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error in RunSlingshot #265

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renyzh5-2 opened this issue Dec 12, 2024 · 2 comments
Open

error in RunSlingshot #265

renyzh5-2 opened this issue Dec 12, 2024 · 2 comments

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@renyzh5-2
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renyzh5-2 commented Dec 12, 2024 •
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Hello, I encountered an issue while running RunSlingshot(). Here is the code. Thanks.

PC_HCC <- RunSlingshot(srt = PC_HCC, group.by = "seurat_clusters", reduction = "umap")
Error in gtable_add_grob():
! grobs must be a single grob or a list of grobs, not a list matrix.
Run rlang::last_trace() to see where the error occurred.
Warning messages:
1: No shared levels found between names(values) of the manual scale and the data's fill values.
2: No shared levels found between names(values) of the manual scale and the data's fill values.
3: Removed 5 rows containing missing values or values outside the scale range (geom_path()).
4: Removed 5 rows containing missing values or values outside the scale range (geom_path()).
rlang::last_trace()
<error/rlang_error>
Error in gtable_add_grob():
! grobs must be a single grob or a list of grobs, not a list matrix.

Backtrace:
▆

  1. └─SCP::RunSlingshot(...)
  2. └─SCP::CellDimPlot(...)
  3. └─base::lapply(...)

  4.   └─SCP (local) FUN(X[[i]], ...)

  5.     └─SCP:::add_grob(gtable, legend, legend.position)

  6.       └─gtable::gtable_add_grob(grobs = grob)

Run rlang::last_trace(drop = FALSE) to see 2 hidden frames.

rlang::last_trace(drop = FALSE)
<error/rlang_error>
Error in gtable_add_grob():
! grobs must be a single grob or a list of grobs, not a list matrix.

Backtrace:
▆

  1. └─SCP::RunSlingshot(...)
  2. └─SCP::CellDimPlot(...)
  3. └─base::lapply(...)

  4.   └─SCP (local) FUN(X[[i]], ...)

  5.     └─SCP:::add_grob(gtable, legend, legend.position)

  6.       └─gtable::gtable_add_grob(grobs = grob)

  7.         └─gtable:::stop_input_type(grobs, "a single grob or a list of grobs")

  8.           └─rlang::abort(message, ..., call = call, arg = arg)

