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brgewbrgew
committedAug 18, 2023
Update non-Actions regression target values for VirtualBox.
1 parent 85fa19e commit 2b17745

8 files changed

+65
-65
lines changed
 

‎tests/testthat/test-alignment.R

+2-2
Original file line numberDiff line numberDiff line change
@@ -86,7 +86,7 @@ test_that("Alignment works on synthetic data", {
8686
batched_cds = cluster_cells(batched_cds, k=10, reduction_method="PCA", resolution=1e-3)
8787
plot_cells(batched_cds, reduction_method="PCA", color_cells_by="partition")
8888

89-
expect_equal(length(unique(partitions(batched_cds, reduction_method="PCA"))), 5)
89+
expect_equal(length(unique(partitions(batched_cds, reduction_method="PCA"))), 4)
9090

9191
#batched_cds = preprocess_cds(batched_cds, num_dim=2, residual_model_formula_str="~cell_type")
9292

@@ -106,7 +106,7 @@ test_that("Alignment works on synthetic data", {
106106
batched_cds = cluster_cells(batched_cds, k=10, reduction_method="Aligned", resolution=1e-3)
107107
plot_cells(batched_cds, reduction_method="Aligned", color_cells_by="batch")
108108

109-
expect_equal(length(unique(partitions(batched_cds, reduction_method="Aligned"))), 10)
109+
expect_equal(length(unique(partitions(batched_cds, reduction_method="Aligned"))), 9)
110110

111111

112112
#plot_cells(batched_cds, reduction_method="PCA", color_cells_by="cluster")

‎tests/testthat/test-cluster_cells.R

+6-7
Original file line numberDiff line numberDiff line change
@@ -56,9 +56,8 @@ test_that("cluster_cells works", {
5656
expect_equal(length(cds@clusters[["UMAP"]]), 3)
5757
expect_equal(length(cds@clusters[["UMAP"]]$cluster_result$optim_res$membership),
5858
nrow(colData(cds)))
59-
expect_equal(cds@clusters[["UMAP"]]$cluster_result$optim_res$membership[[1]],
60-
3)
61-
expect_equal(length(unique(clusters(cds, reduction_method = "UMAP"))), 17)
59+
expect_equal(cds@clusters[["UMAP"]]$cluster_result$optim_res$membership[[1]], 16)
60+
expect_equal(length(unique(clusters(cds, reduction_method = "UMAP"))), 20)
6261

6362
## louvain
6463
cds <- cluster_cells(cds, cluster_method = "louvain", random_seed = 100)
@@ -68,7 +67,7 @@ test_that("cluster_cells works", {
6867
nrow(colData(cds)))
6968
expect_equal(cds@clusters[["UMAP"]]$cluster_result$optim_res$membership[[1]],
7069
1)
71-
expect_equal(length(unique(clusters(cds, reduction_method = "UMAP"))), 8)
70+
expect_equal(length(unique(clusters(cds, reduction_method = "UMAP"))), 11)
7271

7372
# non-standard opts
7473
cds <- cluster_cells(cds, cluster_method = "louvain", k=22, weight = TRUE,
@@ -80,7 +79,7 @@ test_that("cluster_cells works", {
8079
nrow(colData(cds)))
8180
expect_equal(cds@clusters[["UMAP"]]$cluster_result$optim_res$membership[[1]],
8281
1)
83-
expect_equal(length(unique(clusters(cds, reduction_method = "UMAP"))), 12)
82+
expect_equal(length(unique(clusters(cds, reduction_method = "UMAP"))), 13)
8483

8584
### tSNE
8685
##leiden
@@ -102,8 +101,8 @@ test_that("cluster_cells works", {
102101
expect_equal(length(cds@clusters[["tSNE"]]$cluster_result$optim_res$membership),
103102
nrow(colData(cds)))
104103
expect_equal(cds@clusters[["tSNE"]]$cluster_result$optim_res$membership[[1]],
105-
6)
106-
expect_equal(length(unique(clusters(cds, reduction_method = "tSNE"))), 21)
104+
17)
105+
expect_equal(length(unique(clusters(cds, reduction_method = "tSNE"))), 22)
107106

108107
### PCA
109108

‎tests/testthat/test-fit_models.R

+2-1
Original file line numberDiff line numberDiff line change
@@ -9,6 +9,7 @@ skip_not_travis <- function ()
99
skip("Not on Travis")
1010
}
1111

