nn@parameters$name))
expect_equal(res_no_keep_nn@parameters$distance_method, "pearson")
expect_equal(length(res_no_keep_nn@parameters$distance_method), 1)
expect_equal(res_no_keep_nn@parameters$k, 80)
expect_true(is.numeric(res_no_keep_nn@parameters$k))
expect_equal(length(res_no_keep_nn@parameters$k), 1)
expect_equal(res_no_keep_nn@parameters$noise_level, 5e-05)
expect_true(is.numeric(res_no_keep_nn@parameters$noise_level))
expect_equal(length(res_no_keep_nn@parameters$noise_level), 1)
expect_equal(res_no_keep_nn@parameters$fdr, 0.005)
expect_equal(length(res_no_keep_nn@parameters$fdr), 1)
expect_equal(res_no_keep_nn@parameters$row_sum, 1)
expect_true(is.numeric(res_no_keep_nn@parameters$row_sum))
expect_equal(length(res_no_keep_nn@parameters$row_sum), 1)
expect_false(res_no_keep_nn@parameters$no_dknn_filter)
expect_equal(res_no_keep_nn@parameters$seed, 123)
expect_true(is.numeric(res_no_keep_nn@parameters$seed))
expect_equal(length(res_no_keep_nn@parameters$seed), 1)
expect_false(res_no_keep_nn@parameters$keep_nn)
expect_equal(res_no_keep_nn@parameters$k_graph, 5)
expect_true(is.numeric(res_no_keep_nn@parameters$k_graph))
expect_equal(length(res_no_keep_nn@parameters$k_graph), 1)
expect_equal(res_no_keep_nn@parameters$inflation, 1.8)
expect_true(is.numeric(res_no_keep_nn@parameters$inflation))
expect_equal(length(res_no_keep_nn@parameters$inflation), 1)
# =======================================================
# Test parameters in res_no_keep_nn@cluster_number
expect_equal(res_no_keep_nn@gene_clusters_metadata$number, 16)
expect_true(is.numeric(res_no_keep_nn@gene_clusters_metadata$number))
# =======================================================
# Test parameters in res_no_keep_nn@cluster_list
expect_equal(length(res_no_keep_nn@gene_clusters_metadata$cluster_id), 16)
expect_equal(res_no_keep_nn@gene_clusters_metadata$cluster_id, 1:16)
expect_true(is.numeric(res_no_keep_nn@gene_clusters_metadata$cluster_id))
# Remove temporary files
unlink(tmp_dir, recursive = TRUE)
})
test_that("Checking output slots generated by gene_clustering() using keep_nn as TRUE", {
## A rather stringent version
res_keep_nn <- gene_clustering(object = pbmc3k_medium_clust,
inflation = 2.2,
keep_nn = TRUE,
threads = 4,
name = "test")
# =======================================================
# Test name of temporary files
expect_equal(res_keep_nn@parameters$name, "test")
expect_true(file.exists(file.path(res_keep_nn@parameters$output_path,
paste0(res_keep_nn@parameters$name,
".graph_input.txt"))))
expect_true(file.exists(file.path(res_keep_nn@parameters$output_path,
paste0(res_keep_nn@parameters$name,
".graph_out.txt"))))
expect_true(file.exists(file.path(tempdir(), paste0(res_keep_nn@parameters$name,
".graph_input.txt"))))
expect_true(file.exists(file.path(tempdir(), paste0(res_keep_nn@parameters$name,
".graph_input.txt"))))
expect_equal(length(res_keep_nn@parameters$name), 1)
expect_true(is.character(res_keep_nn@parameters$name))
# =======================================================
# Test matrix in res_keep_nn@data
expect_equal(round(sum(res_keep_nn@data), 0), 70172)
expect_equal(round(mean(res_keep_nn@data), 2), 0.64)
expect_equal(round(median(res_keep_nn@data), 2), 0)
expect_equal(round(sd(res_keep_nn@data), 1), 1.3)
expect_equal(round(sum(colMeans(res_keep_nn@data)), 1), 230.8)
expect_equal(round(sum(rowMeans(res_keep_nn@data)), 1), 194.4)
expect_equal(ncol(res_keep_nn@data), 361)