and this is my seurat object: PC_HCC

str(PC_HCC)
Formal class 'Seurat' [package "SeuratObject"] with 13 slots
..@ assays :List of 1
.. ..$ RNA:Formal class 'Assay' [package "SeuratObject"] with 8 slots
.. .. .. ..@ counts :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
.. .. .. .. .. ..@ i : int [1:13871269] 14 16 19 24 28 29 30 38 44 56 ...
.. .. .. .. .. ..@ p : int [1:8785] 0 2324 3794 5049 7002 7960 10133 12336 13575 15726 ...
.. .. .. .. .. ..@ Dim : int [1:2] 20002 8784
.. .. .. .. .. ..@ Dimnames:List of 2
.. .. .. .. .. .. ..$ : chr [1:20002] "OR4F5" "OR4F29" "OR4F16" "SAMD11" ...
.. .. .. .. .. .. ..$ : chr [1:8784] "A011_HCC_1383" "A011_HCC_1746" "A011_HCC_2811" "A011_HCC_3089" ...
.. .. .. .. .. ..@ x : num [1:13871269] 1 1 1 1 3 1 3 1 1 2 ...
.. .. .. .. .. ..@ factors : list()
.. .. .. ..@ data :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
.. .. .. .. .. ..@ i : int [1:13871269] 14 16 19 24 28 29 30 38 44 56 ...
.. .. .. .. .. ..@ p : int [1:8785] 0 2324 3794 5049 7002 7960 10133 12336 13575 15726 ...
.. .. .. .. .. ..@ Dim : int [1:2] 20002 8784
.. .. .. .. .. ..@ Dimnames:List of 2
.. .. .. .. .. .. ..$ : chr [1:20002] "OR4F5" "OR4F29" "OR4F16" "SAMD11" ...
.. .. .. .. .. .. ..$ : chr [1:8784] "A011_HCC_1383" "A011_HCC_1746" "A011_HCC_2811" "A011_HCC_3089" ...
.. .. .. .. .. ..@ x : num [1:13871269] 0.296 0.296 0.296 0.296 0.71 ...
.. .. .. .. .. ..@ factors : list()
.. .. .. ..@ scale.data : num [1:20002, 1:8784] 0 0 0 -0.0676 -0.4298 ...
.. .. .. .. ..- attr(, "dimnames")=List of 2
.. .. .. .. .. ..$ : chr [1:20002] "OR4F5" "OR4F29" "OR4F16" "SAMD11" ...
.. .. .. .. .. ..$ : chr [1:8784] "A011_HCC_1383" "A011_HCC_1746" "A011_HCC_2811" "A011_HCC_3089" ...
.. .. .. ..@ assay.orig : NULL
.. .. .. ..@ var.features : chr [1:2000] "IGLL5" "IGLV3-25" "IGLV3-19" "IGLV2-8" ...
.. .. .. ..@ meta.features:'data.frame': 20002 obs. of 5 variables:
.. .. .. .. ..$ vst.mean : num [1:20002] 0 0 0 0.00569 0.25672 ...
.. .. .. .. ..$ vst.variance : num [1:20002] 0 0 0 0.00589 0.32245 ...
.. .. .. .. ..$ vst.variance.expected : num [1:20002] 0 0 0 0.00693 0.39522 ...
.. .. .. .. ..$ vst.variance.standardized: num [1:20002] 0 0 0 0.849 0.816 ...
.. .. .. .. ..$ vst.variable : logi [1:20002] FALSE FALSE FALSE FALSE FALSE FALSE ...
.. .. .. ..@ misc : list()
.. .. .. ..@ key : Named chr "rna_"
.. .. .. .. ..- attr(, "names")= chr ""
..@ meta.data :'data.frame': 8784 obs. of 11 variables:
.. ..$ orig.ident : chr [1:8784] "A011" "A011" "A011" "A011" ...
.. ..$ nCount_RNA : num [1:8784] 28999 16474 11056 24096 4141 ...
.. ..$ nFeature_RNA : int [1:8784] 2324 1470 1255 1953 958 2173 2203 1239 2151 2258 ...
.. ..$ Sample : chr [1:8784] "A011_HCC" "A011_HCC" "A011_HCC" "A011_HCC" ...
.. ..$ percent.mt : num [1:8784] 1.983 2.537 2.343 0.955 1.111 ...
.. ..$ Cancer_type : chr [1:8784] "HCC" "HCC" "HCC" "HCC" ...
.. ..$ clusters : chr [1:8784] "B_03_MZB1" "B_03_MZB1" "B_03_MZB1" "B_03_MZB1" ...
.. ..$ labels : chr [1:8784] "B cells" "B cells" "B cells" "B cells" ...