12+
library(pryr)
1213

1314
cds <- load_a549()
1415
#cds <- estimate_size_factors(cds)
@@ -321,7 +322,7 @@ test_that("fit_models() can handle cluster in model formulae",{
321322
expression_family = "quasipoisson")
322323
expect_equal(pos_ctrl_gene_fit$status[[1]], "OK")
323324
pos_ctrl_coefs = coefficient_table(pos_ctrl_gene_fit)
324-
expect_equal(pos_ctrl_coefs$estimate[2], -0.0962, tolerance=1e-3)
325+
expect_equal(pos_ctrl_coefs$estimate[2], -0.99, tolerance=1e-2)
325326
})
326327

327328

‎tests/testthat/test-graph_test.R

+3-3
Original file line numberDiff line numberDiff line change
@@ -42,15 +42,15 @@ test_that("test graph_test returns Dex-dependent genes",{
4242
pos_ctrl_gene = test_cds[rowData(cds)$gene_short_name == "che-1",]
4343
pr_test_res = graph_test(pos_ctrl_gene)
4444
expect_equal(pr_test_res$status[1], "OK")
45-
expect_equal(pr_test_res$morans_I, 0.65, tolerance=1e-2)
45+
expect_equal(pr_test_res$morans_I, 0.661, tolerance=1e-2)
4646
expect_equal(pr_test_res$morans_test_statistic, 204.72, tolerance=1e-1)
4747
expect_lt(pr_test_res$p_value[1], 0.05)
4848

4949
neg_ctrl_gene = test_cds[rowData(cds)$gene_short_name == "R02D3.1",]
5050
pr_test_res = graph_test(neg_ctrl_gene)
5151
expect_equal(pr_test_res$status[1], "OK")
52-
expect_equal(pr_test_res$morans_I, -0.00264, tolerance=1e-4)
53-
expect_equal(pr_test_res$morans_test_statistic, -0.731, tolerance=1e-2)
52+
expect_equal(pr_test_res$morans_I, -0.000752, tolerance=1e-5)
53+
expect_equal(pr_test_res$morans_test_statistic, -0.173, tolerance=1e-2)
5454
expect_gt(pr_test_res$p_value[1], 0.05)
5555
})
5656

‎tests/testthat/test-io.R

+2-2
Original file line numberDiff line numberDiff line change
@@ -280,7 +280,7 @@ test_that("save_transform_models and load_transform_models", {
280280
# check UMAP reduced dims matrix and nearest neighbors
281281
expect_equivalent(ncol(reducedDims(cds)[['UMAP']]), 2)
282282
expect_equivalent(nrow(reducedDims(cds)[['UMAP']]), 500)
283-
expect_equivalent(reducedDims(cds)[['UMAP']][[1,1]], 1.96, tol=1e-2)
283+
expect_equivalent(reducedDims(cds)[['UMAP']][[1,1]], 2.7, tol=1e-1)
284284
nn_res <- search_nn_index(query_matrix=reducedDims(cds)[['UMAP']], nn_index=get_cds_nn_index(cds, reduction_method='UMAP', nn_method=nn_method, verbose=FALSE), k=5, nn_control=list(method=nn_method, metric='euclidean', n_trees=50))
285285
expect_equivalent(nn_res[['nn.idx']][[1]], 1)
286286
expect_equivalent(nn_res[['nn.dists']][[1]], 0)
@@ -349,7 +349,7 @@ test_that("save_monocle_objects and load_monocle_objects", {
349349
# check UMAP reduced dims matrix and nearest neighbors
350350
expect_equivalent(ncol(reducedDims(cds)[['UMAP']]), 2)
351351
expect_equivalent(nrow(reducedDims(cds)[['UMAP']]), 500)
352-
expect_equivalent(reducedDims(cds)[['UMAP']][[1,1]], 1.96, tol=1e-2)
352+
expect_equivalent(reducedDims(cds)[['UMAP']][[1,1]], 2.7, tol=1e-1)
353353
nn_res <- search_nn_index(query_matrix=reducedDims(cds)[['UMAP']], nn_index=get_cds_nn_index(cds, reduction_method='UMAP', nn_method=nn_method), k=5, nn_control=list(method=nn_method, metric='euclidean', n_trees=50))
354354
expect_equivalent(nn_res[['nn.idx']][[1]], 1)
355355
expect_equivalent(nn_res[['nn.dists']][[1]], 0)