expect_equal(head(colnames(res_keep_nn@data)), c("GATCTACTGGTGAG-1", "ACAGTGACTCACCC-1", "AGACGTACAGAGGC-1",
"GACGTAACCTGTGA-1", "TATACAGATCCAGA-1", "CGGATAACAGCTCA-1"))
expect_equal(nrow(res_keep_nn@data), 304)
expect_equal(nrow(res_keep_nn@data), length(get_genes(res_keep_nn)))
expect_equal(rownames(res_keep_nn@data), get_genes(res_keep_nn))
expect_equal(rownames(res_keep_nn@data), unlist(res_keep_nn@gene_clusters, use.names = F))
expect_equal(nrow(res_keep_nn@data), length(get_genes(res_keep_nn)))
expect_equal(nrow(res_keep_nn@data), length(unlist(res_keep_nn@gene_clusters)))
expect_equal(round(sum(res_keep_nn@data^2), 1), 238981.3)
expect_true(is.matrix(res_keep_nn@data))
expect_equal(length(res_keep_nn@data), 109744)
# =======================================================
# Test observed distances in res_keep_nn@dbf_output$dknn
expect_equal(round(sum(res_keep_nn@dbf_output$dknn), 1), 1324.4)
expect_equal(round(mean(res_keep_nn@dbf_output$dknn), 1), 0.9)
expect_equal(round(median(res_keep_nn@dbf_output$dknn), 2), 0.89)
expect_equal(round(sd(res_keep_nn@dbf_output$dknn), 2), 0.07)
expect_equal(length(res_keep_nn@dbf_output$dknn), 1531)
expect_equal(round(sum(res_keep_nn@dbf_output$dknn^2), 1), 1152.9)
expect_true(is.numeric(res_keep_nn@dbf_output$dknn))
# =======================================================
# Test simulated distances in res_keep_nn@dbf_output$simulated_dknn
expect_equal(round(sum(res_keep_nn@dbf_output$simulated_dknn), 2), 1335.37)
expect_equal(round(mean(res_keep_nn@dbf_output$simulated_dknn), 2), 0.87)
expect_equal(round(median(res_keep_nn@dbf_output$simulated_dknn), 2), 0.87)
expect_equal(round(sd(res_keep_nn@dbf_output$simulated_dknn), 2), 0.01)
expect_equal(length(res_keep_nn@dbf_output$simulated_dknn), 1531)
expect_equal(round(sum(res_keep_nn@dbf_output$simulated_dknn^2), 2), 1164.85)
expect_true(is.numeric(res_keep_nn@dbf_output$simulated_dknn))
# =======================================================
# Test critical distance in res_keep_nn@critical_distance
expect_equal(round(res_keep_nn@dbf_output$critical_distance, 2), 0.84)
expect_true(is.numeric(res_keep_nn@dbf_output$critical_distance))
expect_equal(length(res_keep_nn@dbf_output$critical_distance), 1)
# =======================================================
# Test gene clusters in res_keep_nn@gene_clusters
expect_equal(sum(as.numeric(names(res_keep_nn@gene_clusters))), 36)
expect_equal(names(res_keep_nn@gene_clusters), as.character(1:8))
expect_equal(length(unlist(res_keep_nn@gene_clusters)), 304)
expect_equal(length(unlist(res_keep_nn@gene_clusters$`1`)), 78)
expect_equal(length(unlist(res_keep_nn@gene_clusters$`2`)), 47)
expect_equal(length(unlist(res_keep_nn@gene_clusters$`3`)), 42)
expect_equal(length(unlist(res_keep_nn@gene_clusters$`4`)), 37)
expect_equal(unlist(res_keep_nn@gene_clusters, use.names = F), get_genes(res_keep_nn))
expect_equal(
unlist(res_keep_nn@gene_clusters$`1`, use.names = F),
get_genes(res_keep_nn, cluster = 1)
)
expect_equal(
unlist(res_keep_nn@gene_clusters$`2`, use.names = F),
get_genes(res_keep_nn, cluster = 2)
)
expect_equal(
unlist(res_keep_nn@gene_clusters$`3`, use.names = F),
get_genes(res_keep_nn, cluster = 3)
)
expect_equal(
unlist(res_keep_nn@gene_clusters$`4`, use.names = F),
get_genes(res_keep_nn, cluster = 4)
)
expect_equal(unlist(res_keep_nn@gene_clusters, use.names = F), rownames(res_keep_nn@data))
expect_true(is.list(res_keep_nn@gene_clusters))
expect_true(is.character(res_keep_nn@gene_clusters$`1`))
