9 Cell Fate and Dynamic Processes

This mainline shifts the analysis story from static identity to directional biology. Once cells have been placed in a baseline manifold, the next question is often whether they lie along a continuum, where terminal states sit, and which transitions are supported by the data.

sclet gathers diffusion-based embeddings, lineage inference, velocity, and fate-oriented methods under the same workflow umbrella. The point is not just to expose more algorithms, but to make the dynamics route readable and reusable as one coherent chapter of analysis.

9.1 Trajectory mainline workflow

If you do not want to stitch together RunDiffusionMap(), RunSlingshot(), RunVelocity(), and RunCellFate() by hand every time, sclet now provides RunTrajectoryWorkflow() as the semantic entry point for this entire analysis mainline.

The point of this wrapper is not to hide the underlying methods. The point is to make the recommended analysis path easier to follow, easier to document, and easier to rerun later.

panc_main <- readRDS("data/pancreas_sub_sce.rds")
panc_main <- RunTrajectoryWorkflow(
  panc_main,
  group = "SubCellType",
  reduction = "UMAP",
  run_diffusion_map = TRUE,
  run_slingshot = TRUE,
  run_velocity = "never",
  run_fate = "never",
  name = "pancreas_main"
)
## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'
## Also defined by 'alabaster.base'
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## Also defined by 'alabaster.base'
## 'as(<dsCMatrix>, "dgTMatrix")' is deprecated.
## Use 'as(as(., "generalMatrix"), "TsparseMatrix")' instead.
## See help("Deprecated") and help("Matrix-deprecated").
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## Also defined by 'alabaster.base'
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## Also defined by 'alabaster.base'
plot_trajectory_overview(
  panc_main,
  id = "pancreas_main",
  panels = c("lineage")
)
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## Also defined by 'alabaster.base'
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## Also defined by 'alabaster.base'

panc <- readRDS("data/pancreas_sub_sce.rds")

panc <- RunSlingshot(sce = panc, group = "SubCellType", reduction = "UMAP")
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RunSlingshot() writes its result back into the unified state layer, so downstream helpers such as plot_lineage() and plot_pseudotime() can consume the recorded trajectory object directly. If needed, you can also check has_trajectory(panc) or inspect get_trajectory(panc).

If you keep multiple trajectory runs in the same object, give them different name values and inspect them explicitly with get_trajectory(panc, id = "your_id").

9.1.1 Lineage plot

p1 <- plot_lineage(panc, group = "SubCellType") + 
  sc_dim_geom_label(
    geom = shadowtext::geom_shadowtext,
    color='black', 
    bg.color='white'
  )
## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'
## Also defined by 'alabaster.base'
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## Also defined by 'alabaster.base'
## displayed selected lineages
p2 <- plot_lineage(panc, group = "SubCellType", lineages = c("Lineage1", "Lineage2"))  + 
  sc_dim_geom_label(
    geom = shadowtext::geom_shadowtext,
    color='black', 
    bg.color='white'
  )
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## Also defined by 'alabaster.base'
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## Also defined by 'alabaster.base'
plot_list(`All Lineages` = p1, `Selected Lineages` = p2, ncol=1)

9.1.2 Pseudotime plot

pp1 <- plot_pseudotime(panc, reduction = "UMAP", lineage = "Lineage1")
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## Also defined by 'alabaster.base'
pp2 <- plot_pseudotime(panc, reduction = "UMAP", lineage = "Lineage2")
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## Also defined by 'alabaster.base'
pp_all <- plot_pseudotime(panc, reduction = "UMAP")
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## Also defined by 'alabaster.base'
plot_list(pp1, pp2, pp_all, design="AABB\nCCCC")

9.1.4 Heatmap

heatmap_genes <- head(unique(rownames(panc)), 10)

## 默认按照拟时间排序
hmp1 <- plot_pseudo_heatmap(panc, features = heatmap_genes, lineage = "Lineage2")

## 可以手动对基因或细胞设置聚类(cluster = TRUE)，此时会打乱pseudotime的排序
hmp2 <- plot_pseudo_heatmap(panc, features = heatmap_genes, lineage = "Lineage2", cluster_columns = TRUE)

## 对基因聚类
hmp3 <- plot_pseudo_heatmap(panc, features = heatmap_genes, lineage = "Lineage2", cluster_rows = TRUE, sort = FALSE)

## 默认排序
hmp4 <- plot_pseudo_heatmap(panc, features = heatmap_genes, lineage = "Lineage2", cluster_rows = FALSE, sort = TRUE)

## 组合起来看就能看到两个参数的设定对行顺序的影响
plot_list(hmp1, hmp2, hmp3, hmp4, ncol=1)

9.2 Diffusion Map for complex trajectories

For very continuous developmental systems, PCA and UMAP are often convenient but not always topology-faithful. RunDiffusionMap() adds a diffusion-based representation that can be tracked like any other reduction in sclet, which is useful when you want a more trajectory-aware geometry before moving on to downstream lineage tools.

panc_dm <- panc

if (!"logcounts" %in% SummarizedExperiment::assayNames(panc_dm) &&
    "counts" %in% SummarizedExperiment::assayNames(panc_dm)) {
  panc_dm <- NormalizeData(panc_dm)
}

if (!"PCA" %in% SingleCellExperiment::reducedDimNames(panc_dm)) {
  dm_features <- rownames(panc_dm)[seq_len(min(500, nrow(panc_dm)))]
  dm_layer <- if ("logcounts" %in% SummarizedExperiment::assayNames(panc_dm)) "logcounts" else "counts"
  panc_dm <- RunPCA(panc_dm, subset_row = dm_features, layer = dm_layer)
}
## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'
## Also defined by 'alabaster.base'
panc_dm <- RunDiffusionMap(panc_dm, n_components = 10, reduction = "PCA")
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head(SingleCellExperiment::reducedDim(panc_dm, "DM")[, 1:3])
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## Also defined by 'alabaster.base'
##                         DC_1        DC_2         DC_3
## CAGCCGAAGCGATATA -0.04762849 -0.02534582 0.0127494749
## AGTGTCATCGCCGTGA  0.01191557  0.05261432 0.0003914782
## GATGAAAAGTTGTAGA -0.04810711 -0.02576844 0.0139306400
## CACAGTACATCCGTGG  0.02733252 -0.01166796 0.0152364853
## CGGAGCTCATTGGGCC -0.04534807 -0.01974909 0.0065963459
## AGAGCTTGTGTGACCC -0.03782034 -0.01332305 0.0002428841
DimPlot(panc_dm, reduction = "DM", mapping = ggplot2::aes(color = SubCellType))
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The velocity and CellRank examples in this section use cached objects generated by the update-data-velocity-fate GitHub Actions workflow. This keeps the book render lightweight: Python-backed basilisk, velociraptor, and CellRank work is done in the data-update workflow, while the book only reads the resulting RDS files.

RNA metabolic process:

  • RNA is synthesized at a rate of alpha
  • RNA is spliced to remove introns and form mature mRNA at rate of beta
  • Mature mRNA is degraded after functioning at rate of gamma

The disruption of the equilibrium between unspliced and spliced RNA indicates whether a gene is in an induced or repressed state.

With RNA-seq, especially the Poly-A enrichment method, the propotion of unspliced RNA obtained is relatively small. Currently, there are also some techinques capable of enriching nascent RNA in single cells, such as scSLAM-seq and scNT-seq.

Although some researchers are skeptical about RNA velocity, it has received significant attention because it can automatically detect the direction of trajectories.

scVelo supports a full dynamical model and various of utility functions (Bergen et al. 2020). It only supports Python and can be run in R using velociraptor.

9.2.1 Example data

This example is adopted from https://www.bioconductor.org/packages/devel/bioc/vignettes/velociraptor/inst/doc/velociraptor.html.

sce <- readRDS("data/hermann-sperm-dynamics.rds")
sce
## class: SingleCellExperiment 
## dim: 2000 300 
## metadata(2): sclet sclet_bookdown_cache
## assays(3): spliced unspliced logcounts
## rownames(2000): ENSMUSG00000117819.1
##   ENSMUSG00000081984.3 ... ENSMUSG00000087185.1
##   ENSMUSG00000086732.1
## rowData names(0):
## colnames(300): CCCATACTCCGAAGAG AATCCAGTCATCTGCC ...
##   GCGCGATAGGCTCATT CTAAGACTCACTATTC
## colData names(11): celltype sizeFactor ...
##   cellrank_fate_X0 cellrank_fate_X1
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## Also defined by 'alabaster.base'
## reducedDimNames(3): PCA .dimred UMAP
## mainExpName: NULL
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## Also defined by 'alabaster.base'
## altExpNames(0):
top_genes <- S4Vectors::metadata(sce)$sclet_bookdown_cache$top_genes
head(top_genes)
## [1] "ENSMUSG00000117819.1" "ENSMUSG00000081984.3"
## [3] "ENSMUSG00000047995.7" "ENSMUSG00000060860.8"
## [5] "ENSMUSG00000100153.2" "ENSMUSG00000090137.8"

9.2.2 Run velocity analysis

sclet wraps the RNA velocity inference via RunVelocity(). Under the hood, it delegates the heavy lifting to scVelo (managed safely via the basilisk/velociraptor Python sandbox) and smoothly registers the outputs to the velocity analysis state.