‎tests/testthat/test-learn_graph.R

+10-10
Original file line numberDiff line numberDiff line change
@@ -33,32 +33,32 @@ test_that("learn_graph stays the same", {
3333
skip_on_travis()
3434
cds <- learn_graph(cds)
3535
expect_is(principal_graph(cds)[["UMAP"]], "igraph")
36-
expect_equal(length(principal_graph(cds)[["UMAP"]]), 63)
37-
expect_equal(as.character(principal_graph(cds)[["UMAP"]][[1]]$Y_1[[1]]), "3")
36+
expect_equal(length(principal_graph(cds)[["UMAP"]]), 33)
37+
expect_equal(as.character(principal_graph(cds)[["UMAP"]][[1]]$Y_1[[1]]), "24")
3838

3939
# Force partition
4040
temp <- rep(c(1,2), length.out=length(partitions(cds)))
4141
names(temp) <- names(partitions(cds))
4242
cds@clusters[["UMAP"]]$partitions <- temp
4343
cds <- learn_graph(cds, use_partition = FALSE)
4444
expect_is(principal_graph(cds)[["UMAP"]], "igraph")
45-
expect_equal(length(principal_graph(cds)[["UMAP"]]), 63)
46-
expect_equal(as.character(principal_graph(cds)[["UMAP"]][[1]]$Y_1[[1]]), "3")
45+
expect_equal(length(principal_graph(cds)[["UMAP"]]), 33)
46+
expect_equal(as.character(principal_graph(cds)[["UMAP"]][[1]]$Y_1[[1]]), "24")
4747

4848
cds <- learn_graph(cds)
4949
expect_is(principal_graph(cds)[["UMAP"]], "igraph")
50-
expect_equal(length(principal_graph(cds)[["UMAP"]]), 104)
51-
expect_equal(as.character(principal_graph(cds)[["UMAP"]][[1]]$Y_1[[1]]), "24")
50+
expect_equal(length(principal_graph(cds)[["UMAP"]]), 74)
51+
expect_equal(as.character(principal_graph(cds)[["UMAP"]][[1]]$Y_1[[1]]), "36")
5252

5353
cds <- learn_graph(cds, close_loop = TRUE)
5454
expect_is(principal_graph(cds)[["UMAP"]], "igraph")
55-
expect_equal(length(principal_graph(cds)[["UMAP"]]), 104)
56-
expect_equal(as.character(principal_graph(cds)[["UMAP"]][[1]]$Y_1[[1]]), "24")
55+
expect_equal(length(principal_graph(cds)[["UMAP"]]), 74)
56+
expect_equal(as.character(principal_graph(cds)[["UMAP"]][[1]]$Y_1[[1]]), "36")
5757

5858
cds <- learn_graph(cds, learn_graph_control = list(prune_graph = FALSE))
5959
expect_is(principal_graph(cds)[["UMAP"]], "igraph")
60-
expect_equal(length(principal_graph(cds)[["UMAP"]]), 216)
61-
expect_equal(as.character(principal_graph(cds)[["UMAP"]][[1]]$Y_1[[1]]), "46")
60+
expect_equal(length(principal_graph(cds)[["UMAP"]]), 144)
61+
expect_equal(as.character(principal_graph(cds)[["UMAP"]][[1]]$Y_1[[1]]), "8")
6262
})
6363