# =======================================================
# Test size of gene clusters in res_keep_nn@gene_clusters_metadata$size
expect_equal(res_keep_nn@gene_clusters_metadata$size, c(`1` = 78L, `2` = 47L, `3` = 42L, `4` = 37L, `5` = 36L, `6` = 24L,
`7` = 23L, `8` = 17L))
expect_true(is.integer(res_keep_nn@gene_clusters_metadata$size))
expect_equal(
res_keep_nn@gene_clusters_metadata$size[1],
c("1" = length(res_keep_nn@gene_clusters$`1`))
)
expect_equal(
res_keep_nn@gene_clusters_metadata$size[2],
c("2" = length(res_keep_nn@gene_clusters$`2`))
)
expect_equal(
res_keep_nn@gene_clusters_metadata$size[3],
c("3" = length(res_keep_nn@gene_clusters$`3`))
)
expect_equal(
res_keep_nn@gene_clusters_metadata$size[4],
c("4" = length(res_keep_nn@gene_clusters$`4`))
)
expect_equal(
res_keep_nn@gene_clusters_metadata$size[1],
c("1" = length(get_genes(res_keep_nn, cluster = 1)))
)
expect_equal(
res_keep_nn@gene_clusters_metadata$size[2],
c("2" = length(get_genes(res_keep_nn, cluster = 2)))
)
expect_equal(
res_keep_nn@gene_clusters_metadata$size[3],
c("3" = length(get_genes(res_keep_nn, cluster = 3)))
)
expect_equal(
res_keep_nn@gene_clusters_metadata$size[4],
c("4" = length(get_genes(res_keep_nn, cluster = 4)))
)
# =======================================================
# Test parameters in res_keep_nn@parameters
expect_true(is.list(res_keep_nn@parameters))
expect_equal(length(res_keep_nn@parameters), 11)
expect_equal(names(res_keep_nn@parameters), c(
"distance_method",
"k",
"noise_level",
"fdr",
"row_sum",
"no_dknn_filter",
"seed",
"keep_nn",
"output_path",
"name",
"inflation"
))
expect_true(is.character(res_keep_nn@parameters$output_path))
expect_equal(length(res_keep_nn@parameters$output_path), 1)
expect_equal(res_keep_nn@parameters$name, "test")
expect_equal(length(res_keep_nn@parameters$name), 1)
expect_equal(res_keep_nn@parameters$distance_method, "pearson")
expect_equal(length(res_keep_nn@parameters$distance_method), 1)
expect_equal(res_keep_nn@parameters$k, 80)
expect_equal(length(res_keep_nn@parameters$k), 1)
expect_equal(res_keep_nn@parameters$noise_level, 5e-05)
expect_equal(length(res_keep_nn@parameters$noise_level), 1)
expect_equal(res_keep_nn@parameters$fdr, 0.005)
expect_equal(length(res_keep_nn@parameters$fdr), 1)
expect_equal(res_keep_nn@parameters$row_sum, 1)
expect_equal(length(res_keep_nn@parameters$row_sum), 1)
expect_false(res_keep_nn@parameters$no_dknn_filter)
expect_equal(res_keep_nn@parameters$seed, 123)
expect_equal(length(res_keep_nn@parameters$seed), 1)
expect_true(res_keep_nn@parameters$keep_nn)
expect_equal(res_keep_nn@parameters$inflation, 2.2)
expect_equal(length(res_keep_nn@parameters$inflation), 1)
# =======================================================
# Test parameters in res_keep_nn@cluster_number
expect_equal(res_keep_nn@gene_clusters_metadata$number, 8)
# =======================================================
# Test parameters in res_keep_nn@cluster_list
expect_equal(length(res_keep_nn@gene_clusters_metadata$cluster_id), 8)
expect_equal(res_keep_nn@gene_clusters_metadata$cluster_id, 1:8)
})
# ==============================================================================
# Test output_path argument
# ==============================================================================
test_that("Checking stop if output directory provided does not exist", {
expect_error(gene_clustering(data = m,
name = "test",
inflation = 2,
output_path = "not_a_directory"))
})
dputhier/dbfmcl documentation built on Dec. 24, 2024, 4:35 p.m.