get_velocity(sce)
## $id
## [1] "velocity"
## 
## $type
## [1] "velocity"
## 
## $status
## [1] "completed"
## 
## $method
## [1] "velociraptor::scvelo"
## 
## $inputs
## $inputs$assays
## [1] "spliced"   "unspliced"
## 
## $inputs$reduction
## [1] "PCA"
## 
## 
## $artifacts
## $artifacts$analysis_key
## [1] "velocity"
## 
## $artifacts$colData
## [1] "velocity_pseudotime" "velocity_confidence"
## [3] "root_cells"          "end_points"         
## 
## $artifacts$reductions
## character(0)
## 
## 
## $params
## $params$mode
## [1] "deterministic"
## 
## $params$subset.row
##    [1] "ENSMUSG00000117819.1"  "ENSMUSG00000081984.3" 
##    [3] "ENSMUSG00000047995.7"  "ENSMUSG00000060860.8" 
##    [5] "ENSMUSG00000100153.2"  "ENSMUSG00000090137.8" 
##    [7] "ENSMUSG00000064220.6"  "ENSMUSG00000064351.1" 
##    [9] "ENSMUSG00000063954.7"  "ENSMUSG00000027505.2" 
##   [11] "ENSMUSG00000059695.4"  "ENSMUSG00000038994.6" 
##   [13] "ENSMUSG00000027431.5"  "ENSMUSG00000018543.8" 
##   [15] "ENSMUSG00000105734.1"  "ENSMUSG00000042800.5" 
##   [17] "ENSMUSG00000022832.11" "ENSMUSG00000048686.4" 
##   [19] "ENSMUSG00000100937.1"  "ENSMUSG00000028259.13"
##   [21] "ENSMUSG00000030976.3"  "ENSMUSG00000079710.10"
##   [23] "ENSMUSG00000020483.14" "ENSMUSG00000094624.1" 
##   [25] "ENSMUSG00000031512.15" "ENSMUSG00000078577.3" 
##   [27] "ENSMUSG00000078554.2"  "ENSMUSG00000048077.6" 
##   [29] "ENSMUSG00000008482.9"  "ENSMUSG00000079666.8" 
##   [31] "ENSMUSG00000041399.3"  "ENSMUSG00000029867.5" 
##   [33] "ENSMUSG00000027564.4"  "ENSMUSG00000070708.5" 
##   [35] "ENSMUSG00000050621.7"  "ENSMUSG00000031991.10"
##   [37] "ENSMUSG00000009093.7"  "ENSMUSG00000047129.11"
##   [39] "ENSMUSG00000085861.1"  "ENSMUSG00000025482.11"
##   [41] "ENSMUSG00000020286.12" "ENSMUSG00000062154.14"
##   [43] "ENSMUSG00000050058.6"  "ENSMUSG00000095384.1" 
##   [45] "ENSMUSG00000051276.4"  "ENSMUSG00000045521.7" 
##   [47] "ENSMUSG00000028264.16" "ENSMUSG00000029723.16"
##   [49] "ENSMUSG00000053184.15" "ENSMUSG00000118396.2" 
##   [51] "ENSMUSG00000021838.17" "ENSMUSG00000029433.16"
##   [53] "ENSMUSG00000047841.8"  "ENSMUSG00000057072.11"
##   [55] "ENSMUSG00000066383.7"  "ENSMUSG00000062028.8" 
##   [57] "ENSMUSG00000044444.6"  "ENSMUSG00000047843.16"
##   [59] "ENSMUSG00000079346.4"  "ENSMUSG00000027938.11"
##   [61] "ENSMUSG00000063971.7"  "ENSMUSG00000041673.12"
##   [63] "ENSMUSG00000045709.11" "ENSMUSG00000028938.9" 
##   [65] "ENSMUSG00000101959.1"  "ENSMUSG00000099863.1" 
##   [67] "ENSMUSG00000032900.15" "ENSMUSG00000027442.10"
##   [69] "ENSMUSG00000038691.5"  "ENSMUSG00000064357.1" 
##   [71] "ENSMUSG00000046755.5"  "ENSMUSG00000024233.10"
##   [73] "ENSMUSG00000008393.9"  "ENSMUSG00000020617.13"
##   [75] "ENSMUSG00000044526.3"  "ENSMUSG00000020945.13"
##   [77] "ENSMUSG00000043629.12" "ENSMUSG00000074748.3" 
##   [79] "ENSMUSG00000066500.5"  "ENSMUSG00000049916.12"
##   [81] "ENSMUSG00000032803.15" "ENSMUSG00000068240.5" 
##   [83] "ENSMUSG00000055826.5"  "ENSMUSG00000038523.10"
##   [85] "ENSMUSG00000059455.3"  "ENSMUSG00000048731.15"
##   [87] "ENSMUSG00000044056.3"  "ENSMUSG00000024430.14"
##   [89] "ENSMUSG00000051113.9"  "ENSMUSG00000095040.2" 
##   [91] "ENSMUSG00000030714.14" "ENSMUSG00000070489.5" 
##   [93] "ENSMUSG00000030859.8"  "ENSMUSG00000022148.16"
##   [95] "ENSMUSG00000053375.8"  "ENSMUSG00000041566.3" 
##   [97] "ENSMUSG00000064358.1"  "ENSMUSG00000061477.4" 
##   [99] "ENSMUSG00000100282.1"  "ENSMUSG00000036438.14"
##  [101] "ENSMUSG00000067909.4"  "ENSMUSG00000021545.5" 
##  [103] "ENSMUSG00000054523.13" "ENSMUSG00000031682.5" 
##  [105] "ENSMUSG00000045942.13" "ENSMUSG00000090117.7" 
##  [107] "ENSMUSG00000037307.11" "ENSMUSG00000050685.5" 
##  [109] "ENSMUSG00000038709.14" "ENSMUSG00000014301.13"
##  [111] "ENSMUSG00000024501.20" "ENSMUSG00000037708.16"
##  [113] "ENSMUSG00000059288.14" "ENSMUSG00000064341.1" 
##  [115] "ENSMUSG00000100862.1"  "ENSMUSG00000027674.16"
##  [117] "ENSMUSG00000027355.15" "ENSMUSG00000074344.7" 
##  [119] "ENSMUSG00000073758.10" "ENSMUSG00000027886.7" 
##  [121] "ENSMUSG00000070563.6"  "ENSMUSG00000055553.16"
##  [123] "ENSMUSG00000026963.4"  "ENSMUSG00000021768.15"
##  [125] "ENSMUSG00000101111.1"  "ENSMUSG00000041540.16"
##  [127] "ENSMUSG00000030858.10" "ENSMUSG00000005803.14"
##  [129] "ENSMUSG00000109864.1"  "ENSMUSG00000056509.10"
##  [131] "ENSMUSG00000091396.2"  "ENSMUSG00000047150.8" 
##  [133] "ENSMUSG00000074435.10" "ENSMUSG00000069971.5" 
##  [135] "ENSMUSG00000089989.10" "ENSMUSG00000010435.7" 
##  [137] "ENSMUSG00000037689.6"  "ENSMUSG00000027606.12"
##  [139] "ENSMUSG00000029477.14" "ENSMUSG00000026592.13"
##  [141] "ENSMUSG00000058935.14" "ENSMUSG00000035085.5" 
##  [143] "ENSMUSG00000060491.14" "ENSMUSG00000095159.2" 
##  [145] "ENSMUSG00000026809.15" "ENSMUSG00000095869.1" 
##  [147] "ENSMUSG00000049154.12" "ENSMUSG00000048655.17"
##  [149] "ENSMUSG00000046173.3"  "ENSMUSG00000021961.6" 
##  [151] "ENSMUSG00000026864.13" "ENSMUSG00000095789.6" 
##  [153] "ENSMUSG00000045336.5"  "ENSMUSG00000020234.10"
##  [155] "ENSMUSG00000001558.5"  "ENSMUSG00000031452.15"
##  [157] "ENSMUSG00000055692.21" "ENSMUSG00000023467.18"
##  [159] "ENSMUSG00000026827.12" "ENSMUSG00000050141.13"
##  [161] "ENSMUSG00000043050.8"  "ENSMUSG00000021415.13"
##  [163] "ENSMUSG00000019876.15" "ENSMUSG00000063480.8" 
##  [165] "ENSMUSG00000036924.3"  "ENSMUSG00000052920.16"
##  [167] "ENSMUSG00000013091.5"  "ENSMUSG00000086361.1" 
##  [169] "ENSMUSG00000073380.2"  "ENSMUSG00000049761.6" 
##  [171] "ENSMUSG00000033949.12" "ENSMUSG00000116210.1" 
##  [173] "ENSMUSG00000073731.12" "ENSMUSG00000047025.5" 
##  [175] "ENSMUSG00000030161.8"  "ENSMUSG00000040883.18"
##  [177] "ENSMUSG00000006941.5"  "ENSMUSG00000072772.3" 
##  [179] "ENSMUSG00000041791.6"  "ENSMUSG00000100684.1" 
##  [181] "ENSMUSG00000043633.6"  "ENSMUSG00000027496.15"
##  [183] "ENSMUSG00000047518.3"  "ENSMUSG00000048573.9" 
##  [185] "ENSMUSG00000023257.3"  "ENSMUSG00000064354.1" 
##  [187] "ENSMUSG00000078127.3"  "ENSMUSG00000090840.2" 
##  [189] "ENSMUSG00000022249.14" "ENSMUSG00000020460.15"
##  [191] "ENSMUSG00000095867.2"  "ENSMUSG00000043859.5" 
##  [193] "ENSMUSG00000028141.11" "ENSMUSG00000110464.1" 
##  [195] "ENSMUSG00000059430.14" "ENSMUSG00000047108.4" 
##  [197] "ENSMUSG00000021585.10" "ENSMUSG00000020270.9" 
##  [199] "ENSMUSG00000101796.1"  "ENSMUSG00000049694.13"
##  [201] "ENSMUSG00000026969.3"  "ENSMUSG00000024397.14"
##  [203] "ENSMUSG00000026182.6"  "ENSMUSG00000034913.10"
##  [205] "ENSMUSG00000061474.11" "ENSMUSG00000044122.15"
##  [207] "ENSMUSG00000028575.11" "ENSMUSG00000021534.8" 
##  [209] "ENSMUSG00000117852.1"  "ENSMUSG00000030421.9" 
##  [211] "ENSMUSG00000036167.16" "ENSMUSG00000039555.14"
##  [213] "ENSMUSG00000017767.3"  "ENSMUSG00000009115.5" 
##  [215] "ENSMUSG00000036244.5"  "ENSMUSG00000035522.3" 
##  [217] "ENSMUSG00000008307.11" "ENSMUSG00000026226.16"
##  [219] "ENSMUSG00000050641.7"  "ENSMUSG00000102070.1" 
##  [221] "ENSMUSG00000028427.13" "ENSMUSG00000032530.14"
##  [223] "ENSMUSG00000048206.6"  "ENSMUSG00000061633.3" 
##  [225] "ENSMUSG00000007907.4"  "ENSMUSG00000004633.17"
##  [227] "ENSMUSG00000046957.5"  "ENSMUSG00000022501.6" 
##  [229] "ENSMUSG00000027480.12" "ENSMUSG00000030629.15"
##  [231] "ENSMUSG00000020622.17" "ENSMUSG00000089781.2" 
##  [233] "ENSMUSG00000040541.8"  "ENSMUSG00000026940.3" 
##  [235] "ENSMUSG00000099353.7"  "ENSMUSG00000046750.17"
##  [237] "ENSMUSG00000021203.15" "ENSMUSG00000070999.2" 
##  [239] "ENSMUSG00000062651.4"  "ENSMUSG00000033213.16"
##  [241] "ENSMUSG00000101894.1"  "ENSMUSG00000045378.5" 
##  [243] "ENSMUSG00000020940.13" "ENSMUSG00000090202.1" 
##  [245] "ENSMUSG00000002240.12" "ENSMUSG00000031509.10"
##  [247] "ENSMUSG00000019945.10" "ENSMUSG00000030344.11"
##  [249] "ENSMUSG00000038015.6"  "ENSMUSG00000038180.11"
##  [251] "ENSMUSG00000070332.4"  "ENSMUSG00000067367.9" 
##  [253] "ENSMUSG00000017720.2"  "ENSMUSG00000097522.1" 
##  [255] "ENSMUSG00000012405.16" "ENSMUSG00000085940.1" 
##  [257] "ENSMUSG00000032110.4"  "ENSMUSG00000090273.3" 
##  [259] "ENSMUSG00000078161.8"  "ENSMUSG00000001175.15"
##  [261] "ENSMUSG00000048994.2"  "ENSMUSG00000058173.12"
##  [263] "ENSMUSG00000007591.15" "ENSMUSG00000024059.10"
##  [265] "ENSMUSG00000055891.7"  "ENSMUSG00000004455.16"
##  [267] "ENSMUSG00000050089.13" "ENSMUSG00000066878.5" 
##  [269] "ENSMUSG00000041068.6"  "ENSMUSG00000038997.4" 
##  [271] "ENSMUSG00000030206.13" "ENSMUSG00000070392.5" 
##  [273] "ENSMUSG00000028332.13" "ENSMUSG00000062867.13"
##  [275] "ENSMUSG00000043036.13" "ENSMUSG00000116615.1" 
##  [277] "ENSMUSG00000029678.8"  "ENSMUSG00000002308.16"
##  [279] "ENSMUSG00000003518.13" "ENSMUSG00000062825.15"
##  [281] "ENSMUSG00000020096.20" "ENSMUSG00000089743.7" 
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##  [881] "ENSMUSG00000022812.14" "ENSMUSG00000082652.1" 