6464

‎tests/testthat/test-order_cells.R

+30-30
Original file line numberDiff line numberDiff line change
@@ -36,21 +36,21 @@ cds <- learn_graph(cds)
3636
test_that("order_cells works", {
3737
skip_on_travis()
3838
cds <- order_cells(cds, root_pr_nodes = "Y_1")
39-
expect_equal(max(pseudotime(cds)), 16.5, tol = 1e-1)
39+
expect_equal(max(pseudotime(cds)), 11.9, tol = 1e-1)
4040
expect_equal(min(pseudotime(cds)), 0)
41-
expect_equal(as.numeric(pseudotime(cds)[1]), 0.111, tol = 1e-2)
41+
expect_equal(as.numeric(pseudotime(cds)[1]), 0.0538, tol = 1e-3)
4242
cds <- order_cells(cds, root_pr_nodes = c("Y_1", "Y_10"))
43-
expect_equal(max(pseudotime(cds)), 9.08, tol = 1e-2)
43+
expect_equal(max(pseudotime(cds)), 6.34, tol = 1e-2)
4444
expect_equal(min(pseudotime(cds)), 0)
45-
expect_equal(as.numeric(pseudotime(cds)[1]), 0.111, tol = 1e-2)
45+
expect_equal(as.numeric(pseudotime(cds)[1]), 0.0538, tol = 1e-3)
4646
cds <- order_cells(cds, root_cells = "G07_B02_RT_587")
47-
expect_equal(max(pseudotime(cds)), 14.9, tol = 1e-1)
47+
expect_equal(max(pseudotime(cds)), 13.2, tol = 1e-1)
4848
expect_equal(min(pseudotime(cds)), 0)
49-
expect_equal(as.numeric(pseudotime(cds)[1]), 2.18, tol = 1e-2)
49+
expect_equal(as.numeric(pseudotime(cds)[1]), 1.5, tol = 1e-1)
5050
cds <- order_cells(cds, root_cells = c("G07_B02_RT_587", "F06_A01_RT_598"))
51-
expect_equal(max(pseudotime(cds)), 8.89, tol = 1e-2)
51+
expect_equal(max(pseudotime(cds)), 7.26, tol = 1e-2)
5252
expect_equal(min(pseudotime(cds)), 0)
53-
expect_equal(as.numeric(pseudotime(cds)[1]), 2.18, tol = 1e-2)
53+
expect_equal(as.numeric(pseudotime(cds)[1]), 1.5, tol = 1e-1)
5454
})
5555

5656
cds <- reduce_dimension(cds, max_components = 3, umap.fast_sgd=FALSE)
@@ -62,19 +62,19 @@ test_that("order_cells works 3d", {
6262
cds <- order_cells(cds, root_pr_nodes = "Y_1")
6363
expect_equal(max(pseudotime(cds)), 10.0, tol = 1e-1)
6464
expect_equal(min(pseudotime(cds)), 0)
65-
expect_equal(as.numeric(pseudotime(cds)[1]), 9.67e-7, tol = 1e-8)
65+
expect_equal(as.numeric(pseudotime(cds)[1]), 0.664, tol = 1e-3)
6666
cds <- order_cells(cds, root_pr_nodes = c("Y_1", "Y_10"))
67-
expect_equal(max(pseudotime(cds)), 7.69, tol = 1e-2)
67+
expect_equal(max(pseudotime(cds)), 8.64, tol = 1e-2)
6868
expect_equal(min(pseudotime(cds)), 0)
69-
expect_equal(as.numeric(pseudotime(cds)[1]), 9.67e-7, tol = 1e-8)
69+
expect_equal(as.numeric(pseudotime(cds)[1]), 0.664, tol = 1e-3)
7070
cds <- order_cells(cds, root_cells = "G07_B02_RT_587")
71-
expect_equal(max(pseudotime(cds)), 13.4, tol = 1e-1)
71+
expect_equal(max(pseudotime(cds)), 10.4, tol = 1e-1)
7272
expect_equal(min(pseudotime(cds)), 0)
73-
expect_equal(as.numeric(pseudotime(cds)[1]), 3.17, tol = 1e-1)
73+
expect_equal(as.numeric(pseudotime(cds)[1]), 0.664, tol = 1e-3)
7474
cds <- order_cells(cds, root_cells = c("G07_B02_RT_587", "F06_A01_RT_598"))
7575
expect_equal(max(pseudotime(cds)), 10.2, tol = 1e-1)
7676
expect_equal(min(pseudotime(cds)), 0)
77-
expect_equal(as.numeric(pseudotime(cds)[1]), 3.17, tol = 1e-1)
77+
expect_equal(as.numeric(pseudotime(cds)[1]), 0.664, tol = 1e-3)
7878
})
7979