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# Set verbosity to 0
set_verbosity(0)
load_example_dataset("7871581/files/pbmc3k_medium")
pbmc3k_medium_clust <- select_genes(data = pbmc3k_medium,
distance_method = "pearson")
test_that("Checking output slots generated by gene_clustering() using keep_nn as FALSE", {
# Create output directory
tmp_dir <- tempdir()
dir.create(tmp_dir, recursive = TRUE, showWarnings = FALSE)
## A rather stringent version
res_no_keep_nn <- gene_clustering(object = pbmc3k_medium_clust,
inflation = 1.8,
keep_nn = FALSE,
s = 5,
threads = 6,
output_path = tmp_dir)
# =======================================================
# Test name of temporary files
expect_true(file.exists(file.path(res_no_keep_nn@parameters$output_path,
paste0(res_no_keep_nn@parameters$name,
".graph_input.txt"))))
expect_true(file.exists(file.path(res_no_keep_nn@parameters$output_path,
paste0(res_no_keep_nn@parameters$name,
".graph_out.txt"))))
expect_equal(length(res_no_keep_nn@parameters$name), 1)
expect_true(is.character(res_no_keep_nn@parameters$name))
# =======================================================
# Test matrix in res_no_keep_nn@data
expect_equal(round(sum(res_no_keep_nn@data), 0), 70172)
expect_equal(round(mean(res_no_keep_nn@data), 6), 0.639414)
expect_equal(round(median(res_no_keep_nn@data), 6), 0)
expect_equal(round(sd(res_no_keep_nn@data), 6), 1.329959)
expect_equal(round(sum(colMeans(res_no_keep_nn@data)), 1), 230.8)
expect_equal(round(sum(rowMeans(res_no_keep_nn@data)), 4), 194.382)
expect_equal(ncol(res_no_keep_nn@data), 361)
expect_equal(head(colnames(res_no_keep_nn@data)), c("GATCTACTGGTGAG-1", "ACAGTGACTCACCC-1", "AGACGTACAGAGGC-1",
"GACGTAACCTGTGA-1", "TATACAGATCCAGA-1", "CGGATAACAGCTCA-1"))
expect_equal(tail(colnames(res_no_keep_nn@data)), c("GGCATATGGGGAGT-1", "TTACGTACGTTCAG-1", "GGAACACTTCAGAC-1",
"ATCATCTGACACCA-1", "ACGAACTGGCTATG-1", "TAACACCTTGTTTC-1"))
expect_equal(nrow(res_no_keep_nn@data), 304)
expect_equal(nrow(res_no_keep_nn@data), length(get_genes(res_no_keep_nn)))
expect_equal(rownames(res_no_keep_nn@data), get_genes(res_no_keep_nn))
expect_equal(rownames(res_no_keep_nn@data), unlist(res_no_keep_nn@gene_clusters, use.names = F))
expect_equal(nrow(res_no_keep_nn@data), length(get_genes(res_no_keep_nn)))
expect_equal(nrow(res_no_keep_nn@data), length(unlist(res_no_keep_nn@gene_clusters)))
expect_equal(round(sum(res_no_keep_nn@data^2), 1), 238981.3)
expect_true(is.matrix(res_no_keep_nn@data))
expect_equal(length(res_no_keep_nn@data), 109744)
# =======================================================
# Test observed distances in res_no_keep_nn@dbf_output$dknn
expect_equal(round(sum(res_no_keep_nn@dbf_output$dknn), 3), 1324.35)
expect_equal(round(mean(res_no_keep_nn@dbf_output$dknn), 7), 0.8650231)
expect_equal(round(median(res_no_keep_nn@dbf_output$dknn), 7), 0.886363)
expect_equal(round(sd(res_no_keep_nn@dbf_output$dknn), 6), 0.069147)
expect_equal(length(res_no_keep_nn@dbf_output$dknn), 1531)
expect_equal(round(sum(res_no_keep_nn@dbf_output$dknn^2), 2), 1152.91)
# =======================================================
# Test simulated distances in res_no_keep_nn@dbf_output$simulated_dknn
expect_equal(round(sum(res_no_keep_nn@dbf_output$simulated_dknn), 3), 1335.374)
expect_equal(round(mean(res_no_keep_nn@dbf_output$simulated_dknn), 7), 0.8722235)
expect_equal(round(median(res_no_keep_nn@dbf_output$simulated_dknn), 7), 0.8722685)
expect_equal(round(sd(res_no_keep_nn@dbf_output$simulated_dknn), 6), 0.008386)
expect_equal(length(res_no_keep_nn@dbf_output$simulated_dknn), 1531)