.. ..$ RNA_snn_res.0.2 : Factor w/ 9 levels "0","1","2","3",..: 7 2 2 2 2 2 7 2 2 7 ...
.. ..$ seurat_clusters : Factor w/ 7 levels "0","1","2","3",..: 1 1 6 1 1 1 2 1 4 3 ...
.. ..$ RNA_snn_res.0.13: Factor w/ 7 levels "0","1","2","3",..: 1 1 6 1 1 1 2 1 4 3 ...
..@ active.assay: chr "RNA"
..@ active.ident: Factor w/ 7 levels "0","1","2","3",..: 1 1 6 1 1 1 2 1 4 3 ...
.. ..- attr(, "names")= chr [1:8784] "A011_HCC_1383" "A011_HCC_1746" "A011_HCC_2811" "A011_HCC_3089" ...
..@ graphs :List of 2
.. ..$ RNA_nn :Formal class 'Graph' [package "SeuratObject"] with 7 slots
.. .. .. ..@ assay.used: chr "RNA"
.. .. .. ..@ i : int [1:175680] 0 9 14 146 783 1079 1263 1310 2064 2720 ...
.. .. .. ..@ p : int [1:8785] 0 21 31 76 132 135 153 253 269 310 ...
.. .. .. ..@ Dim : int [1:2] 8784 8784
.. .. .. ..@ Dimnames :List of 2
.. .. .. .. ..$ : chr [1:8784] "A011_HCC_1383" "A011_HCC_1746" "A011_HCC_2811" "A011_HCC_3089" ...
.. .. .. .. ..$ : chr [1:8784] "A011_HCC_1383" "A011_HCC_1746" "A011_HCC_2811" "A011_HCC_3089" ...
.. .. .. ..@ x : num [1:175680] 1 1 1 1 1 1 1 1 1 1 ...
.. .. .. ..@ factors : list()
.. ..$ RNA_snn:Formal class 'Graph' [package "SeuratObject"] with 7 slots
.. .. .. ..@ assay.used: chr "RNA"
.. .. .. ..@ i : int [1:664882] 0 5 146 642 783 845 1719 2064 2381 2417 ...
.. .. .. ..@ p : int [1:8785] 0 38 95 153 281 325 377 579 645 742 ...
.. .. .. ..@ Dim : int [1:2] 8784 8784
.. .. .. ..@ Dimnames :List of 2
.. .. .. .. ..$ : chr [1:8784] "A011_HCC_1383" "A011_HCC_1746" "A011_HCC_2811" "A011_HCC_3089" ...
.. .. .. .. ..$ : chr [1:8784] "A011_HCC_1383" "A011_HCC_1746" "A011_HCC_2811" "A011_HCC_3089" ...
.. .. .. ..@ x : num [1:664882] 1 0.0811 0.0811 0.0811 0.1429 ...
.. .. .. ..@ factors : list()
..@ neighbors : list()
..@ reductions :List of 4
.. ..$ pca :Formal class 'DimReduc' [package "SeuratObject"] with 9 slots
.. .. .. ..@ cell.embeddings : num [1:8784, 1:50] 2.99 3.92 1.76 3.24 2.96 ...
.. .. .. .. ..- attr(, "dimnames")=List of 2
.. .. .. .. .. ..$ : chr [1:8784] "A011_HCC_1383" "A011_HCC_1746" "A011_HCC_2811" "A011_HCC_3089" ...
.. .. .. .. .. ..$ : chr [1:50] "PC_1" "PC_2" "PC_3" "PC_4" ...
.. .. .. ..@ feature.loadings : num [1:2000, 1:50] -0.00249 0.00332 0.00139 0.00106 0.0021 ...
.. .. .. .. ..- attr(, "dimnames")=List of 2
.. .. .. .. .. ..$ : chr [1:2000] "IGLL5" "IGLV3-25" "IGLV3-19" "IGLV2-8" ...
.. .. .. .. .. ..$ : chr [1:50] "PC_1" "PC_2" "PC_3" "PC_4" ...
.. .. .. ..@ feature.loadings.projected: num[0 , 0 ]
.. .. .. ..@ assay.used : chr "RNA"
.. .. .. ..@ global : logi FALSE
.. .. .. ..@ stdev : num [1:50] 10.43 5.24 4.44 3.7 3.63 ...
.. .. .. ..@ jackstraw :Formal class 'JackStrawData' [package "SeuratObject"] with 4 slots
.. .. .. .. .. ..@ empirical.p.values : num[0 , 0 ]
.. .. .. .. .. ..@ fake.reduction.scores : num[0 , 0 ]
.. .. .. .. .. ..@ empirical.p.values.full: num[0 , 0 ]
.. .. .. .. .. ..@ overall.p.values : num[0 , 0 ]
.. .. .. ..@ misc :List of 1
.. .. .. .. ..$ total.variance: num 1370
.. .. .. ..@ key : chr "PC_"
.. ..$ umap :Formal class 'DimReduc' [package "SeuratObject"] with 9 slots