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##  [891] "ENSMUSG00000038943.16" "ENSMUSG00000041623.17"
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##  [903] "ENSMUSG00000042607.15" "ENSMUSG00000033053.4" 
##  [905] "ENSMUSG00000022657.9"  "ENSMUSG00000033502.15"
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##  [909] "ENSMUSG00000022400.9"  "ENSMUSG00000112913.1" 
##  [911] "ENSMUSG00000040485.5"  "ENSMUSG00000093945.1" 
##  [913] "ENSMUSG00000084901.6"  "ENSMUSG00000087611.1" 
##  [915] "ENSMUSG00000006241.16" "ENSMUSG00000020650.15"
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##  [919] "ENSMUSG00000030403.9"  "ENSMUSG00000043319.5" 
##  [921] "ENSMUSG00000048416.15" "ENSMUSG00000025231.17"
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##  [929] "ENSMUSG00000034349.14" "ENSMUSG00000072722.2" 
##  [931] "ENSMUSG00000094036.1"  "ENSMUSG00000022783.11"
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##  [935] "ENSMUSG00000085037.1"  "ENSMUSG00000028845.15"
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##  [947] "ENSMUSG00000024712.9"  "ENSMUSG00000106086.1" 
##  [949] "ENSMUSG00000096405.3"  "ENSMUSG00000050043.16"
##  [951] "ENSMUSG00000025794.9"  "ENSMUSG00000025245.14"
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##  [957] "ENSMUSG00000045193.13" "ENSMUSG00000030189.15"
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##  [961] "ENSMUSG00000024193.8"  "ENSMUSG00000020462.14"
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##  [967] "ENSMUSG00000040888.10" "ENSMUSG00000110665.1" 
##  [969] "ENSMUSG00000074677.11" "ENSMUSG00000025156.17"
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##  [973] "ENSMUSG00000028441.12" "ENSMUSG00000013593.12"
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##  [977] "ENSMUSG00000038570.15" "ENSMUSG00000029229.8" 
##  [979] "ENSMUSG00000020180.10" "ENSMUSG00000031085.16"
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##  [983] "ENSMUSG00000029620.4"  "ENSMUSG00000055943.5" 
##  [985] "ENSMUSG00000056912.12" "ENSMUSG00000029155.16"
##  [987] "ENSMUSG00000004667.18" "ENSMUSG00000055882.8" 
##  [989] "ENSMUSG00000087250.2"  "ENSMUSG00000043421.8" 
##  [991] "ENSMUSG00000100708.1"  "ENSMUSG00000035133.9" 
##  [993] "ENSMUSG00000052099.14" "ENSMUSG00000024663.20"
##  [995] "ENSMUSG00000024905.15" "ENSMUSG00000000171.5" 
##  [997] "ENSMUSG00000115761.1"  "ENSMUSG00000024758.15"
##  [999] "ENSMUSG00000000579.14" "ENSMUSG00000044957.3" 
## [1001] "ENSMUSG00000026585.13" "ENSMUSG00000028572.13"
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## [1005] "ENSMUSG00000001687.15" "ENSMUSG00000059447.13"
## [1007] "ENSMUSG00000037072.15" "ENSMUSG00000023873.13"
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## [1011] "ENSMUSG00000026989.5"  "ENSMUSG00000063089.4" 
## [1013] "ENSMUSG00000031181.2"  "ENSMUSG00000042396.10"
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## [1017] "ENSMUSG00000051185.9"  "ENSMUSG00000034813.18"
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## [1029] "ENSMUSG00000006715.11" "ENSMUSG00000022769.9" 
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## [1039] "ENSMUSG00000020420.8"  "ENSMUSG00000017802.14"
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## [1055] "ENSMUSG00000032171.7"  "ENSMUSG00000080725.9" 
## [1057] "ENSMUSG00000061689.15" "ENSMUSG00000024145.6" 
## [1059] "ENSMUSG00000034165.16" "ENSMUSG00000096001.2" 
## [1061] "ENSMUSG00000025486.17" "ENSMUSG00000060073.9" 
## [1063] "ENSMUSG00000096769.7"  "ENSMUSG00000059972.7" 
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## [1071] "ENSMUSG00000094811.7"  "ENSMUSG00000101683.6" 
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## [1077] "ENSMUSG00000026966.6"  "ENSMUSG00000096650.7" 
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## [1083] "ENSMUSG00000034473.14" "ENSMUSG00000055302.5" 
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## [1087] "ENSMUSG00000027341.10" "ENSMUSG00000096372.1" 
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## [1107] "ENSMUSG00000038594.9"  "ENSMUSG00000052906.7" 
## [1109] "ENSMUSG00000021572.9"  "ENSMUSG00000072692.7" 
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## [1897] "ENSMUSG00000093617.1"  "ENSMUSG00000032666.16"
## [1899] "ENSMUSG00000062438.4"  "ENSMUSG00000078652.9" 
## [1901] "ENSMUSG00000021196.14" "ENSMUSG00000032254.10"
## [1903] "ENSMUSG00000110343.1"  "ENSMUSG00000102045.1" 
## [1905] "ENSMUSG00000061887.14" "ENSMUSG00000027018.11"
## [1907] "ENSMUSG00000048701.13" "ENSMUSG00000099681.1" 
## [1909] "ENSMUSG00000029517.13" "ENSMUSG00000086817.1" 
## [1911] "ENSMUSG00000040714.14" "ENSMUSG00000022710.17"
## [1913] "ENSMUSG00000043415.5"  "ENSMUSG00000114334.1" 
## [1915] "ENSMUSG00000031996.17" "ENSMUSG00000022103.10"
## [1917] "ENSMUSG00000026646.16" "ENSMUSG00000091970.3" 
## [1919] "ENSMUSG00000115284.1"  "ENSMUSG00000032966.14"
## [1921] "ENSMUSG00000052273.4"  "ENSMUSG00000020993.9" 
## [1923] "ENSMUSG00000085100.1"  "ENSMUSG00000021997.4" 
## [1925] "ENSMUSG00000075524.3"  "ENSMUSG00000032232.14"
## [1927] "ENSMUSG00000093383.1"  "ENSMUSG00000033671.18"
## [1929] "ENSMUSG00000036411.10" "ENSMUSG00000020974.6" 
## [1931] "ENSMUSG00000097841.2"  "ENSMUSG00000083380.1" 
## [1933] "ENSMUSG00000090063.6"  "ENSMUSG00000107305.1" 
## [1935] "ENSMUSG00000038453.17" "ENSMUSG00000029504.5" 
## [1937] "ENSMUSG00000118491.1"  "ENSMUSG00000049692.7" 
## [1939] "ENSMUSG00000026643.16" "ENSMUSG00000021671.9" 
## [1941] "ENSMUSG00000028567.8"  "ENSMUSG00000106549.1" 
## [1943] "ENSMUSG00000021086.5"  "ENSMUSG00000050912.15"
## [1945] "ENSMUSG00000095785.2"  "ENSMUSG00000117000.1" 
## [1947] "ENSMUSG00000020612.16" "ENSMUSG00000090713.2" 
## [1949] "ENSMUSG00000027306.15" "ENSMUSG00000029875.5" 
## [1951] "ENSMUSG00000056383.10" "ENSMUSG00000026882.1" 
## [1953] "ENSMUSG00000037443.13" "ENSMUSG00000101634.6" 
## [1955] "ENSMUSG00000027823.9"  "ENSMUSG00000023075.9" 
## [1957] "ENSMUSG00000028447.11" "ENSMUSG00000027940.18"
## [1959] "ENSMUSG00000070372.11" "ENSMUSG00000024259.9" 
## [1961] "ENSMUSG00000106876.1"  "ENSMUSG00000027131.3" 
## [1963] "ENSMUSG00000107895.1"  "ENSMUSG00000106918.3" 
## [1965] "ENSMUSG00000020986.13" "ENSMUSG00000038374.10"
## [1967] "ENSMUSG00000042688.16" "ENSMUSG00000040822.7" 
## [1969] "ENSMUSG00000095452.2"  "ENSMUSG00000090379.1" 
## [1971] "ENSMUSG00000067038.6"  "ENSMUSG00000055762.16"
## [1973] "ENSMUSG00000030590.15" "ENSMUSG00000087258.1" 
## [1975] "ENSMUSG00000020576.10" "ENSMUSG00000046229.10"
## [1977] "ENSMUSG00000033953.10" "ENSMUSG00000037972.7" 
## [1979] "ENSMUSG00000057110.15" "ENSMUSG00000022555.12"
## [1981] "ENSMUSG00000026941.16" "ENSMUSG00000010376.15"
## [1983] "ENSMUSG00000096901.7"  "ENSMUSG00000029131.14"
## [1985] "ENSMUSG00000060407.6"  "ENSMUSG00000049295.17"
## [1987] "ENSMUSG00000078935.1"  "ENSMUSG00000075232.6" 
## [1989] "ENSMUSG00000022111.9"  "ENSMUSG00000030264.14"
## [1991] "ENSMUSG00000085044.1"  "ENSMUSG00000037364.12"
## [1993] "ENSMUSG00000020463.15" "ENSMUSG00000029707.6" 
## [1995] "ENSMUSG00000111028.1"  "ENSMUSG00000019878.8" 
## [1997] "ENSMUSG00000022965.8"  "ENSMUSG00000085759.1" 
## [1999] "ENSMUSG00000087185.1"  "ENSMUSG00000086732.1" 
## 
## 
## $summary
## $summary$n_features
## [1] 2000
## 
## $summary$n_cells
## [1] 300
## 
## 
## $results
## class: SingleCellExperiment 
## dim: 2000 300 
## metadata(4): neighbors velocity_params velocity_graph
##   velocity_graph_neg
## assays(6): X spliced ... Mu velocity
## rownames(2000): ENSMUSG00000117819.1
##   ENSMUSG00000081984.3 ... ENSMUSG00000087185.1
##   ENSMUSG00000086732.1
## rowData names(4): velocity_gamma velocity_qreg_ratio
##   velocity_r2 velocity_genes
## colnames(300): CCCATACTCCGAAGAG AATCCAGTCATCTGCC ...
##   GCGCGATAGGCTCATT CTAAGACTCACTATTC
## colData names(7): velocity_self_transition root_cells
##   ... velocity_confidence
##   velocity_confidence_transition
## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'
## Also defined by 'alabaster.base'
## reducedDimNames(1): X_pca
## mainExpName: NULL
## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'