expect_equal(round(sum(res_no_keep_nn@dbf_output$simulated_dknn^2), 2), 1164.85)
expect_true(is.numeric(res_no_keep_nn@dbf_output$simulated_dknn))
# =======================================================
# Test critical distance in res_no_keep_nn@critical_distance
expect_equal(round(res_no_keep_nn@dbf_output$critical_distance, 7), 0.8369334)
expect_equal(length(res_no_keep_nn@dbf_output$critical_distance), 1)
# =======================================================
# Test gene clusters in res_no_keep_nn@gene_clusters
expect_equal(sum(as.numeric(names(res_no_keep_nn@gene_clusters))), 136)
expect_equal(names(res_no_keep_nn@gene_clusters), as.character(1:16))
expect_equal(length(unlist(res_no_keep_nn@gene_clusters)), 304)
expect_equal(length(unlist(res_no_keep_nn@gene_clusters$`1`)), 63)
expect_equal(length(unlist(res_no_keep_nn@gene_clusters$`2`)), 37)
expect_equal(length(unlist(res_no_keep_nn@gene_clusters$`3`)), 34)
expect_equal(length(unlist(res_no_keep_nn@gene_clusters$`4`)), 29)
expect_equal(length(unlist(res_no_keep_nn@gene_clusters$`10`)), 12)
expect_equal(unlist(res_no_keep_nn@gene_clusters, use.names = F), get_genes(res_no_keep_nn))
expect_equal(
unlist(res_no_keep_nn@gene_clusters$`1`, use.names = F),
get_genes(res_no_keep_nn, cluster = 1)
)
expect_equal(
unlist(res_no_keep_nn@gene_clusters$`2`, use.names = F),
get_genes(res_no_keep_nn, cluster = 2)
)
expect_equal(
unlist(res_no_keep_nn@gene_clusters$`3`, use.names = F),
get_genes(res_no_keep_nn, cluster = 3)
)
expect_equal(
unlist(res_no_keep_nn@gene_clusters$`4`, use.names = F),
get_genes(res_no_keep_nn, cluster = 4)
)
expect_equal(unlist(res_no_keep_nn@gene_clusters, use.names = F), rownames(res_no_keep_nn@data))
expect_true(is.list(res_no_keep_nn@gene_clusters))
expect_true(is.character(res_no_keep_nn@gene_clusters$`1`))
# =======================================================
# Test size of gene clusters in res_no_keep_nn@gene_clusters_metadata$size
expect_equal(res_no_keep_nn@gene_clusters_metadata$size, c(`1` = 63L, `2` = 37L, `3` = 34L, `4` = 29L, `5` = 26L, `6` = 24L,
`7` = 21L, `8` = 14L, `9` = 14L, `10` = 12L, `11` = 7L, `12` = 6L,
`13` = 5L, `14` = 5L, `15` = 4L, `16` = 3L))
expect_true(is.integer(res_no_keep_nn@gene_clusters_metadata$size))
expect_equal(
res_no_keep_nn@gene_clusters_metadata$size[1],
c("1" = length(res_no_keep_nn@gene_clusters$`1`))
)
expect_equal(
res_no_keep_nn@gene_clusters_metadata$size[2],
c("2" = length(res_no_keep_nn@gene_clusters$`2`))
)
expect_equal(
res_no_keep_nn@gene_clusters_metadata$size[3],
c("3" = length(res_no_keep_nn@gene_clusters$`3`))
)
expect_equal(
res_no_keep_nn@gene_clusters_metadata$size[4],
c("4" = length(res_no_keep_nn@gene_clusters$`4`))
)
expect_equal(
res_no_keep_nn@gene_clusters_metadata$size[1],
c("1" = length(get_genes(res_no_keep_nn, cluster = 1)))
)
expect_equal(
res_no_keep_nn@gene_clusters_metadata$size[2],
c("2" = length(get_genes(res_no_keep_nn, cluster = 2)))
)
expect_equal(
res_no_keep_nn@gene_clusters_metadata$size[3],
c("3" = length(get_genes(res_no_keep_nn, cluster = 3)))
)
expect_equal(
res_no_keep_nn@gene_clusters_metadata$size[4],
c("4" = length(get_genes(res_no_keep_nn, cluster = 4)))
)
# =======================================================
# Test parameters in res_no_keep_nn@parameters
expect_true(is.list(res_no_keep_nn@parameters))
expect_equal(length(res_no_keep_nn@parameters), 12)
expect_equal(names(res_no_keep_nn@parameters), c(
"distance_method",
"k",
"noise_level",
"fdr",
"row_sum",
"no_dknn_filter",
"seed",
"keep_nn",
"k_graph",
"output_path",
"name",
"inflation"
))
expect_equal(res_no_keep_nn@parameters$output_path, tmp_dir)