8080
cds <- cluster_cells(cds, random_seed = 100)
@@ -83,21 +83,21 @@ cds <- learn_graph(cds)
8383
test_that("order_cells works leiden", {
8484
skip_on_travis()
8585
cds <- order_cells(cds, root_pr_nodes = "Y_1")
86-
expect_equal(max(pseudotime(cds)), 6.35, tol = 1e-2)
86+
expect_equal(max(pseudotime(cds)), 9.94, tol = 1e-2)
8787
expect_equal(min(pseudotime(cds)), 0)
88-
expect_equal(as.numeric(pseudotime(cds)[1]), 1.94, tol = 1e-2)
88+
expect_equal(as.numeric(pseudotime(cds)[1]), 4.49, tol = 1e-2)
8989
cds <- order_cells(cds, root_pr_nodes = c("Y_1", "Y_2"))
90-
expect_equal(max(pseudotime(cds)), 3.76, tol = 1e-2)
90+
expect_equal(max(pseudotime(cds)), 4.72, tol = 1e-2)
9191
expect_equal(min(pseudotime(cds)), 0)
92-
expect_equal(as.numeric(pseudotime(cds)[1]), 1.94, tol = 1e-2)
92+
expect_equal(as.numeric(pseudotime(cds)[1]), 4.35, tol = 1e-2)
9393
cds <- order_cells(cds, root_cells = "G07_B02_RT_587")
94-
expect_equal(max(pseudotime(cds)), 6.35, tol = 1e-2)
94+
expect_equal(max(pseudotime(cds)), 8.03, tol = 1e-2)
9595
expect_equal(min(pseudotime(cds)), 0)
96-
expect_equal(as.numeric(pseudotime(cds)[1]), 1.94 , tol = 1e-2)
96+
expect_equal(as.numeric(pseudotime(cds)[1]), 0.121 , tol = 1e-3)
9797
cds <- order_cells(cds, root_cells = c("G07_B02_RT_587", "F06_A01_RT_598"))
98-
expect_equal(max(pseudotime(cds)), 4.15, tol = 1e-2)
98+
expect_equal(max(pseudotime(cds)), 5.85, tol = 1e-2)
9999
expect_equal(min(pseudotime(cds)), 0)
100-
expect_equal(as.numeric(pseudotime(cds)[1]), 1.94 , tol = 1e-2)
100+
expect_equal(as.numeric(pseudotime(cds)[1]), 0.121 , tol = 1e-3)
101101
})
102102

103103
cds <- reduce_dimension(cds, max_components = 3, umap.fast_sgd=FALSE)
@@ -107,21 +107,21 @@ cds <- learn_graph(cds)
107107
test_that("order_cells works leiden 3d", {
108108
skip_on_travis()
109109
cds <- order_cells(cds, root_pr_nodes = "Y_1")
110-
expect_equal(max(pseudotime(cds)), 6.35, tol = 1e-1)
110+
expect_equal(max(pseudotime(cds)), 9.94, tol = 1e-2)
111111
expect_equal(min(pseudotime(cds)), 0)
112-
expect_equal(as.numeric(pseudotime(cds)[1]), 1.94, tol = 1e-2)
112+
expect_equal(as.numeric(pseudotime(cds)[1]), 4.49, tol = 1e-2)
113113
cds <- order_cells(cds, root_pr_nodes = c("Y_1", "Y_2"))
114-
expect_equal(max(pseudotime(cds)), 3.76, tol = 1e-2)
114+
expect_equal(max(pseudotime(cds)), 4.72, tol = 1e-2)
115115
expect_equal(min(pseudotime(cds)), 0)
116-
expect_equal(as.numeric(pseudotime(cds)[1]), 1.94, tol = 1e-2)
116+
expect_equal(as.numeric(pseudotime(cds)[1]), 4.35, tol = 1e-2)
117117
cds <- order_cells(cds, root_cells = "G07_B02_RT_587")
118-
expect_equal(max(pseudotime(cds)), 6.35, tol = 1e-2)
118+
expect_equal(max(pseudotime(cds)), 8.03, tol = 1e-2)
119119
expect_equal(min(pseudotime(cds)), 0)
120-
expect_equal(as.numeric(pseudotime(cds)[1]), 1.94, tol = 1e-2)
120+
expect_equal(as.numeric(pseudotime(cds)[1]), 0.121, tol = 1e-3)
121121
cds <- order_cells(cds, root_cells = c("G07_B02_RT_587", "F06_A01_RT_598"))
122-
expect_equal(max(pseudotime(cds)), 4.15, tol = 1e-2)
122+
expect_equal(max(pseudotime(cds)), 5.85, tol = 1e-2)
123123
expect_equal(min(pseudotime(cds)), 0)
124-
expect_equal(as.numeric(pseudotime(cds)[1]), 1.94, tol = 1e-2)
124+
expect_equal(as.numeric(pseudotime(cds)[1]), 0.121, tol = 1e-3)
125125
})
126126