## Also defined by 'alabaster.base'
## altExpNames(0):
## 
## $reductions
## character(0)
## 
## $coldata_fields
## [1] "velocity_pseudotime" "velocity_confidence"
## [3] "root_cells"          "end_points"         
## 
## $created_at
## [1] "2026-06-14 21:02:19 UTC"
## 
## $mode
## [1] "deterministic"
## 
## $use.dimred
## [1] "PCA"
## 
## $subset.row
##    [1] "ENSMUSG00000117819.1"  "ENSMUSG00000081984.3" 
##    [3] "ENSMUSG00000047995.7"  "ENSMUSG00000060860.8" 
##    [5] "ENSMUSG00000100153.2"  "ENSMUSG00000090137.8" 
##    [7] "ENSMUSG00000064220.6"  "ENSMUSG00000064351.1" 
##    [9] "ENSMUSG00000063954.7"  "ENSMUSG00000027505.2" 
##   [11] "ENSMUSG00000059695.4"  "ENSMUSG00000038994.6" 
##   [13] "ENSMUSG00000027431.5"  "ENSMUSG00000018543.8" 
##   [15] "ENSMUSG00000105734.1"  "ENSMUSG00000042800.5" 
##   [17] "ENSMUSG00000022832.11" "ENSMUSG00000048686.4" 
##   [19] "ENSMUSG00000100937.1"  "ENSMUSG00000028259.13"
##   [21] "ENSMUSG00000030976.3"  "ENSMUSG00000079710.10"
##   [23] "ENSMUSG00000020483.14" "ENSMUSG00000094624.1" 
##   [25] "ENSMUSG00000031512.15" "ENSMUSG00000078577.3" 
##   [27] "ENSMUSG00000078554.2"  "ENSMUSG00000048077.6" 
##   [29] "ENSMUSG00000008482.9"  "ENSMUSG00000079666.8" 
##   [31] "ENSMUSG00000041399.3"  "ENSMUSG00000029867.5" 
##   [33] "ENSMUSG00000027564.4"  "ENSMUSG00000070708.5" 
##   [35] "ENSMUSG00000050621.7"  "ENSMUSG00000031991.10"
##   [37] "ENSMUSG00000009093.7"  "ENSMUSG00000047129.11"
##   [39] "ENSMUSG00000085861.1"  "ENSMUSG00000025482.11"
##   [41] "ENSMUSG00000020286.12" "ENSMUSG00000062154.14"
##   [43] "ENSMUSG00000050058.6"  "ENSMUSG00000095384.1" 
##   [45] "ENSMUSG00000051276.4"  "ENSMUSG00000045521.7" 
##   [47] "ENSMUSG00000028264.16" "ENSMUSG00000029723.16"
##   [49] "ENSMUSG00000053184.15" "ENSMUSG00000118396.2" 
##   [51] "ENSMUSG00000021838.17" "ENSMUSG00000029433.16"
##   [53] "ENSMUSG00000047841.8"  "ENSMUSG00000057072.11"
##   [55] "ENSMUSG00000066383.7"  "ENSMUSG00000062028.8" 
##   [57] "ENSMUSG00000044444.6"  "ENSMUSG00000047843.16"
##   [59] "ENSMUSG00000079346.4"  "ENSMUSG00000027938.11"
##   [61] "ENSMUSG00000063971.7"  "ENSMUSG00000041673.12"
##   [63] "ENSMUSG00000045709.11" "ENSMUSG00000028938.9" 
##   [65] "ENSMUSG00000101959.1"  "ENSMUSG00000099863.1" 
##   [67] "ENSMUSG00000032900.15" "ENSMUSG00000027442.10"
##   [69] "ENSMUSG00000038691.5"  "ENSMUSG00000064357.1" 
##   [71] "ENSMUSG00000046755.5"  "ENSMUSG00000024233.10"
##   [73] "ENSMUSG00000008393.9"  "ENSMUSG00000020617.13"
##   [75] "ENSMUSG00000044526.3"  "ENSMUSG00000020945.13"
##   [77] "ENSMUSG00000043629.12" "ENSMUSG00000074748.3" 
##   [79] "ENSMUSG00000066500.5"  "ENSMUSG00000049916.12"
##   [81] "ENSMUSG00000032803.15" "ENSMUSG00000068240.5" 
##   [83] "ENSMUSG00000055826.5"  "ENSMUSG00000038523.10"
##   [85] "ENSMUSG00000059455.3"  "ENSMUSG00000048731.15"
##   [87] "ENSMUSG00000044056.3"  "ENSMUSG00000024430.14"
##   [89] "ENSMUSG00000051113.9"  "ENSMUSG00000095040.2" 
##   [91] "ENSMUSG00000030714.14" "ENSMUSG00000070489.5" 
##   [93] "ENSMUSG00000030859.8"  "ENSMUSG00000022148.16"
##   [95] "ENSMUSG00000053375.8"  "ENSMUSG00000041566.3" 
##   [97] "ENSMUSG00000064358.1"  "ENSMUSG00000061477.4" 
##   [99] "ENSMUSG00000100282.1"  "ENSMUSG00000036438.14"
##  [101] "ENSMUSG00000067909.4"  "ENSMUSG00000021545.5" 
##  [103] "ENSMUSG00000054523.13" "ENSMUSG00000031682.5" 
##  [105] "ENSMUSG00000045942.13" "ENSMUSG00000090117.7" 
##  [107] "ENSMUSG00000037307.11" "ENSMUSG00000050685.5" 
##  [109] "ENSMUSG00000038709.14" "ENSMUSG00000014301.13"
##  [111] "ENSMUSG00000024501.20" "ENSMUSG00000037708.16"
##  [113] "ENSMUSG00000059288.14" "ENSMUSG00000064341.1" 
##  [115] "ENSMUSG00000100862.1"  "ENSMUSG00000027674.16"
##  [117] "ENSMUSG00000027355.15" "ENSMUSG00000074344.7" 
##  [119] "ENSMUSG00000073758.10" "ENSMUSG00000027886.7" 
##  [121] "ENSMUSG00000070563.6"  "ENSMUSG00000055553.16"
##  [123] "ENSMUSG00000026963.4"  "ENSMUSG00000021768.15"
##  [125] "ENSMUSG00000101111.1"  "ENSMUSG00000041540.16"
##  [127] "ENSMUSG00000030858.10" "ENSMUSG00000005803.14"
##  [129] "ENSMUSG00000109864.1"  "ENSMUSG00000056509.10"
##  [131] "ENSMUSG00000091396.2"  "ENSMUSG00000047150.8" 
##  [133] "ENSMUSG00000074435.10" "ENSMUSG00000069971.5" 
##  [135] "ENSMUSG00000089989.10" "ENSMUSG00000010435.7" 
##  [137] "ENSMUSG00000037689.6"  "ENSMUSG00000027606.12"
##  [139] "ENSMUSG00000029477.14" "ENSMUSG00000026592.13"
##  [141] "ENSMUSG00000058935.14" "ENSMUSG00000035085.5" 
##  [143] "ENSMUSG00000060491.14" "ENSMUSG00000095159.2" 
##  [145] "ENSMUSG00000026809.15" "ENSMUSG00000095869.1" 
##  [147] "ENSMUSG00000049154.12" "ENSMUSG00000048655.17"
##  [149] "ENSMUSG00000046173.3"  "ENSMUSG00000021961.6" 
##  [151] "ENSMUSG00000026864.13" "ENSMUSG00000095789.6" 
##  [153] "ENSMUSG00000045336.5"  "ENSMUSG00000020234.10"
##  [155] "ENSMUSG00000001558.5"  "ENSMUSG00000031452.15"
##  [157] "ENSMUSG00000055692.21" "ENSMUSG00000023467.18"
##  [159] "ENSMUSG00000026827.12" "ENSMUSG00000050141.13"
##  [161] "ENSMUSG00000043050.8"  "ENSMUSG00000021415.13"
##  [163] "ENSMUSG00000019876.15" "ENSMUSG00000063480.8" 
##  [165] "ENSMUSG00000036924.3"  "ENSMUSG00000052920.16"
##  [167] "ENSMUSG00000013091.5"  "ENSMUSG00000086361.1" 
##  [169] "ENSMUSG00000073380.2"  "ENSMUSG00000049761.6" 
##  [171] "ENSMUSG00000033949.12" "ENSMUSG00000116210.1" 
##  [173] "ENSMUSG00000073731.12" "ENSMUSG00000047025.5" 
##  [175] "ENSMUSG00000030161.8"  "ENSMUSG00000040883.18"
##  [177] "ENSMUSG00000006941.5"  "ENSMUSG00000072772.3" 
##  [179] "ENSMUSG00000041791.6"  "ENSMUSG00000100684.1" 
##  [181] "ENSMUSG00000043633.6"  "ENSMUSG00000027496.15"
##  [183] "ENSMUSG00000047518.3"  "ENSMUSG00000048573.9" 
##  [185] "ENSMUSG00000023257.3"  "ENSMUSG00000064354.1" 
##  [187] "ENSMUSG00000078127.3"  "ENSMUSG00000090840.2" 
##  [189] "ENSMUSG00000022249.14" "ENSMUSG00000020460.15"
##  [191] "ENSMUSG00000095867.2"  "ENSMUSG00000043859.5" 
##  [193] "ENSMUSG00000028141.11" "ENSMUSG00000110464.1" 
##  [195] "ENSMUSG00000059430.14" "ENSMUSG00000047108.4" 
##  [197] "ENSMUSG00000021585.10" "ENSMUSG00000020270.9" 
##  [199] "ENSMUSG00000101796.1"  "ENSMUSG00000049694.13"
##  [201] "ENSMUSG00000026969.3"  "ENSMUSG00000024397.14"
##  [203] "ENSMUSG00000026182.6"  "ENSMUSG00000034913.10"
##  [205] "ENSMUSG00000061474.11" "ENSMUSG00000044122.15"
##  [207] "ENSMUSG00000028575.11" "ENSMUSG00000021534.8" 
##  [209] "ENSMUSG00000117852.1"  "ENSMUSG00000030421.9" 
##  [211] "ENSMUSG00000036167.16" "ENSMUSG00000039555.14"
##  [213] "ENSMUSG00000017767.3"  "ENSMUSG00000009115.5" 
##  [215] "ENSMUSG00000036244.5"  "ENSMUSG00000035522.3" 
##  [217] "ENSMUSG00000008307.11" "ENSMUSG00000026226.16"
##  [219] "ENSMUSG00000050641.7"  "ENSMUSG00000102070.1" 
##  [221] "ENSMUSG00000028427.13" "ENSMUSG00000032530.14"
##  [223] "ENSMUSG00000048206.6"  "ENSMUSG00000061633.3" 
##  [225] "ENSMUSG00000007907.4"  "ENSMUSG00000004633.17"
##  [227] "ENSMUSG00000046957.5"  "ENSMUSG00000022501.6" 
##  [229] "ENSMUSG00000027480.12" "ENSMUSG00000030629.15"
##  [231] "ENSMUSG00000020622.17" "ENSMUSG00000089781.2" 
##  [233] "ENSMUSG00000040541.8"  "ENSMUSG00000026940.3" 
##  [235] "ENSMUSG00000099353.7"  "ENSMUSG00000046750.17"
##  [237] "ENSMUSG00000021203.15" "ENSMUSG00000070999.2" 
##  [239] "ENSMUSG00000062651.4"  "ENSMUSG00000033213.16"
##  [241] "ENSMUSG00000101894.1"  "ENSMUSG00000045378.5" 
##  [243] "ENSMUSG00000020940.13" "ENSMUSG00000090202.1" 
##  [245] "ENSMUSG00000002240.12" "ENSMUSG00000031509.10"
##  [247] "ENSMUSG00000019945.10" "ENSMUSG00000030344.11"
##  [249] "ENSMUSG00000038015.6"  "ENSMUSG00000038180.11"
##  [251] "ENSMUSG00000070332.4"  "ENSMUSG00000067367.9" 
##  [253] "ENSMUSG00000017720.2"  "ENSMUSG00000097522.1" 
##  [255] "ENSMUSG00000012405.16" "ENSMUSG00000085940.1" 
##  [257] "ENSMUSG00000032110.4"  "ENSMUSG00000090273.3" 
##  [259] "ENSMUSG00000078161.8"  "ENSMUSG00000001175.15"
##  [261] "ENSMUSG00000048994.2"  "ENSMUSG00000058173.12"
##  [263] "ENSMUSG00000007591.15" "ENSMUSG00000024059.10"
##  [265] "ENSMUSG00000055891.7"  "ENSMUSG00000004455.16"
##  [267] "ENSMUSG00000050089.13" "ENSMUSG00000066878.5" 
##  [269] "ENSMUSG00000041068.6"  "ENSMUSG00000038997.4" 
##  [271] "ENSMUSG00000030206.13" "ENSMUSG00000070392.5" 
##  [273] "ENSMUSG00000028332.13" "ENSMUSG00000062867.13"
##  [275] "ENSMUSG00000043036.13" "ENSMUSG00000116615.1" 
##  [277] "ENSMUSG00000029678.8"  "ENSMUSG00000002308.16"
##  [279] "ENSMUSG00000003518.13" "ENSMUSG00000062825.15"
##  [281] "ENSMUSG00000020096.20" "ENSMUSG00000089743.7" 
##  [283] "ENSMUSG00000028484.16" "ENSMUSG00000030385.4" 
##  [285] "ENSMUSG00000029909.6"  "ENSMUSG00000026931.10"
##  [287] "ENSMUSG00000030077.11" "ENSMUSG00000021499.12"
##  [289] "ENSMUSG00000058690.14" "ENSMUSG00000090206.8" 
##  [291] "ENSMUSG00000045004.3"  "ENSMUSG00000022982.10"
##  [293] "ENSMUSG00000070979.5"  "ENSMUSG00000040681.16"
##  [295] "ENSMUSG00000094975.1"  "ENSMUSG00000014529.9" 
##  [297] "ENSMUSG00000062075.13" "ENSMUSG00000021590.7" 
##  [299] "ENSMUSG00000040456.2"  "ENSMUSG00000029682.5" 
##  [301] "ENSMUSG00000022674.15" "ENSMUSG00000022993.7" 
##  [303] "ENSMUSG00000020636.14" "ENSMUSG00000097638.1" 
##  [305] "ENSMUSG00000029607.14" "ENSMUSG00000093394.1" 
##  [307] "ENSMUSG00000045022.6"  "ENSMUSG00000024532.13"
##  [309] "ENSMUSG00000040576.8"  "ENSMUSG00000114630.1" 
##  [311] "ENSMUSG00000086467.2"  "ENSMUSG00000031651.5" 
##  [313] "ENSMUSG00000099422.4"  "ENSMUSG00000003153.10"
##  [315] "ENSMUSG00000009549.14" "ENSMUSG00000073257.3" 
##  [317] "ENSMUSG00000095533.7"  "ENSMUSG00000036992.10"
##  [319] "ENSMUSG00000042200.3"  "ENSMUSG00000096666.2" 
##  [321] "ENSMUSG00000047044.7"  "ENSMUSG00000035165.14"
##  [323] "ENSMUSG00000081604.5"  "ENSMUSG00000010044.12"
##  [325] "ENSMUSG00000063129.1"  "ENSMUSG00000094843.2" 
##  [327] "ENSMUSG00000096153.1"  "ENSMUSG00000028832.11"
##  [329] "ENSMUSG00000028287.4"  "ENSMUSG00000118504.1" 
##  [331] "ENSMUSG00000029182.10" "ENSMUSG00000037418.6" 
##  [333] "ENSMUSG00000012042.9"  "ENSMUSG00000045886.7" 
##  [335] "ENSMUSG00000097075.3"  "ENSMUSG00000045620.7" 
##  [337] "ENSMUSG00000023806.10" "ENSMUSG00000030654.9" 
##  [339] "ENSMUSG00000056486.18" "ENSMUSG00000109657.1" 
##  [341] "ENSMUSG00000057719.11" "ENSMUSG00000100727.6" 
##  [343] "ENSMUSG00000051728.7"  "ENSMUSG00000086046.1" 
##  [345] "ENSMUSG00000040919.13" "ENSMUSG00000038165.8" 
##  [347] "ENSMUSG00000095546.7"  "ENSMUSG00000081406.4" 
##  [349] "ENSMUSG00000015242.14" "ENSMUSG00000026743.16"
##  [351] "ENSMUSG00000017049.4"  "ENSMUSG00000059891.14"
##  [353] "ENSMUSG00000015962.5"  "ENSMUSG00000071726.2" 
##  [355] "ENSMUSG00000092522.1"  "ENSMUSG00000090369.3" 
##  [357] "ENSMUSG00000026831.16" "ENSMUSG00000085580.1" 
##  [359] "ENSMUSG00000037894.13" "ENSMUSG00000026622.15"
##  [361] "ENSMUSG00000030688.15" "ENSMUSG00000056987.8" 
##  [363] "ENSMUSG00000022641.15" "ENSMUSG00000027956.11"
##  [365] "ENSMUSG00000061099.12" "ENSMUSG00000028716.15"
##  [367] "ENSMUSG00000003923.14" "ENSMUSG00000030968.3" 
##  [369] "ENSMUSG00000022749.8"  "ENSMUSG00000030301.17"
##  [371] "ENSMUSG00000020048.13" "ENSMUSG00000028533.10"
##  [373] "ENSMUSG00000045989.4"  "ENSMUSG00000024223.3" 
##  [375] "ENSMUSG00000034689.2"  "ENSMUSG00000028492.13"
##  [377] "ENSMUSG00000107598.1"  "ENSMUSG00000020681.14"
##  [379] "ENSMUSG00000043429.7"  "ENSMUSG00000072605.10"
##  [381] "ENSMUSG00000001666.8"  "ENSMUSG00000064363.1" 
##  [383] "ENSMUSG00000010841.13" "ENSMUSG00000051674.15"
##  [385] "ENSMUSG00000044556.3"  "ENSMUSG00000036533.9" 
##  [387] "ENSMUSG00000051896.4"  "ENSMUSG00000118506.1" 
##  [389] "ENSMUSG00000095110.1"  "ENSMUSG00000057173.8" 
##  [391] "ENSMUSG00000024510.6"  "ENSMUSG00000079022.10"
##  [393] "ENSMUSG00000029484.12" "ENSMUSG00000091849.7" 
##  [395] "ENSMUSG00000031971.15" "ENSMUSG00000030137.8" 
##  [397] "ENSMUSG00000102096.1"  "ENSMUSG00000020696.18"
##  [399] "ENSMUSG00000026107.11" "ENSMUSG00000032278.11"
##  [401] "ENSMUSG00000019732.14" "ENSMUSG00000027793.6" 
##  [403] "ENSMUSG00000029044.9"  "ENSMUSG00000001089.14"
##  [405] "ENSMUSG00000029752.12" "ENSMUSG00000028520.12"
##  [407] "ENSMUSG00000079409.8"  "ENSMUSG00000028873.16"
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##  [953] "ENSMUSG00000038503.15" "ENSMUSG00000022800.14"
##  [955] "ENSMUSG00000094052.2"  "ENSMUSG00000107141.1" 
##  [957] "ENSMUSG00000045193.13" "ENSMUSG00000030189.15"
##  [959] "ENSMUSG00000099923.2"  "ENSMUSG00000093993.7" 
##  [961] "ENSMUSG00000024193.8"  "ENSMUSG00000020462.14"
##  [963] "ENSMUSG00000094802.7"  "ENSMUSG00000022744.12"
##  [965] "ENSMUSG00000096468.7"  "ENSMUSG00000024853.10"
##  [967] "ENSMUSG00000040888.10" "ENSMUSG00000110665.1" 
##  [969] "ENSMUSG00000074677.11" "ENSMUSG00000025156.17"
##  [971] "ENSMUSG00000020415.16" "ENSMUSG00000106741.3" 
##  [973] "ENSMUSG00000028441.12" "ENSMUSG00000013593.12"
##  [975] "ENSMUSG00000096867.1"  "ENSMUSG00000048039.8" 
##  [977] "ENSMUSG00000038570.15" "ENSMUSG00000029229.8" 
##  [979] "ENSMUSG00000020180.10" "ENSMUSG00000031085.16"
##  [981] "ENSMUSG00000092074.2"  "ENSMUSG00000024217.10"
##  [983] "ENSMUSG00000029620.4"  "ENSMUSG00000055943.5" 
##  [985] "ENSMUSG00000056912.12" "ENSMUSG00000029155.16"
##  [987] "ENSMUSG00000004667.18" "ENSMUSG00000055882.8" 
##  [989] "ENSMUSG00000087250.2"  "ENSMUSG00000043421.8" 
##  [991] "ENSMUSG00000100708.1"  "ENSMUSG00000035133.9" 
##  [993] "ENSMUSG00000052099.14" "ENSMUSG00000024663.20"
##  [995] "ENSMUSG00000024905.15" "ENSMUSG00000000171.5" 
##  [997] "ENSMUSG00000115761.1"  "ENSMUSG00000024758.15"
##  [999] "ENSMUSG00000000579.14" "ENSMUSG00000044957.3" 
## [1001] "ENSMUSG00000026585.13" "ENSMUSG00000028572.13"
## [1003] "ENSMUSG00000104960.1"  "ENSMUSG00000107073.1" 
## [1005] "ENSMUSG00000001687.15" "ENSMUSG00000059447.13"
## [1007] "ENSMUSG00000037072.15" "ENSMUSG00000023873.13"
## [1009] "ENSMUSG00000100837.7"  "ENSMUSG00000079652.8" 
## [1011] "ENSMUSG00000026989.5"  "ENSMUSG00000063089.4" 
## [1013] "ENSMUSG00000031181.2"  "ENSMUSG00000042396.10"
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## [1017] "ENSMUSG00000051185.9"  "ENSMUSG00000034813.18"
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## [1021] "ENSMUSG00000087524.1"  "ENSMUSG00000042564.13"
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## [1025] "ENSMUSG00000099531.1"  "ENSMUSG00000029602.11"
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## [1029] "ENSMUSG00000006715.11" "ENSMUSG00000022769.9" 
## [1031] "ENSMUSG00000103840.1"  "ENSMUSG00000006143.12"
## [1033] "ENSMUSG00000079334.8"  "ENSMUSG00000068686.12"
## [1035] "ENSMUSG00000025724.12" "ENSMUSG00000083896.8" 
## [1037] "ENSMUSG00000038696.14" "ENSMUSG00000043153.6" 
## [1039] "ENSMUSG00000020420.8"  "ENSMUSG00000017802.14"
## [1041] "ENSMUSG00000070883.3"  "ENSMUSG00000030647.8" 
## [1043] "ENSMUSG00000027985.14" "ENSMUSG00000100557.1" 
## [1045] "ENSMUSG00000022141.7"  "ENSMUSG00000100372.1" 
## [1047] "ENSMUSG00000060794.8"  "ENSMUSG00000029191.16"
## [1049] "ENSMUSG00000042726.14" "ENSMUSG00000058603.10"
## [1051] "ENSMUSG00000038347.15" "ENSMUSG00000091255.1" 
## [1053] "ENSMUSG00000019996.17" "ENSMUSG00000099740.1" 
## [1055] "ENSMUSG00000032171.7"  "ENSMUSG00000080725.9" 
## [1057] "ENSMUSG00000061689.15" "ENSMUSG00000024145.6" 
## [1059] "ENSMUSG00000034165.16" "ENSMUSG00000096001.2" 
## [1061] "ENSMUSG00000025486.17" "ENSMUSG00000060073.9" 
## [1063] "ENSMUSG00000096769.7"  "ENSMUSG00000059972.7" 
## [1065] "ENSMUSG00000095413.1"  "ENSMUSG00000029685.15"
## [1067] "ENSMUSG00000051437.4"  "ENSMUSG00000034706.16"
## [1069] "ENSMUSG00000058183.14" "ENSMUSG00000020624.3" 
## [1071] "ENSMUSG00000094811.7"  "ENSMUSG00000101683.6" 
## [1073] "ENSMUSG00000027459.16" "ENSMUSG00000034192.5" 
## [1075] "ENSMUSG00000054405.14" "ENSMUSG00000071041.4" 
## [1077] "ENSMUSG00000026966.6"  "ENSMUSG00000096650.7" 
## [1079] "ENSMUSG00000052748.14" "ENSMUSG00000073795.11"
## [1081] "ENSMUSG00000087260.5"  "ENSMUSG00000110332.1" 
## [1083] "ENSMUSG00000034473.14" "ENSMUSG00000055302.5" 
## [1085] "ENSMUSG00000054115.11" "ENSMUSG00000014470.4" 
## [1087] "ENSMUSG00000027341.10" "ENSMUSG00000096372.1" 
## [1089] "ENSMUSG00000068219.8"  "ENSMUSG00000029423.10"
## [1091] "ENSMUSG00000101051.6"  "ENSMUSG00000021337.8" 
## [1093] "ENSMUSG00000039704.7"  "ENSMUSG00000047441.4" 
## [1095] "ENSMUSG00000049339.16" "ENSMUSG00000069041.8" 
## [1097] "ENSMUSG00000025613.13" "ENSMUSG00000005233.16"
## [1099] "ENSMUSG00000034031.5"  "ENSMUSG00000034401.16"
## [1101] "ENSMUSG00000038095.15" "ENSMUSG00000090935.10"
## [1103] "ENSMUSG00000003166.20" "ENSMUSG00000073001.3" 
## [1105] "ENSMUSG00000029564.12" "ENSMUSG00000025043.3" 
## [1107] "ENSMUSG00000038594.9"  "ENSMUSG00000052906.7" 
## [1109] "ENSMUSG00000021572.9"  "ENSMUSG00000072692.7" 
## [1111] "ENSMUSG00000092519.2"  "ENSMUSG00000022174.8" 
## [1113] "ENSMUSG00000032294.17" "ENSMUSG00000036480.9" 
## [1115] "ENSMUSG00000015222.18" "ENSMUSG00000029701.15"
## [1117] "ENSMUSG00000116554.1"  "ENSMUSG00000030465.19"
## [1119] "ENSMUSG00000035578.16" "ENSMUSG00000022021.14"
## [1121] "ENSMUSG00000043060.8"  "ENSMUSG00000090685.1" 
## [1123] "ENSMUSG00000022892.11" "ENSMUSG00000033307.7" 
## [1125] "ENSMUSG00000031919.6"  "ENSMUSG00000020018.6" 
## [1127] "ENSMUSG00000029550.11" "ENSMUSG00000071788.5" 
## [1129] "ENSMUSG00000049881.13" "ENSMUSG00000028868.13"
## [1131] "ENSMUSG00000003200.10" "ENSMUSG00000035232.8" 
## [1133] "ENSMUSG00000022972.10" "ENSMUSG00000026339.18"
## [1135] "ENSMUSG00000023051.11" "ENSMUSG00000097424.2" 
## [1137] "ENSMUSG00000114412.1"  "ENSMUSG00000036921.2" 
## [1139] "ENSMUSG00000036463.8"  "ENSMUSG00000102416.4" 
## [1141] "ENSMUSG00000053914.9"  "ENSMUSG00000107214.3" 