.. .. .. ..@ cell.embeddings : num [1:8784, 1:2] 4.861 4.683 -0.133 0.807 4.909 ...
.. .. .. .. ..- attr(, "scaled:center")= num [1:2] 4.21 -1.41
.. .. .. .. ..- attr(, "dimnames")=List of 2
.. .. .. .. .. ..$ : chr [1:8784] "A011_HCC_1383" "A011_HCC_1746" "A011_HCC_2811" "A011_HCC_3089" ...
.. .. .. .. .. ..$ : chr [1:2] "umap_1" "umap_2"
.. .. .. ..@ feature.loadings : num[0 , 0 ]
.. .. .. ..@ feature.loadings.projected: num[0 , 0 ]
.. .. .. ..@ assay.used : chr "RNA"
.. .. .. ..@ global : logi TRUE
.. .. .. ..@ stdev : num(0)
.. .. .. ..@ jackstraw :Formal class 'JackStrawData' [package "SeuratObject"] with 4 slots
.. .. .. .. .. ..@ empirical.p.values : num[0 , 0 ]
.. .. .. .. .. ..@ fake.reduction.scores : num[0 , 0 ]
.. .. .. .. .. ..@ empirical.p.values.full: num[0 , 0 ]
.. .. .. .. .. ..@ overall.p.values : num[0 , 0 ]
.. .. .. ..@ misc : list()
.. .. .. ..@ key : chr "umap_"
.. ..$ tsne :Formal class 'DimReduc' [package "SeuratObject"] with 9 slots
.. .. .. ..@ cell.embeddings : num [1:8784, 1:2] -12.6 -23.5 -13.7 18.8 -20.8 ...
.. .. .. .. ..- attr(, "dimnames")=List of 2
.. .. .. .. .. ..$ : chr [1:8784] "A011_HCC_1383" "A011_HCC_1746" "A011_HCC_2811" "A011_HCC_3089" ...
.. .. .. .. .. ..$ : chr [1:2] "tSNE_1" "tSNE_2"
.. .. .. ..@ feature.loadings : num[0 , 0 ]
.. .. .. ..@ feature.loadings.projected: num[0 , 0 ]
.. .. .. ..@ assay.used : chr "RNA"
.. .. .. ..@ global : logi TRUE
.. .. .. ..@ stdev : num(0)
.. .. .. ..@ jackstraw :Formal class 'JackStrawData' [package "SeuratObject"] with 4 slots
.. .. .. .. .. ..@ empirical.p.values : num[0 , 0 ]
.. .. .. .. .. ..@ fake.reduction.scores : num[0 , 0 ]
.. .. .. .. .. ..@ empirical.p.values.full: num[0 , 0 ]
.. .. .. .. .. ..@ overall.p.values : num[0 , 0 ]
.. .. .. ..@ misc : list()
.. .. .. ..@ key : chr "tSNE_"
.. ..$ harmony:Formal class 'DimReduc' [package "SeuratObject"] with 9 slots
.. .. .. ..@ cell.embeddings : num [1:8784, 1:50] 2.59 4 1.15 3.43 3.03 ...
.. .. .. .. ..- attr(, "dimnames")=List of 2
.. .. .. .. .. ..$ : chr [1:8784] "A011_HCC_1383" "A011_HCC_1746" "A011_HCC_2811" "A011_HCC_3089" ...
.. .. .. .. .. ..$ : chr [1:50] "harmony_1" "harmony_2" "harmony_3" "harmony_4" ...
.. .. .. ..@ feature.loadings : num [1:20002, 1:50] 0 0 0 956 -16169 ...
.. .. .. .. ..- attr(, "dimnames")=List of 2
.. .. .. .. .. ..$ : chr [1:20002] "OR4F5" "OR4F29" "OR4F16" "SAMD11" ...
.. .. .. .. .. ..$ : chr [1:50] "harmony_1" "harmony_2" "harmony_3" "harmony_4" ...
.. .. .. ..@ feature.loadings.projected: num [1:20002, 1:50] 0 0 0 956 -16169 ...
.. .. .. .. ..- attr(*, "dimnames")=List of 2
.. .. .. .. .. ..$ : chr [1:20002] "OR4F5" "OR4F29" "OR4F16" "SAMD11" ...
.. .. .. .. .. ..$ : chr [1:50] "harmony_1" "harmony_2" "harmony_3" "harmony_4" ...
.. .. .. ..@ assay.used : chr "RNA"
.. .. .. ..@ global : logi FALSE
.. .. .. ..@ stdev : num [1:50] 10.16 3.75 3.47 2.96 2.97 ...
.. .. .. ..@ jackstraw :Formal class 'JackStrawData' [package "SeuratObject"] with 4 slots
.. .. .. .. .. ..@ empirical.p.values : num[0 , 0 ]