expect_true(is.character(res_no_keep_nn@parameters$output_path))
expect_equal(length(res_no_keep_nn@parameters$output_path), 1)
expect_true(is.character(res_no_keep_nn@parameters$name))
expect_equal(length(res_no_keep_nn@parameters$name), 1)
expect_equal(nchar(res_no_keep_nn@parameters$name), 10)
expect_true(grepl("[[:alnum:]]+", res_no_keep_nn@parameters$name))
expect_equal(res_no_keep_nn@parameters$distance_method, "pearson")
expect_equal(length(res_no_keep_nn@parameters$distance_method), 1)
expect_equal(res_no_keep_nn@parameters$k, 80)
expect_true(is.numeric(res_no_keep_nn@parameters$k))
expect_equal(length(res_no_keep_nn@parameters$k), 1)
expect_equal(res_no_keep_nn@parameters$noise_level, 5e-05)
expect_true(is.numeric(res_no_keep_nn@parameters$noise_level))
expect_equal(length(res_no_keep_nn@parameters$noise_level), 1)
expect_equal(res_no_keep_nn@parameters$fdr, 0.005)
expect_equal(length(res_no_keep_nn@parameters$fdr), 1)
expect_equal(res_no_keep_nn@parameters$row_sum, 1)
expect_true(is.numeric(res_no_keep_nn@parameters$row_sum))
expect_equal(length(res_no_keep_nn@parameters$row_sum), 1)
expect_false(res_no_keep_nn@parameters$no_dknn_filter)
expect_equal(res_no_keep_nn@parameters$seed, 123)
expect_true(is.numeric(res_no_keep_nn@parameters$seed))
expect_equal(length(res_no_keep_nn@parameters$seed), 1)
expect_false(res_no_keep_nn@parameters$keep_nn)
expect_equal(res_no_keep_nn@parameters$k_graph, 5)
expect_true(is.numeric(res_no_keep_nn@parameters$k_graph))
expect_equal(length(res_no_keep_nn@parameters$k_graph), 1)
expect_equal(res_no_keep_nn@parameters$inflation, 1.8)
expect_true(is.numeric(res_no_keep_nn@parameters$inflation))
expect_equal(length(res_no_keep_nn@parameters$inflation), 1)
# =======================================================
# Test parameters in res_no_keep_nn@cluster_number
expect_equal(res_no_keep_nn@gene_clusters_metadata$number, 16)
expect_true(is.numeric(res_no_keep_nn@gene_clusters_metadata$number))
# =======================================================
# Test parameters in res_no_keep_nn@cluster_list
expect_equal(length(res_no_keep_nn@gene_clusters_metadata$cluster_id), 16)
expect_equal(res_no_keep_nn@gene_clusters_metadata$cluster_id, 1:16)
expect_true(is.numeric(res_no_keep_nn@gene_clusters_metadata$cluster_id))
# Remove temporary files
unlink(tmp_dir, recursive = TRUE)
})
test_that("Checking output slots generated by gene_clustering() using keep_nn as TRUE", {
## A rather stringent version
res_keep_nn <- gene_clustering(object = pbmc3k_medium_clust,
inflation = 2.2,
keep_nn = TRUE,
threads = 4,
name = "test")
# =======================================================
# Test name of temporary files
expect_equal(res_keep_nn@parameters$name, "test")
expect_true(file.exists(file.path(res_keep_nn@parameters$output_path,
paste0(res_keep_nn@parameters$name,
".graph_input.txt"))))
expect_true(file.exists(file.path(res_keep_nn@parameters$output_path,
paste0(res_keep_nn@parameters$name,
".graph_out.txt"))))
expect_true(file.exists(file.path(tempdir(), paste0(res_keep_nn@parameters$name,
".graph_input.txt"))))
expect_true(file.exists(file.path(tempdir(), paste0(res_keep_nn@parameters$name,
".graph_input.txt"))))
expect_equal(length(res_keep_nn@parameters$name), 1)
expect_true(is.character(res_keep_nn@parameters$name))
# =======================================================
# Test matrix in res_keep_nn@data
expect_equal(round(sum(res_keep_nn@data), 0), 70172)
expect_equal(round(mean(res_keep_nn@data), 2), 0.64)
expect_equal(round(median(res_keep_nn@data), 2), 0)