## [1143] "ENSMUSG00000091906.2"  "ENSMUSG00000036574.5" 
## [1145] "ENSMUSG00000100963.1"  "ENSMUSG00000021483.8" 
## [1147] "ENSMUSG00000054717.7"  "ENSMUSG00000032671.5" 
## [1149] "ENSMUSG00000042672.15" "ENSMUSG00000042320.17"
## [1151] "ENSMUSG00000025287.15" "ENSMUSG00000006412.10"
## [1153] "ENSMUSG00000107478.1"  "ENSMUSG00000116976.1" 
## [1155] "ENSMUSG00000033102.15" "ENSMUSG00000000247.11"
## [1157] "ENSMUSG00000020904.11" "ENSMUSG00000029003.11"
## [1159] "ENSMUSG00000041923.15" "ENSMUSG00000031782.15"
## [1161] "ENSMUSG00000112654.1"  "ENSMUSG00000093950.2" 
## [1163] "ENSMUSG00000066979.6"  "ENSMUSG00000101801.6" 
## [1165] "ENSMUSG00000033963.16" "ENSMUSG00000086898.1" 
## [1167] "ENSMUSG00000028642.7"  "ENSMUSG00000049387.10"
## [1169] "ENSMUSG00000002043.17" "ENSMUSG00000059395.4" 
## [1171] "ENSMUSG00000037573.5"  "ENSMUSG00000103328.1" 
## [1173] "ENSMUSG00000020214.10" "ENSMUSG00000070283.4" 
## [1175] "ENSMUSG00000101155.6"  "ENSMUSG00000100121.1" 
## [1177] "ENSMUSG00000106013.4"  "ENSMUSG00000049354.8" 
## [1179] "ENSMUSG00000022753.15" "ENSMUSG00000079299.3" 
## [1181] "ENSMUSG00000037017.15" "ENSMUSG00000094294.2" 
## [1183] "ENSMUSG00000032204.13" "ENSMUSG00000100240.1" 
## [1185] "ENSMUSG00000100431.2"  "ENSMUSG00000049491.15"
## [1187] "ENSMUSG00000094258.7"  "ENSMUSG00000020633.14"
## [1189] "ENSMUSG00000031458.8"  "ENSMUSG00000089982.7" 
## [1191] "ENSMUSG00000035021.13" "ENSMUSG00000030990.18"
## [1193] "ENSMUSG00000028451.12" "ENSMUSG00000085486.2" 
## [1195] "ENSMUSG00000026523.14" "ENSMUSG00000004341.8" 
## [1197] "ENSMUSG00000002228.7"  "ENSMUSG00000031608.13"
## [1199] "ENSMUSG00000002949.15" "ENSMUSG00000112141.1" 
## [1201] "ENSMUSG00000079619.2"  "ENSMUSG00000023286.16"
## [1203] "ENSMUSG00000101915.1"  "ENSMUSG00000028383.17"
## [1205] "ENSMUSG00000083287.4"  "ENSMUSG00000025903.14"
## [1207] "ENSMUSG00000070493.3"  "ENSMUSG00000033174.17"
## [1209] "ENSMUSG00000037001.10" "ENSMUSG00000059208.15"
## [1211] "ENSMUSG00000039202.12" "ENSMUSG00000021771.14"
## [1213] "ENSMUSG00000002957.11" "ENSMUSG00000056815.1" 
## [1215] "ENSMUSG00000100872.2"  "ENSMUSG00000089887.2" 
## [1217] "ENSMUSG00000057506.5"  "ENSMUSG00000054966.13"
## [1219] "ENSMUSG00000032336.17" "ENSMUSG00000056919.9" 
## [1221] "ENSMUSG00000103935.1"  "ENSMUSG00000082398.1" 
## [1223] "ENSMUSG00000114441.1"  "ENSMUSG00000036743.4" 
## [1225] "ENSMUSG00000027569.15" "ENSMUSG00000043091.9" 
## [1227] "ENSMUSG00000084804.1"  "ENSMUSG00000031950.7" 
## [1229] "ENSMUSG00000050087.3"  "ENSMUSG00000093752.1" 
## [1231] "ENSMUSG00000028328.13" "ENSMUSG00000118311.1" 
## [1233] "ENSMUSG00000003721.14" "ENSMUSG00000081739.3" 
## [1235] "ENSMUSG00000063145.10" "ENSMUSG00000031270.1" 
## [1237] "ENSMUSG00000021790.12" "ENSMUSG00000085431.7" 
## [1239] "ENSMUSG00000053194.2"  "ENSMUSG00000028184.12"
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## [1243] "ENSMUSG00000086587.7"  "ENSMUSG00000031818.12"
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## [1247] "ENSMUSG00000032399.8"  "ENSMUSG00000074247.10"
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## [1251] "ENSMUSG00000046282.7"  "ENSMUSG00000027364.14"
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## [1257] "ENSMUSG00000024959.14" "ENSMUSG00000021986.9" 
## [1259] "ENSMUSG00000038515.10" "ENSMUSG00000026778.13"
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## [1267] "ENSMUSG00000082843.2"  "ENSMUSG00000073643.11"
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## [1271] "ENSMUSG00000047368.4"  "ENSMUSG00000050435.2" 
## [1273] "ENSMUSG00000030978.10" "ENSMUSG00000018362.14"
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## [1279] "ENSMUSG00000117104.1"  "ENSMUSG00000109228.2" 
## [1281] "ENSMUSG00000069118.3"  "ENSMUSG00000037236.16"
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## [1291] "ENSMUSG00000002210.11" "ENSMUSG00000029103.16"
## [1293] "ENSMUSG00000115656.1"  "ENSMUSG00000032475.15"
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## [1297] "ENSMUSG00000036427.5"  "ENSMUSG00000092586.8" 
## [1299] "ENSMUSG00000026499.5"  "ENSMUSG00000022884.15"
## [1301] "ENSMUSG00000091792.1"  "ENSMUSG00000100559.1" 
## [1303] "ENSMUSG00000057047.5"  "ENSMUSG00000021977.11"
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## [1309] "ENSMUSG00000095493.2"  "ENSMUSG00000027520.15"
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## [1313] "ENSMUSG00000060161.9"  "ENSMUSG00000032221.14"
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## [1317] "ENSMUSG00000006310.10" "ENSMUSG00000035142.18"
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## [1323] "ENSMUSG00000093923.7"  "ENSMUSG00000080268.4" 
## [1325] "ENSMUSG00000061928.6"  "ENSMUSG00000008813.13"
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## [1331] "ENSMUSG00000047215.14" "ENSMUSG00000066278.6" 
## [1333] "ENSMUSG00000028563.16" "ENSMUSG00000046949.16"
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## [1343] "ENSMUSG00000115372.1"  "ENSMUSG00000048100.13"
## [1345] "ENSMUSG00000040659.3"  "ENSMUSG00000064307.13"
## [1347] "ENSMUSG00000115896.1"  "ENSMUSG00000117497.1" 
## [1349] "ENSMUSG00000052738.14" "ENSMUSG00000052403.11"
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## [1355] "ENSMUSG00000015335.16" "ENSMUSG00000051695.6" 
## [1357] "ENSMUSG00000024076.10" "ENSMUSG00000021101.2" 
## [1359] "ENSMUSG00000109293.1"  "ENSMUSG00000025257.5" 
## [1361] "ENSMUSG00000083381.1"  "ENSMUSG00000027331.15"
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## [1367] "ENSMUSG00000099354.6"  "ENSMUSG00000047446.18"
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## [1371] "ENSMUSG00000057113.13" "ENSMUSG00000055547.4" 
## [1373] "ENSMUSG00000118339.1"  "ENSMUSG00000048516.2" 
## [1375] "ENSMUSG00000039477.16" "ENSMUSG00000017716.15"
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## [1381] "ENSMUSG00000028337.14" "ENSMUSG00000015443.9" 
## [1383] "ENSMUSG00000107144.1"  "ENSMUSG00000074634.12"
## [1385] "ENSMUSG00000031762.7"  "ENSMUSG00000028945.9" 
## [1387] "ENSMUSG00000028560.11" "ENSMUSG00000061392.2" 
## [1389] "ENSMUSG00000049902.6"  "ENSMUSG00000029552.19"
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## [1395] "ENSMUSG00000022681.15" "ENSMUSG00000037913.12"
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## [1401] "ENSMUSG00000021846.9"  "ENSMUSG00000031453.16"
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## [1409] "ENSMUSG00000037910.2"  "ENSMUSG00000020212.14"
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## [1425] "ENSMUSG00000058076.12" "ENSMUSG00000030708.14"
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## [1433] "ENSMUSG00000084349.3"  "ENSMUSG00000036551.6" 
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## [1437] "ENSMUSG00000032412.8"  "ENSMUSG00000085088.1" 
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## [1441] "ENSMUSG00000026301.16" "ENSMUSG00000101009.6" 
## [1443] "ENSMUSG00000096898.2"  "ENSMUSG00000087360.2" 
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## [1455] "ENSMUSG00000042229.9"  "ENSMUSG00000018925.3" 
## [1457] "ENSMUSG00000018040.9"  "ENSMUSG00000005575.16"
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## [1463] "ENSMUSG00000086607.7"  "ENSMUSG00000090136.4" 
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## [1467] "ENSMUSG00000055357.8"  "ENSMUSG00000032405.10"
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## [1473] "ENSMUSG00000091422.8"  "ENSMUSG00000025027.18"
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## [1943] "ENSMUSG00000021086.5"  "ENSMUSG00000050912.15"
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## [1949] "ENSMUSG00000027306.15" "ENSMUSG00000029875.5" 
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## [1955] "ENSMUSG00000027823.9"  "ENSMUSG00000023075.9" 
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## [1975] "ENSMUSG00000020576.10" "ENSMUSG00000046229.10"
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## [1979] "ENSMUSG00000057110.15" "ENSMUSG00000022555.12"
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## [1983] "ENSMUSG00000096901.7"  "ENSMUSG00000029131.14"
## [1985] "ENSMUSG00000060407.6"  "ENSMUSG00000049295.17"
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## [1989] "ENSMUSG00000022111.9"  "ENSMUSG00000030264.14"
## [1991] "ENSMUSG00000085044.1"  "ENSMUSG00000037364.12"
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## [1995] "ENSMUSG00000111028.1"  "ENSMUSG00000019878.8" 
## [1997] "ENSMUSG00000022965.8"  "ENSMUSG00000085759.1" 
## [1999] "ENSMUSG00000087185.1"  "ENSMUSG00000086732.1" 
## 
## $timestamp
## [1] "2026-06-14 21:02:19 UTC"

