choose_cells/ERROR: calculateLW: the reduced dims matrix has too few rows/No principal graph for UMAP calculated.

[HaixJiang]

When I extract the branch through the interactive interface, I can't graph_test to the cds_subset. The error is as follows:

> cds_subset <- choose_cells(mycds)
> subset_pr_test_res <- graph_test(cds_subset, neighbor_graph = "principal_graph",cores = 4)
Error in calculateLW(cds = cds, k = k, neighbor_graph = neighbor_graph,  :
  calculateLW: the reduced dims matrix has too few rows
>
> cds_sub <- choose_graph_segments(cds)
Error: No principal graph for UMAP calculated. Please run learn_graph with reduction_method = UMAP before running choose_graph_segments.
> cds_sub <- choose_graph_segments(mycds)
> subset_pr_test_res <- graph_test(cds_sub, neighbor_graph = "principal_graph",cores = 4)
Error: No dimensionality reduction for UMAP calculated. Please run reduce_dimension with reduction_method = UMAP before running graph_test.
> cds_sub@int_colData@listData$reducedDims@listData$UMAP

** traceback():**

3: stop("calculateLW: the reduced dims matrix has too few rows")
2: calculateLW(cds = cds, k = k, neighbor_graph = neighbor_graph,
       reduction_method = reduction_method, verbose = verbose, nn_control = nn_control)
1: graph_test(cds_subset, neighbor_graph = "principal_graph", cores = 4)

sessionInfo():

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods
[8] base
other attached packages:
 [1] shiny_1.8.0                 Matrix_1.6-1.1
 [3] dplyr_1.1.3                 ggplot2_3.4.4
 [5] SeuratObject_4.1.4          Seurat_4.4.0
 [7] monocle3_1.3.4              SingleCellExperiment_1.24.0
 [9] SummarizedExperiment_1.32.0 GenomicRanges_1.54.1
[11] GenomeInfoDb_1.38.0         IRanges_2.36.0
[13] S4Vectors_0.40.1            MatrixGenerics_1.14.0
[15] matrixStats_1.0.0           Biobase_2.62.0
[17] BiocGenerics_0.48.0

loaded via a namespace (and not attached):
  [1] RColorBrewer_1.1-3        jsonlite_1.8.7
  [3] magrittr_2.0.3            spatstat.utils_3.0-4
  [5] farver_2.1.1              nloptr_2.0.3
  [7] ragg_1.2.6                zlibbioc_1.48.0
  [9] vctrs_0.6.4               ROCR_1.0-11
 [11] memoise_2.0.1             DelayedMatrixStats_1.24.0
 [13] minqa_1.2.6               spatstat.explore_3.2-5
 [15] RCurl_1.98-1.12           terra_1.7-55
 [17] htmltools_0.5.7           S4Arrays_1.2.0
 [19] SparseArray_1.2.0         sass_0.4.7
 [21] sctransform_0.4.1         parallelly_1.36.0
 [23] bslib_0.5.1               KernSmooth_2.23-22
 [25] htmlwidgets_1.6.2         ica_1.0-3
 [27] plyr_1.8.9                cachem_1.0.8
 [29] plotly_4.10.3             zoo_1.8-12
 [31] igraph_1.5.1              mime_0.12
 [33] lifecycle_1.0.4           pkgconfig_2.0.3
 [35] R6_2.5.1                  fastmap_1.1.1
 [37] GenomeInfoDbData_1.2.11   fitdistrplus_1.1-11
 [39] future_1.33.0             digest_0.6.33
 [41] colorspace_2.1-0          patchwork_1.1.3
 [43] tensor_1.5                irlba_2.3.5.1
 [45] textshaping_0.3.7         labeling_0.4.3
 [47] progressr_0.14.0          fansi_1.0.5
 [49] spatstat.sparse_3.0-3     httr_1.4.7
 [51] polyclip_1.10-6           abind_1.4-5
 [53] compiler_4.3.1            proxy_0.4-27
 [55] withr_2.5.2               MASS_7.3-60
 [57] DelayedArray_0.28.0       tools_4.3.1
 [59] lmtest_0.9-40             httpuv_1.6.12
 [61] future.apply_1.11.0       goftest_1.2-3
 [63] glue_1.6.2                nlme_3.1-163
 [65] promises_1.2.1            grid_4.3.1
 [67] Rtsne_0.17                cluster_2.1.4
 [69] reshape2_1.4.4            generics_0.1.3
 [71] gtable_0.3.4              spatstat.data_3.0-3
 [73] tidyr_1.3.0               data.table_1.14.8
 [75] sp_2.1-1                  utf8_1.2.4
 [77] XVector_0.42.0            spatstat.geom_3.2-7
 [79] RcppAnnoy_0.0.21          ggrepel_0.9.4
 [81] RANN_2.6.1                pillar_1.9.0
 [83] stringr_1.5.1             later_1.3.1
 [85] splines_4.3.1             lattice_0.22-5
 [87] survival_3.5-7            deldir_1.0-9
 [89] tidyselect_1.2.0          miniUI_0.1.1.1
 [91] pbapply_1.7-2             gridExtra_2.3
 [93] scattermore_1.2           leidenbase_0.1.25
 [95] stringi_1.8.1             lazyeval_0.2.2
 [97] boot_1.3-28.1             codetools_0.2-19
 [99] tibble_3.2.1              cli_3.6.1
[101] uwot_0.1.16               systemfonts_1.0.5
[103] xtable_1.8-4              reticulate_1.34.0
[105] jquerylib_0.1.4           munsell_0.5.0
[107] Rcpp_1.0.11               globals_0.16.2
[109] spatstat.random_3.2-1     png_0.1-8
[111] parallel_4.3.1            ellipsis_0.3.2
[113] assertthat_0.2.1          sparseMatrixStats_1.14.0
[115] bitops_1.0-7              lme4_1.1-34
[117] listenv_0.9.0             viridisLite_0.4.2
[119] scales_1.2.1              ggridges_0.5.4
[121] leiden_0.4.3              purrr_1.0.2
[123] crayon_1.5.2              rlang_1.1.2
[125] cowplot_1.1.1