expect_equal(round(sd(res_keep_nn@data), 1), 1.3)
expect_equal(round(sum(colMeans(res_keep_nn@data)), 1), 230.8)
expect_equal(round(sum(rowMeans(res_keep_nn@data)), 1), 194.4)
expect_equal(ncol(res_keep_nn@data), 361)
expect_equal(head(colnames(res_keep_nn@data)), c("GATCTACTGGTGAG-1", "ACAGTGACTCACCC-1", "AGACGTACAGAGGC-1",
"GACGTAACCTGTGA-1", "TATACAGATCCAGA-1", "CGGATAACAGCTCA-1"))
expect_equal(nrow(res_keep_nn@data), 304)
expect_equal(nrow(res_keep_nn@data), length(get_genes(res_keep_nn)))
expect_equal(rownames(res_keep_nn@data), get_genes(res_keep_nn))
expect_equal(rownames(res_keep_nn@data), unlist(res_keep_nn@gene_clusters, use.names = F))
expect_equal(nrow(res_keep_nn@data), length(get_genes(res_keep_nn)))
expect_equal(nrow(res_keep_nn@data), length(unlist(res_keep_nn@gene_clusters)))
expect_equal(round(sum(res_keep_nn@data^2), 1), 238981.3)
expect_true(is.matrix(res_keep_nn@data))
expect_equal(length(res_keep_nn@data), 109744)
# =======================================================
# Test observed distances in res_keep_nn@dbf_output$dknn
expect_equal(round(sum(res_keep_nn@dbf_output$dknn), 1), 1324.4)
expect_equal(round(mean(res_keep_nn@dbf_output$dknn), 1), 0.9)
expect_equal(round(median(res_keep_nn@dbf_output$dknn), 2), 0.89)
expect_equal(round(sd(res_keep_nn@dbf_output$dknn), 2), 0.07)
expect_equal(length(res_keep_nn@dbf_output$dknn), 1531)
expect_equal(round(sum(res_keep_nn@dbf_output$dknn^2), 1), 1152.9)
expect_true(is.numeric(res_keep_nn@dbf_output$dknn))
# =======================================================
# Test simulated distances in res_keep_nn@dbf_output$simulated_dknn
expect_equal(round(sum(res_keep_nn@dbf_output$simulated_dknn), 2), 1335.37)
expect_equal(round(mean(res_keep_nn@dbf_output$simulated_dknn), 2), 0.87)
expect_equal(round(median(res_keep_nn@dbf_output$simulated_dknn), 2), 0.87)
expect_equal(round(sd(res_keep_nn@dbf_output$simulated_dknn), 2), 0.01)
expect_equal(length(res_keep_nn@dbf_output$simulated_dknn), 1531)
expect_equal(round(sum(res_keep_nn@dbf_output$simulated_dknn^2), 2), 1164.85)
expect_true(is.numeric(res_keep_nn@dbf_output$simulated_dknn))
# =======================================================
# Test critical distance in res_keep_nn@critical_distance
expect_equal(round(res_keep_nn@dbf_output$critical_distance, 2), 0.84)
expect_true(is.numeric(res_keep_nn@dbf_output$critical_distance))
expect_equal(length(res_keep_nn@dbf_output$critical_distance), 1)
# =======================================================
# Test gene clusters in res_keep_nn@gene_clusters
expect_equal(sum(as.numeric(names(res_keep_nn@gene_clusters))), 36)
expect_equal(names(res_keep_nn@gene_clusters), as.character(1:8))
expect_equal(length(unlist(res_keep_nn@gene_clusters)), 304)
expect_equal(length(unlist(res_keep_nn@gene_clusters$`1`)), 78)
expect_equal(length(unlist(res_keep_nn@gene_clusters$`2`)), 47)
expect_equal(length(unlist(res_keep_nn@gene_clusters$`3`)), 42)
expect_equal(length(unlist(res_keep_nn@gene_clusters$`4`)), 37)
expect_equal(unlist(res_keep_nn@gene_clusters, use.names = F), get_genes(res_keep_nn))
expect_equal(
unlist(res_keep_nn@gene_clusters$`1`, use.names = F),
get_genes(res_keep_nn, cluster = 1)
)
expect_equal(
unlist(res_keep_nn@gene_clusters$`2`, use.names = F),
get_genes(res_keep_nn, cluster = 2)
)
expect_equal(
unlist(res_keep_nn@gene_clusters$`3`, use.names = F),
get_genes(res_keep_nn, cluster = 3)
)
expect_equal(
unlist(res_keep_nn@gene_clusters$`4`, use.names = F),
get_genes(res_keep_nn, cluster = 4)
)
expect_equal(unlist(res_keep_nn@gene_clusters, use.names = F), rownames(res_keep_nn@data))