9.2.3 Visualize velocity-based trajectory

Once the velocity state is recorded, visualizing it is a breeze. You can use VelocityPlot() to draw the dynamic stream or arrows over any active dimensionality reduction space (like UMAP or t-SNE).

# Project the cached velocity stream onto the UMAP embedding
VelocityPlot(sce, reduction = "UMAP")
## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'
## Also defined by 'alabaster.base'
## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'
## Also defined by 'alabaster.base'
## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'
## Also defined by 'alabaster.base'
## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'
## Also defined by 'alabaster.base'
## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'
## Also defined by 'alabaster.base'
## Installing pyenv ...
## Done! pyenv has been installed to '/home/runner/.local/share/r-reticulate/pyenv/bin/pyenv'.
## Using Python: /home/runner/.pyenv/versions/3.12.10/bin/python3.12
## Creating virtual environment '/home/runner/.cache/R/basilisk/1.24.0/velociraptor/1.22.0/env' ...
## + /home/runner/.pyenv/versions/3.12.10/bin/python3.12 -m venv /home/runner/.cache/R/basilisk/1.24.0/velociraptor/1.22.0/env
## Done!
## Installing packages: pip, wheel, setuptools
## + /home/runner/.cache/R/basilisk/1.24.0/velociraptor/1.22.0/env/bin/python -m pip install --upgrade pip wheel setuptools
## Installing packages: 'anndata==0.11.4', 'array-api-compat==1.12.0', 'click==8.2.1', 'contourpy==1.3.2', 'cycler==0.12.1', 'fonttools==4.58.5', 'h5py==3.14.0', 'joblib==1.5.1', 'kiwisolver==1.4.8', 'legacy-api-wrap==1.4.1', 'llvmlite==0.44.0', 'loompy==3.0.8', 'matplotlib==3.10.3', 'natsort==8.4.0', 'networkx==3.5', 'numba==0.61.2', 'numpy==2.2.6', 'numpy-groupies==0.11.3', 'packaging==25.0', 'pandas==2.3.1', 'patsy==1.0.1', 'pillow==11.3.0', 'pip==25.1.1', 'pynndescent==0.5.13', 'pyparsing==3.2.3', 'python-dateutil==2.9.0.post0', 'pytz==2025.2', 'scanpy==1.11.3', 'scikit-learn==1.7.0', 'scipy==1.15.3', 'scvelo==0.3.3', 'seaborn==0.13.2', 'session-info2==0.1.2', 'setuptools==80.9.0', 'six==1.17.0', 'statsmodels==0.14.5', 'threadpoolctl==3.6.0', 'tqdm==4.67.1', 'typing_extensions==4.14.1', 'tzdata==2025.2', 'umap-learn==0.5.9.post2', 'wheel==0.45.1'
## + /home/runner/.cache/R/basilisk/1.24.0/velociraptor/1.22.0/env/bin/python -m pip install --upgrade --no-user 'anndata==0.11.4' 'array-api-compat==1.12.0' 'click==8.2.1' 'contourpy==1.3.2' 'cycler==0.12.1' 'fonttools==4.58.5' 'h5py==3.14.0' 'joblib==1.5.1' 'kiwisolver==1.4.8' 'legacy-api-wrap==1.4.1' 'llvmlite==0.44.0' 'loompy==3.0.8' 'matplotlib==3.10.3' 'natsort==8.4.0' 'networkx==3.5' 'numba==0.61.2' 'numpy==2.2.6' 'numpy-groupies==0.11.3' 'packaging==25.0' 'pandas==2.3.1' 'patsy==1.0.1' 'pillow==11.3.0' 'pip==25.1.1' 'pynndescent==0.5.13' 'pyparsing==3.2.3' 'python-dateutil==2.9.0.post0' 'pytz==2025.2' 'scanpy==1.11.3' 'scikit-learn==1.7.0' 'scipy==1.15.3' 'scvelo==0.3.3' 'seaborn==0.13.2' 'session-info2==0.1.2' 'setuptools==80.9.0' 'six==1.17.0' 'statsmodels==0.14.5' 'threadpoolctl==3.6.0' 'tqdm==4.67.1' 'typing_extensions==4.14.1' 'tzdata==2025.2' 'umap-learn==0.5.9.post2' 'wheel==0.45.1'
## Virtual environment '/home/runner/.cache/R/basilisk/1.24.0/velociraptor/1.22.0/env' successfully created.
## For native R and reading and writing of H5AD files, an R
## <AnnData> object, and conversion to <SingleCellExperiment>
## or <Seurat> objects, check out the anndataR package:
## ℹ Install it from Bioconductor with
##   `BiocManager::install("anndataR")`
## ℹ See more at <https://bioconductor.org/packages/anndataR/>
## This message is displayed once per session.
## ℹ Using the 'X' assay as the X matrix
## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'
## Also defined by 'alabaster.base'
## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'
## Also defined by 'alabaster.base'
## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'
## Also defined by 'alabaster.base'
## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'
## Also defined by 'alabaster.base'
## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'
## Also defined by 'alabaster.base'
## computing velocity embedding
##     finished (0:00:00) --> added
##     'velocity_target', embedded velocity vectors (adata.obsm)

9.3 CellRank: Advanced Fate Mapping

When standard trajectory tools (like Slingshot) struggle with complex, cyclic, or highly heterogeneous developmental processes, CellRank shines. CellRank elegantly combines directed RNA velocity data with undirected transcriptomic similarity to robustly infer terminal states and cellular fate probabilities.

sclet brings the full power of CellRank directly to your SCE object, again utilizing the isolated basilisk Python environment to prevent dependency conflicts.

9.3.1 Run CellRank

RunCellFate() is the user-facing entry point for fate mapping in sclet. At the moment it dispatches to CellRank, automatically senses the upstream velocity run, and records the resulting terminal states, named fate probabilities, and lineage drivers in the shared state contract.