127127

‎tests/testthat/test-reduce_dimension.R

+10-10
Original file line numberDiff line numberDiff line change
@@ -27,25 +27,25 @@ test_that("reduce_dimension runs", {
2727
cds <- reduce_dimension(cds, umap.fast_sgd=FALSE, cores=1)
2828
expect_equal(nrow(reducedDims(cds)$UMAP), nrow(colData(cds)))
2929
expect_equal(ncol(reducedDims(cds)$UMAP), 2)
30-
expect_equal(as.numeric(reducedDims(cds)$UMAP[1,1]), -2.86,
30+
expect_equal(as.numeric(reducedDims(cds)$UMAP[1,1]), 2.26,
3131
tolerance = 1e-2)
3232

3333
cds <- reduce_dimension(cds, max_components = 3, umap.fast_sgd=FALSE, cores=1, reduction_method = "UMAP")
3434
expect_equal(nrow(reducedDims(cds)$UMAP), nrow(colData(cds)))
3535
expect_equal(ncol(reducedDims(cds)$UMAP), 3)
36-
expect_equal(as.numeric(reducedDims(cds)$UMAP[1,1]), 1.69,
37-
tolerance = 1e-2)
36+
expect_equal(as.numeric(reducedDims(cds)$UMAP[1,1]), 0.265,
37+
tolerance = 1e-3)
3838

3939
cds <- reduce_dimension(cds, reduction_method = "tSNE")
4040
expect_equal(nrow(reducedDims(cds)$tSNE), nrow(colData(cds)))
4141
expect_equal(ncol(reducedDims(cds)$tSNE), 2)
42-
expect_equal(as.numeric(reducedDims(cds)$tSNE[1,1]), -1.16,
42+
expect_equal(as.numeric(reducedDims(cds)$tSNE[1,1]), -3.74,
4343
tolerance = 1e-2)
4444

4545
cds <- reduce_dimension(cds, max_components = 3, reduction_method = "tSNE")
4646
expect_equal(nrow(reducedDims(cds)$tSNE), nrow(colData(cds)))
4747
expect_equal(ncol(reducedDims(cds)$tSNE), 3)
48-
expect_equal(as.numeric(reducedDims(cds)$tSNE[1,1]), -4.29,
48+
expect_equal(as.numeric(reducedDims(cds)$tSNE[1,1]), -5.29,
4949
tolerance = 1e-2)
5050

5151
cds <- reduce_dimension(cds, reduction_method = "PCA")
@@ -57,14 +57,14 @@ test_that("reduce_dimension runs", {
5757
cds <- reduce_dimension(cds, umap.fast_sgd=FALSE, cores=1, preprocess_method = "LSI")
5858
expect_equal(nrow(reducedDims(cds)$UMAP), nrow(colData(cds)))
5959
expect_equal(ncol(reducedDims(cds)$UMAP), 2)
60-
expect_equal(as.numeric(reducedDims(cds)$UMAP[1,1]), -0.163,
61-
tolerance = 1e-3)
60+
expect_equal(as.numeric(reducedDims(cds)$UMAP[1,1]), -1.21,
61+
tolerance = 1e-2)
6262

6363
cds <- reduce_dimension(cds, reduction_method = "tSNE", preprocess_method = "LSI")
6464
expect_equal(nrow(reducedDims(cds)$tSNE), nrow(colData(cds)))
6565
expect_equal(ncol(reducedDims(cds)$tSNE), 2)
66-
expect_equal(as.numeric(reducedDims(cds)$tSNE[1,1]), -2.15,
67-
tolerance = 1e-2)
66+
expect_equal(as.numeric(reducedDims(cds)$tSNE[1,1]), 0.738,
67+
tolerance = 1e-3)
6868

6969
# check model
7070
set.seed(100)
@@ -78,7 +78,7 @@ test_that("reduce_dimension runs", {
7878
expect_equal(cds@reduce_dim_aux[['UMAP']][['model']][['umap_min_dist']], 0.1, tol=1e-1)
7979
expect_equal(cds@reduce_dim_aux[['UMAP']][['model']][['umap_n_neighbors']], 15, tol=1e1)
8080
expect_equal(cds@reduce_dim_aux[['UMAP']][['model']][['umap_fast_sgd']], FALSE)
81-
expect_equal(cds@reduce_dim_aux[['UMAP']][['model']][['umap_model']][['embedding']][[1,1]], -1.80, tol=1e-1)
81+
expect_equal(cds@reduce_dim_aux[['UMAP']][['model']][['umap_model']][['embedding']][[1,1]], 2.03, tol=1e-2)
8282
expect_equal(cds@reduce_dim_aux[['UMAP']][['model']][['umap_model']][['n_neighbors']][[1]], 15, tol=1e1)
8383

8484

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