.. .. .. .. .. ..@ fake.reduction.scores : num[0 , 0 ]
.. .. .. .. .. ..@ empirical.p.values.full: num[0 , 0 ]
.. .. .. .. .. ..@ overall.p.values : num[0 , 0 ]
.. .. .. ..@ misc : list()
.. .. .. ..@ key : chr "harmony_"
..@ images : list()
..@ project.name: chr "SeuratProject"
..@ misc : list()
..@ version :Classes 'package_version', 'numeric_version' hidden list of 1
.. ..$ : int [1:3] 4 0 2
..@ commands :List of 11
.. ..$ RunUMAP.RNA.pca :Formal class 'SeuratCommand' [package "SeuratObject"] with 5 slots
.. .. .. ..@ name : chr "RunUMAP.RNA.pca"
.. .. .. ..@ time.stamp : POSIXct[1:1], format: "2024-12-12 08:20:05"
.. .. .. ..@ assay.used : chr "RNA"
.. .. .. ..@ call.string: chr "RunUMAP(., dims = 1:20, reduction = "pca", )"
.. .. .. ..@ params :List of 25
.. .. .. .. ..$ dims : int [1:20] 1 2 3 4 5 6 7 8 9 10 ...
.. .. .. .. ..$ reduction : chr "pca"
.. .. .. .. ..$ assay : chr "RNA"
.. .. .. .. ..$ slot : chr "data"
.. .. .. .. ..$ umap.method : chr "uwot"
.. .. .. .. ..$ return.model : logi FALSE
.. .. .. .. ..$ n.neighbors : int 30
.. .. .. .. ..$ n.components : int 2
.. .. .. .. ..$ metric : chr "cosine"
.. .. .. .. ..$ learning.rate : num 1
.. .. .. .. ..$ min.dist : num 0.3
.. .. .. .. ..$ spread : num 1
.. .. .. .. ..$ set.op.mix.ratio : num 1
.. .. .. .. ..$ local.connectivity : int 1
.. .. .. .. ..$ repulsion.strength : num 1
.. .. .. .. ..$ negative.sample.rate: int 5
.. .. .. .. ..$ uwot.sgd : logi FALSE
.. .. .. .. ..$ seed.use : int 42
.. .. .. .. ..$ angular.rp.forest : logi FALSE
.. .. .. .. ..$ densmap : logi FALSE
.. .. .. .. ..$ dens.lambda : num 2
.. .. .. .. ..$ dens.frac : num 0.3
.. .. .. .. ..$ dens.var.shift : num 0.1
.. .. .. .. ..$ verbose : logi TRUE
.. .. .. .. ..$ reduction.name : chr "umap"
.. ..$ FindNeighbors.RNA.pca :Formal class 'SeuratCommand' [package "SeuratObject"] with 5 slots
.. .. .. ..@ name : chr "FindNeighbors.RNA.pca"
.. .. .. ..@ time.stamp : POSIXct[1:1], format: "2024-12-12 08:21:33"
.. .. .. ..@ assay.used : chr "RNA"
.. .. .. ..@ call.string: chr "FindNeighbors(., dims = 1:20, reduction = "pca")"
.. .. .. ..@ params :List of 16
.. .. .. .. ..$ reduction : chr "pca"
.. .. .. .. ..$ dims : int [1:20] 1 2 3 4 5 6 7 8 9 10 ...
.. .. .. .. ..$ assay : chr "RNA"
.. .. .. .. ..$ k.param : num 20
.. .. .. .. ..$ return.neighbor: logi FALSE
.. .. .. .. ..$ compute.SNN : logi TRUE
.. .. .. .. ..$ prune.SNN : num 0.0667
.. .. .. .. ..$ nn.method : chr "annoy"
.. .. .. .. ..$ n.trees : num 50
.. .. .. .. ..$ annoy.metric : chr "euclidean"
.. .. .. .. ..$ nn.eps : num 0
.. .. .. .. ..$ verbose : logi TRUE
.. .. .. .. ..$ do.plot : logi FALSE
.. .. .. .. ..$ graph.name : chr [1:2] "RNA_nn" "RNA_snn"
.. .. .. .. ..$ l2.norm : logi FALSE
.. .. .. .. ..$ cache.index : logi FALSE
.. ..$ NormalizeData.RNA :Formal class 'SeuratCommand' [package "SeuratObject"] with 5 slots
.. .. .. ..@ name : chr "NormalizeData.RNA"
.. .. .. ..@ time.stamp : POSIXct[1:1], format: "2024-12-12 09:00:14"
.. .. .. ..@ assay.used : chr "RNA"
.. .. .. ..@ call.string: chr [1:2] "NormalizeData(PC_HCC, normalization.method = "LogNormalize", " " scale.factor = 10000)"