expect_true(is.list(res_keep_nn@gene_clusters))
expect_true(is.character(res_keep_nn@gene_clusters$`1`))
# =======================================================
# Test size of gene clusters in res_keep_nn@gene_clusters_metadata$size
expect_equal(res_keep_nn@gene_clusters_metadata$size, c(`1` = 78L, `2` = 47L, `3` = 42L, `4` = 37L, `5` = 36L, `6` = 24L,
`7` = 23L, `8` = 17L))
expect_true(is.integer(res_keep_nn@gene_clusters_metadata$size))
expect_equal(
res_keep_nn@gene_clusters_metadata$size[1],
c("1" = length(res_keep_nn@gene_clusters$`1`))
)
expect_equal(
res_keep_nn@gene_clusters_metadata$size[2],
c("2" = length(res_keep_nn@gene_clusters$`2`))
)
expect_equal(
res_keep_nn@gene_clusters_metadata$size[3],
c("3" = length(res_keep_nn@gene_clusters$`3`))
)
expect_equal(
res_keep_nn@gene_clusters_metadata$size[4],
c("4" = length(res_keep_nn@gene_clusters$`4`))
)
expect_equal(
res_keep_nn@gene_clusters_metadata$size[1],
c("1" = length(get_genes(res_keep_nn, cluster = 1)))
)
expect_equal(
res_keep_nn@gene_clusters_metadata$size[2],
c("2" = length(get_genes(res_keep_nn, cluster = 2)))
)
expect_equal(
res_keep_nn@gene_clusters_metadata$size[3],
c("3" = length(get_genes(res_keep_nn, cluster = 3)))
)
expect_equal(
res_keep_nn@gene_clusters_metadata$size[4],
c("4" = length(get_genes(res_keep_nn, cluster = 4)))
)
# =======================================================
# Test parameters in res_keep_nn@parameters
expect_true(is.list(res_keep_nn@parameters))
expect_equal(length(res_keep_nn@parameters), 11)
expect_equal(names(res_keep_nn@parameters), c(
"distance_method",
"k",
"noise_level",
"fdr",
"row_sum",
"no_dknn_filter",
"seed",
"keep_nn",
"output_path",
"name",
"inflation"
))
expect_true(is.character(res_keep_nn@parameters$output_path))
expect_equal(length(res_keep_nn@parameters$output_path), 1)
expect_equal(res_keep_nn@parameters$name, "test")
expect_equal(length(res_keep_nn@parameters$name), 1)
expect_equal(res_keep_nn@parameters$distance_method, "pearson")
expect_equal(length(res_keep_nn@parameters$distance_method), 1)
expect_equal(res_keep_nn@parameters$k, 80)
expect_equal(length(res_keep_nn@parameters$k), 1)
expect_equal(res_keep_nn@parameters$noise_level, 5e-05)
expect_equal(length(res_keep_nn@parameters$noise_level), 1)
expect_equal(res_keep_nn@parameters$fdr, 0.005)
expect_equal(length(res_keep_nn@parameters$fdr), 1)
expect_equal(res_keep_nn@parameters$row_sum, 1)
expect_equal(length(res_keep_nn@parameters$row_sum), 1)
expect_false(res_keep_nn@parameters$no_dknn_filter)
expect_equal(res_keep_nn@parameters$seed, 123)
expect_equal(length(res_keep_nn@parameters$seed), 1)
expect_true(res_keep_nn@parameters$keep_nn)
expect_equal(res_keep_nn@parameters$inflation, 2.2)
expect_equal(length(res_keep_nn@parameters$inflation), 1)
# =======================================================
# Test parameters in res_keep_nn@cluster_number
expect_equal(res_keep_nn@gene_clusters_metadata$number, 8)
# =======================================================
# Test parameters in res_keep_nn@cluster_list
expect_equal(length(res_keep_nn@gene_clusters_metadata$cluster_id), 8)
expect_equal(res_keep_nn@gene_clusters_metadata$cluster_id, 1:8)
})
# ==============================================================================
# Test output_path argument
# ==============================================================================
test_that("Checking stop if output directory provided does not exist", {
expect_error(gene_clustering(data = m,
name = "test",
inflation = 2,
output_path = "not_a_directory"))
})
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