# Inspect the cached CellRank analysis state
get_cellrank(sce, id = "cellrank")
## $id
## [1] "cellrank"
## 
## $type
## [1] "trajectory"
## 
## $status
## [1] "completed"
## 
## $method
## [1] "CellRank"
## 
## $inputs
## $inputs$reduction
## [1] "PCA"
## 
## $inputs$cluster_key
## [1] "cluster"
## 
## $inputs$velocity_id
## [1] "velocity"
## 
## 
## $artifacts
## $artifacts$analysis_key
## [1] "cellrank"
## 
## $artifacts$terminal_state_col
## [1] "cellrank_terminal_states"
## 
## $artifacts$fate_probability_cols
## [1] "cellrank_fate_X0" "cellrank_fate_X1"
## 
## $artifacts$fate_probability_names
## [1] "0" "1"
## 
## $artifacts$has_lineage_drivers
## [1] TRUE
## 
## 
## $params
## list()
## 
## $summary
## $summary$n_terminal_states
## [1] 2
## 
## $summary$n_fate_dimensions
## [1] 2
## 
## $summary$n_lineage_drivers
## [1] 4000
## 
## 
## $reduction
## [1] "PCA"
## 
## $cluster_key
## [1] "cluster"
## 
## $terminal_states
##   [1] NA  NA  NA  "0" NA  NA  "1" NA  NA  NA  NA  NA  NA 
##  [14] NA  "0" NA  NA  NA  NA  NA  "1" NA  NA  NA  NA  "1"
##  [27] NA  "0" "1" NA  "0" NA  "0" NA  "0" NA  NA  "0" NA 
##  [40] NA  "0" NA  NA  NA  NA  "0" NA  NA  NA  "0" NA  NA 
##  [53] NA  "0" NA  NA  NA  NA  NA  NA  NA  NA  NA  "1" NA 
##  [66] NA  "0" NA  NA  NA  NA  NA  NA  NA  "1" NA  "0" NA 
##  [79] NA  NA  NA  NA  "1" NA  "0" "1" "0" NA  NA  "0" NA 
##  [92] "0" NA  "0" NA  NA  NA  NA  NA  NA  NA  "0" NA  NA 
## [105] "1" NA  NA  "1" NA  NA  NA  "1" NA  NA  NA  "1" NA 
## [118] "1" NA  NA  NA  "1" NA  "0" "0" NA  NA  NA  NA  NA 
## [131] NA  NA  "1" NA  "1" NA  NA  NA  NA  NA  NA  NA  NA 
## [144] "1" NA  NA  NA  NA  NA  "1" NA  NA  "1" NA  NA  "1"
## [157] NA  NA  NA  NA  NA  "1" "0" NA  NA  "1" NA  NA  NA 
## [170] NA  NA  "0" NA  NA  NA  NA  NA  "1" NA  NA  NA  NA 
## [183] NA  NA  NA  NA  "0" NA  NA  NA  NA  NA  NA  NA  "1"
## [196] NA  NA  NA  NA  NA  "1" NA  NA  NA  NA  NA  "0" "0"
## [209] "1" NA  NA  NA  "0" NA  NA  NA  NA  NA  NA  NA  NA 
## [222] NA  NA  NA  NA  NA  NA  NA  NA  NA  NA  NA  NA  NA 
## [235] NA  "1" NA  NA  NA  NA  NA  NA  NA  NA  NA  NA  NA 
## [248] NA  NA  NA  NA  NA  NA  NA  NA  NA  NA  NA  NA  NA 
## [261] NA  NA  NA  NA  NA  NA  NA  NA  NA  NA  NA  "1" NA 
## [274] NA  NA  "1" NA  NA  NA  NA  NA  NA  NA  NA  NA  "0"
## [287] NA  NA  "1" NA  NA  NA  "0" NA  NA  NA  NA  "0" NA 
## [300] NA 
## 
## $absorption_probs
##        cellrank_fate_X0 cellrank_fate_X1
##   [1,]       0.99702079      0.002979403
##   [2,]       0.99554624      0.004453895
##   [3,]       0.99467236      0.005327871
##   [4,]       1.00000000      0.000000000
##   [5,]       0.93386362      0.066128651
##   [6,]       0.93386457      0.066127800
##   [7,]       0.00000000      1.000000000
##   [8,]       0.93386484      0.066127578
##   [9,]       0.93386475      0.066127619
##  [10,]       0.99821091      0.001789189
##  [11,]       0.93387051      0.066121807
##  [12,]       0.93386347      0.066128800
##  [13,]       0.93386447      0.066127933
##  [14,]       0.93386322      0.066129000
##  [15,]       1.00000000      0.000000000
##  [16,]       0.99687145      0.003128671
##  [17,]       0.93386289      0.066129439
##  [18,]       0.93386504      0.066127104
##  [19,]       0.93386285      0.066129504
##  [20,]       0.97175552      0.028242821
##  [21,]       0.00000000      1.000000000
##  [22,]       0.93386475      0.066127553
##  [23,]       0.93385668      0.066135557
##  [24,]       0.93386069      0.066131591
##  [25,]       0.93385716      0.066135183
##  [26,]       0.00000000      1.000000000
##  [27,]       0.93386478      0.066127350
##  [28,]       1.00000000      0.000000000
##  [29,]       0.00000000      1.000000000
##  [30,]       0.93390299      0.066089163
##  [31,]       1.00000000      0.000000000
##  [32,]       0.93334962      0.066642696
##  [33,]       1.00000000      0.000000000
##  [34,]       0.93386041      0.066131935
##  [35,]       1.00000000      0.000000000
##  [36,]       0.93384886      0.066143499
##  [37,]       0.93387567      0.066116468
##  [38,]       1.00000000      0.000000000
##  [39,]       0.93386501      0.066127389
##  [40,]       0.93386190      0.066130472
##  [41,]       1.00000000      0.000000000
##  [42,]       0.93386967      0.066122668
##  [43,]       0.93386332      0.066128985
##  [44,]       0.93386477      0.066127432
##  [45,]       0.93386470      0.066127596
##  [46,]       1.00000000      0.000000000
##  [47,]       0.93386426      0.066128167
##  [48,]       0.92909910      0.070893316
##  [49,]       0.93386470      0.066127504
##  [50,]       1.00000000      0.000000000
##  [51,]       0.99265539      0.007344720
##  [52,]       0.93386473      0.066127449
##  [53,]       0.93386485      0.066127382
##  [54,]       1.00000000      0.000000000
##  [55,]       0.93386459      0.066127637
##  [56,]       0.93386497      0.066127416
##  [57,]       0.93386104      0.066131268
##  [58,]       0.99432502      0.005675160
##  [59,]       0.98319042      0.016809800
##  [60,]       0.93386624      0.066125988
##  [61,]       0.93382855      0.066163772
##  [62,]       0.93381615      0.066176161
##  [63,]       0.93386400      0.066128318
##  [64,]       0.00000000      1.000000000
##  [65,]       0.93386327      0.066129077
##  [66,]       0.12193963      0.878060505
##  [67,]       1.00000000      0.000000000
##  [68,]       0.93386515      0.066127189
##  [69,]       0.97653877      0.023461592
##  [70,]       0.93390455      0.066087669
##  [71,]       0.89391967      0.106080512
##  [72,]       0.93386482      0.066127613
##  [73,]       0.93386417      0.066128020
##  [74,]       0.93386473      0.066127690
##  [75,]       0.00000000      1.000000000
##  [76,]       0.93385851      0.066133787
##  [77,]       1.00000000      0.000000000
##  [78,]       0.93386474      0.066127388
##  [79,]       0.99423855      0.005761593
##  [80,]       0.93386219      0.066130014
##  [81,]       0.93386440      0.066127872
##  [82,]       0.93389593      0.066096448
##  [83,]       0.00000000      1.000000000
##  [84,]       0.93386491      0.066127466
##  [85,]       1.00000000      0.000000000
##  [86,]       0.00000000      1.000000000
##  [87,]       1.00000000      0.000000000
##  [88,]       0.62144752      0.378553150
##  [89,]       0.93386492      0.066127349
##  [90,]       1.00000000      0.000000000
##  [91,]       0.93386485      0.066127480
##  [92,]       1.00000000      0.000000000
##  [93,]       0.93386415      0.066128151
##  [94,]       1.00000000      0.000000000
##  [95,]       0.93386451      0.066127718
##  [96,]       0.93386425      0.066128103
##  [97,]       0.93386145      0.066130878
##  [98,]       0.93386377      0.066128505
##  [99,]       0.93386314      0.066129165
## [100,]       0.93385296      0.066139439
## [101,]       0.93386964      0.066122581
## [102,]       1.00000000      0.000000000
## [103,]       0.93386467      0.066127536
## [104,]       0.93387900      0.066112932
## [105,]       0.00000000      1.000000000
## [106,]       0.93386574      0.066126516
## [107,]       0.76093938      0.239061206
## [108,]       0.00000000      1.000000000
## [109,]       0.99692364      0.003076577
## [110,]       0.99418059      0.005819583
## [111,]       0.93386499      0.066127398
## [112,]       0.00000000      1.000000000
## [113,]       0.93386441      0.066127765
## [114,]       0.93386062      0.066131732
## [115,]       0.93386472      0.066127466
## [116,]       0.00000000      1.000000000
## [117,]       0.62985065      0.370149977
## [118,]       0.00000000      1.000000000
## [119,]       0.93387443      0.066117638
## [120,]       0.99355631      0.006443791
## [121,]       0.93386112      0.066131163
## [122,]       0.00000000      1.000000000
## [123,]       0.93386467      0.066127510
## [124,]       1.00000000      0.000000000
## [125,]       1.00000000      0.000000000
## [126,]       0.93387900      0.066112932
## [127,]       0.93386471      0.066127502
## [128,]       0.92666452      0.073327867
## [129,]       0.93386477      0.066127395
## [130,]       0.08816117      0.911838925
## [131,]       0.93386452      0.066127757
## [132,]       0.93386451      0.066127732
## [133,]       0.00000000      1.000000000
## [134,]       0.66998783      0.330012701
## [135,]       0.00000000      1.000000000
## [136,]       0.92329507      0.076705143
## [137,]       0.93386401      0.066128299
## [138,]       0.93386549      0.066126907
## [139,]       0.93385910      0.066133087
## [140,]       0.93385648      0.066135847
## [141,]       0.93383087      0.066161453
## [142,]       0.78929234      0.210708332
## [143,]       0.93385465      0.066137592
## [144,]       0.00000000      1.000000000
## [145,]       0.93386058      0.066131662
## [146,]       0.99388134      0.006118856
## [147,]       0.32868802      0.671312246
## [148,]       0.93387187      0.066120268
## [149,]       0.93386101      0.066131304
## [150,]       0.00000000      1.000000000
## [151,]       0.93402744      0.065965193
## [152,]       0.82595531      0.174044967
## [153,]       0.00000000      1.000000000
## [154,]       0.93386430      0.066127947
## [155,]       0.99560129      0.004399008
## [156,]       0.00000000      1.000000000
## [157,]       0.93076723      0.069225101
## [158,]       0.93385871      0.066133570
## [159,]       0.93385845      0.066133796
## [160,]       0.93384925      0.066143148
## [161,]       0.83934038      0.160660113
## [162,]       0.00000000      1.000000000
## [163,]       1.00000000      0.000000000
## [164,]       0.93388986      0.066102114
## [165,]       0.93390455      0.066087669
## [166,]       0.00000000      1.000000000
## [167,]       0.93386466      0.066127466
## [168,]       0.93386202      0.066130302
## [169,]       0.93386097      0.066131330
## [170,]       0.93386463      0.066127532
## [171,]       0.93389418      0.066097984
## [172,]       1.00000000      0.000000000
## [173,]       0.93386388      0.066128410
## [174,]       0.93386482      0.066127526
## [175,]       0.93387697      0.066115044
## [176,]       0.97710740      0.022892836
## [177,]       0.93386463      0.066127732
## [178,]       0.00000000      1.000000000
## [179,]       0.93379778      0.066194510
## [180,]       0.93388457      0.066107405
## [181,]       0.93386488      0.066127517
## [182,]       0.93387586      0.066116270
## [183,]       0.98860737      0.011392952
## [184,]       0.93388617      0.066105799
## [185,]       0.93386369      0.066128570
## [186,]       0.93386480      0.066127342
## [187,]       1.00000000      0.000000000
## [188,]       0.99491412      0.005086141
## [189,]       0.93386521      0.066127201
## [190,]       0.93386861      0.066123469
## [191,]       0.93386491      0.066127320
## [192,]       0.93324070      0.066751603
## [193,]       0.93346054      0.066531775
## [194,]       0.93386631      0.066125851
## [195,]       0.00000000      1.000000000
## [196,]       0.93386826      0.066123973
## [197,]       0.93314359      0.066848698
## [198,]       0.93385959      0.066132667
## [199,]       0.93382122      0.066171084
## [200,]       0.93380224      0.066189999
## [201,]       0.00000000      1.000000000
## [202,]       0.93336645      0.066625819
## [203,]       0.93387447      0.066117714
## [204,]       0.93387034      0.066121963
## [205,]       0.93390455      0.066087669
## [206,]       0.93386436      0.066128009
## [207,]       1.00000000      0.000000000
## [208,]       1.00000000      0.000000000
## [209,]       0.00000000      1.000000000
## [210,]       0.93390063      0.066091497
## [211,]       0.93387379      0.066118474
## [212,]       0.93386486      0.066127430
## [213,]       1.00000000      0.000000000
## [214,]       0.93386348      0.066128881
## [215,]       0.93386792      0.066124133
## [216,]       0.93390455      0.066087669
## [217,]       0.97959613      0.020404196
## [218,]       0.93386457      0.066127872
## [219,]       0.93386389      0.066128432
## [220,]       0.43064670      0.569353785
## [221,]       0.93386260      0.066129732
## [222,]       0.93386454      0.066127741
## [223,]       0.93386480      0.066127294
## [224,]       0.93386456      0.066127878
## [225,]       0.93384971      0.066142662
## [226,]       0.93390455      0.066087669
## [227,]       0.93386378      0.066128468
## [228,]       0.93386468      0.066127649
## [229,]       0.93390455      0.066087669
## [230,]       0.93385860      0.066133708
## [231,]       0.93386475      0.066127389
## [232,]       0.93386476      0.066127395
## [233,]       0.93386542      0.066126994
## [234,]       0.93386694      0.066125346
## [235,]       0.93386174      0.066130530
## [236,]       0.00000000      1.000000000
## [237,]       0.93386486      0.066127334
## [238,]       0.93386963      0.066122531
## [239,]       0.93386388      0.066128496
## [240,]       0.93390666      0.066085586
## [241,]       0.93386798      0.066124090
## [242,]       0.93387223      0.066119877
## [243,]       0.93386587      0.066126336
## [244,]       0.93386568      0.066126724
## [245,]       0.93386091      0.066131338
## [246,]       0.93385774      0.066134686
## [247,]       0.93386518      0.066127233
## [248,]       0.93387518      0.066117064
## [249,]       0.93386574      0.066126619
## [250,]       0.93386420      0.066128089
## [251,]       0.93389725      0.066094850
## [252,]       0.93389941      0.066092710
## [253,]       0.93386033      0.066132036
## [254,]       0.93386460      0.066127767
## [255,]       0.93386477      0.066127364
## [256,]       0.93386482      0.066127579
## [257,]       0.93386757      0.066124483
## [258,]       0.93386453      0.066127648
## [259,]       0.93386472      0.066127488
## [260,]       0.99576620      0.004234121
## [261,]       0.93384366      0.066148669
## [262,]       0.93386614      0.066126079
## [263,]       0.93386263      0.066129711
## [264,]       0.93386094      0.066131360
## [265,]       0.95671778      0.043282381
## [266,]       0.93213050      0.067861904
## [267,]       0.93390455      0.066087669
## [268,]       0.93386442      0.066127835
## [269,]       0.93329078      0.066701493
## [270,]       0.93386193      0.066130405
## [271,]       0.93386488      0.066127555
## [272,]       0.00000000      1.000000000
## [273,]       0.93386458      0.066127765
## [274,]       0.93386478      0.066127339
## [275,]       0.93386791      0.066124141
## [276,]       0.00000000      1.000000000
## [277,]       0.93386432      0.066127959
## [278,]       0.93387005      0.066122216
## [279,]       0.93389706      0.066095000
## [280,]       0.93386468      0.066127554
## [281,]       0.93386663      0.066125559
## [282,]       0.93386333      0.066128969
## [283,]       0.93386516      0.066127066
## [284,]       0.93386429      0.066127986
## [285,]       0.07872847      0.921271639
## [286,]       1.00000000      0.000000000
## [287,]       0.93385327      0.066139061
## [288,]       0.93386467      0.066127714
## [289,]       0.00000000      1.000000000
## [290,]       0.93386795      0.066124025
## [291,]       0.93386482      0.066127309
## [292,]       0.93392455      0.066067751
## [293,]       1.00000000      0.000000000
## [294,]       0.93386686      0.066125288
## [295,]       0.93386481      0.066127662
## [296,]       0.93386522      0.066127216
## [297,]       0.93376035      0.066231961
## [298,]       1.00000000      0.000000000
## [299,]       0.90631186      0.093680681
## [300,]       0.99499636      0.005003830
## 
## $terminal_state_col
## [1] "cellrank_terminal_states"
## 
## $fate_probability_cols
## [1] "cellrank_fate_X0" "cellrank_fate_X1"
## 
## $fate_probability_names
## [1] "0" "1"
## 
## $lineage_drivers
## # A tibble: 4,000 × 7
##    gene    lineage     corr     pval    qval  ci_low ci_high
##    <chr>   <chr>      <dbl>    <dbl>   <dbl>   <dbl>   <dbl>
##  1 ENSMUS… 0       -0.147   1.10e- 2 1.54e-2 -0.256  -0.0339
##  2 ENSMUS… 0       -0.00858 8.82e- 1 8.91e-1 -0.122   0.105 
##  3 ENSMUS… 0        0.344   6.75e-10 5.47e-9  0.240   0.440 
##  4 ENSMUS… 0       -0.306   5.17e- 8 2.21e-7 -0.405  -0.200 
##  5 ENSMUS… 0       -0.203   3.86e- 4 7.02e-4 -0.309  -0.0920
##  6 ENSMUS… 0        0.248   1.30e- 5 3.06e-5  0.138   0.351 
##  7 ENSMUS… 0        0.0138  8.12e- 1 8.24e-1 -0.0996  0.127 
##  8 ENSMUS… 0       -0.341   9.82e-10 7.70e-9 -0.437  -0.236 
##  9 ENSMUS… 0       -0.141   1.47e- 2 2.01e-2 -0.250  -0.0278
## 10 ENSMUS… 0        0.320   1.09e- 8 5.87e-8  0.215   0.418 
## # ℹ 3,990 more rows
## 
## $created_at
## [1] "2026-06-14 21:17:16 UTC"
## 
## $timestamp
## [1] "2026-06-14 21:17:16 UTC"

The resulting terminal state assignments and directional fate probabilities are written directly into colData(sce). In addition, sclet now provides fate-specific plotting helpers following the plot_<module>_<type> convention, so you do not need to manually reconstruct the plotting data frame after every run.

p_prob <- plot_fate_probability(sce, fate = 1, reduction = "UMAP", id = "cellrank")
## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'
## Also defined by 'alabaster.base'
## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'
## Also defined by 'alabaster.base'
p_term <- plot_fate_terminal_states(sce, reduction = "UMAP", id = "cellrank")
## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'
## Also defined by 'alabaster.base'
## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'
## Also defined by 'alabaster.base'
plot_list(`Fate Probability` = p_prob, `Terminal States` = p_term)

cr <- get_cellrank(sce, id = "cellrank")
driver_lineage <- if (!is.null(cr$artifacts$fate_probability_names)) {
  cr$artifacts$fate_probability_names[[1]]
} else {
  cr$fate_probability_names[[1]]
}

plot_fate_driver_trends(sce, lineage = driver_lineage, top_n = 4)

9.4 Workflow shell for velocity and fate

When spliced/unspliced assays are available, the same trajectory mainline can extend from lineage inference to velocity and fate mapping:

sce <- RunTrajectoryWorkflow(
  sce,
  group = "cluster",
  reduction = "PCA",
  run_diffusion_map = FALSE,
  run_slingshot = FALSE,
  run_velocity = "auto",
  run_fate = "auto",
  name = "germline_main"
)

plot_trajectory_overview(
  sce,
  id = "germline_main",
  panels = c("velocity", "terminal_states", "fate_probability")
)

9.5 Velocity Latent Time

When scVelo is run in dynamical mode, it infers a latent time for each cell — a pseudotime ordering derived from the RNA velocity field itself, not from a separate trajectory method. plot_velocity_latent_time() colors cells on an embedding by this inferred temporal progression.

{r velocity-latent, eval=FALSE} # requires scVelo dynamical mode latent time plot_velocity_latent_time( sce, reduction = "UMAP", id = "germline_main_velocity" )

References

Bergen, Volker, Marius Lange, Stefan Peidli, F. Alexander Wolf, and Fabian J. Theis. 2020. “Generalizing RNA Velocity to Transient Cell States Through Dynamical Modeling.” Nature Biotechnology 38 (12): 1408–14. https://doi.org/10.1038/s41587-020-0591-3.