.. .. .. ..@ params :List of 5
.. .. .. .. ..$ assay : chr "RNA"
.. .. .. .. ..$ normalization.method: chr "LogNormalize"
.. .. .. .. ..$ scale.factor : num 10000
.. .. .. .. ..$ margin : num 1
.. .. .. .. ..$ verbose : logi TRUE
.. ..$ FindVariableFeatures.RNA :Formal class 'SeuratCommand' [package "SeuratObject"] with 5 slots
.. .. .. ..@ name : chr "FindVariableFeatures.RNA"
.. .. .. ..@ time.stamp : POSIXct[1:1], format: "2024-12-12 09:00:16"
.. .. .. ..@ assay.used : chr "RNA"
.. .. .. ..@ call.string: chr "FindVariableFeatures(., selection.method = "vst", nfeatures = 2000)"
.. .. .. ..@ params :List of 12
.. .. .. .. ..$ assay : chr "RNA"
.. .. .. .. ..$ selection.method : chr "vst"
.. .. .. .. ..$ loess.span : num 0.3
.. .. .. .. ..$ clip.max : chr "auto"
.. .. .. .. ..$ mean.function :function (mat, display_progress)
.. .. .. .. ..$ dispersion.function:function (mat, display_progress)
.. .. .. .. ..$ num.bin : num 20
.. .. .. .. ..$ binning.method : chr "equal_width"
.. .. .. .. ..$ nfeatures : num 2000
.. .. .. .. ..$ mean.cutoff : num [1:2] 0.1 8
.. .. .. .. ..$ dispersion.cutoff : num [1:2] 1 Inf
.. .. .. .. ..$ verbose : logi TRUE
.. ..$ ScaleData.RNA :Formal class 'SeuratCommand' [package "SeuratObject"] with 5 slots
.. .. .. ..@ name : chr "ScaleData.RNA"
.. .. .. ..@ time.stamp : POSIXct[1:1], format: "2024-12-12 09:00:25"
.. .. .. ..@ assay.used : chr "RNA"
.. .. .. ..@ call.string: chr "ScaleData(., features = rownames(PC_HCC))"
.. .. .. ..@ params :List of 10
.. .. .. .. ..$ features : chr [1:20002] "OR4F5" "OR4F29" "OR4F16" "SAMD11" ...
.. .. .. .. ..$ assay : chr "RNA"
.. .. .. .. ..$ model.use : chr "linear"
.. .. .. .. ..$ use.umi : logi FALSE
.. .. .. .. ..$ do.scale : logi TRUE
.. .. .. .. ..$ do.center : logi TRUE
.. .. .. .. ..$ scale.max : num 10
.. .. .. .. ..$ block.size : num 1000
.. .. .. .. ..$ min.cells.to.block: num 3000
.. .. .. .. ..$ verbose : logi TRUE
.. ..$ RunPCA.RNA :Formal class 'SeuratCommand' [package "SeuratObject"] with 5 slots
.. .. .. ..@ name : chr "RunPCA.RNA"
.. .. .. ..@ time.stamp : POSIXct[1:1], format: "2024-12-12 09:00:30"
.. .. .. ..@ assay.used : chr "RNA"
.. .. .. ..@ call.string: chr [1:2] "RunPCA(PC_HCC, features = VariableFeatures(object = PC_HCC), " " reduction.name = "pca")"
.. .. .. ..@ params :List of 11
.. .. .. .. ..$ assay : chr "RNA"
.. .. .. .. ..$ features : chr [1:2000] "IGLL5" "IGLV3-25" "IGLV3-19" "IGLV2-8" ...
.. .. .. .. ..$ npcs : num 50
.. .. .. .. ..$ rev.pca : logi FALSE
.. .. .. .. ..$ weight.by.var : logi TRUE
.. .. .. .. ..$ verbose : logi TRUE
.. .. .. .. ..$ ndims.print : int [1:5] 1 2 3 4 5
.. .. .. .. ..$ nfeatures.print: num 30
.. .. .. .. ..$ reduction.name : chr "pca"
.. .. .. .. ..$ reduction.key : chr "PC_"
.. .. .. .. ..$ seed.use : num 42
.. ..$ Seurat..ProjectDim.RNA.harmony:Formal class 'SeuratCommand' [package "SeuratObject"] with 5 slots
.. .. .. ..@ name : chr "Seurat::ProjectDim.RNA.harmony"
.. .. .. ..@ time.stamp : POSIXct[1:1], format: "2024-12-12 09:00:36"
.. .. .. ..@ assay.used : chr "RNA"
.. .. .. ..@ call.string: chr [1:2] "Seurat::ProjectDim(object, reduction = reduction.save, overwrite = TRUE, " " verbose = FALSE)"
.. .. .. ..@ params :List of 7
.. .. .. .. ..$ reduction : chr "harmony"
.. .. .. .. ..$ assay : chr "RNA"
.. .. .. .. ..$ dims.print : int [1:5] 1 2 3 4 5
.. .. .. .. ..$ nfeatures.print: num 20
.. .. .. .. ..$ overwrite : logi TRUE
.. .. .. .. ..$ do.center : logi FALSE
.. .. .. .. ..$ verbose : logi FALSE
.. ..$ RunUMAP.RNA.harmony :Formal class 'SeuratCommand' [package "SeuratObject"] with 5 slots
.. .. .. ..@ name : chr "RunUMAP.RNA.harmony"
.. .. .. ..@ time.stamp : POSIXct[1:1], format: "2024-12-12 09:02:22"
.. .. .. ..@ assay.used : chr "RNA"
.. .. .. ..@ call.string: chr "RunUMAP(., dims = 1:20, reduction = "harmony")"
.. .. .. ..@ params :List of 25
.. .. .. .. ..$ dims : int [1:20] 1 2 3 4 5 6 7 8 9 10 ...
.. .. .. .. ..$ reduction : chr "harmony"
.. .. .. .. ..$ assay : chr "RNA"
.. .. .. .. ..$ slot : chr "data"
.. .. .. .. ..$ umap.method : chr "uwot"
.. .. .. .. ..$ return.model : logi FALSE
.. .. .. .. ..$ n.neighbors : int 30
.. .. .. .. ..$ n.components : int 2
.. .. .. .. ..$ metric : chr "cosine"
.. .. .. .. ..$ learning.rate : num 1
.. .. .. .. ..$ min.dist : num 0.3
.. .. .. .. ..$ spread : num 1
.. .. .. .. ..$ set.op.mix.ratio : num 1
.. .. .. .. ..$ local.connectivity : int 1
.. .. .. .. ..$ repulsion.strength : num 1
.. .. .. .. ..$ negative.sample.rate: int 5
.. .. .. .. ..$ uwot.sgd : logi FALSE
.. .. .. .. ..$ seed.use : int 42
.. .. .. .. ..$ angular.rp.forest : logi FALSE
.. .. .. .. ..$ densmap : logi FALSE
.. .. .. .. ..$ dens.lambda : num 2
.. .. .. .. ..$ dens.frac : num 0.3
.. .. .. .. ..$ dens.var.shift : num 0.1
.. .. .. .. ..$ verbose : logi TRUE
.. .. .. .. ..$ reduction.name : chr "umap"
.. ..$ RunTSNE :Formal class 'SeuratCommand' [package "SeuratObject"] with 5 slots
.. .. .. ..@ name : chr "RunTSNE"
.. .. .. ..@ time.stamp : POSIXct[1:1], format: "2024-12-12 09:02:56"
.. .. .. ..@ assay.used : chr "RNA"
.. .. .. ..@ call.string: chr "RunTSNE(., reduction = "harmony", dims = 1:20)"
.. .. .. ..@ params :List of 8
.. .. .. .. ..$ reduction : chr "harmony"
.. .. .. .. ..$ cells : chr [1:8784] "A011_HCC_1383" "A011_HCC_1746" "A011_HCC_2811" "A011_HCC_3089" ...
.. .. .. .. ..$ dims : int [1:20] 1 2 3 4 5 6 7 8 9 10 ...
.. .. .. .. ..$ seed.use : num 1
.. .. .. .. ..$ tsne.method : chr "Rtsne"
.. .. .. .. ..$ dim.embed : num 2
.. .. .. .. ..$ reduction.name: chr "tsne"
.. .. .. .. ..$ reduction.key : chr "tSNE_"
.. ..$ FindNeighbors.RNA.harmony :Formal class 'SeuratCommand' [package "SeuratObject"] with 5 slots
.. .. .. ..@ name : chr "FindNeighbors.RNA.harmony"
.. .. .. ..@ time.stamp : POSIXct[1:1], format: "2024-12-12 09:02:58"
.. .. .. ..@ assay.used : chr "RNA"
.. .. .. ..@ call.string: chr "FindNeighbors(., reduction = "harmony", dims = 1:20)"
.. .. .. ..@ params :List of 16
.. .. .. .. ..$ reduction : chr "harmony"
.. .. .. .. ..$ dims : int [1:20] 1 2 3 4 5 6 7 8 9 10 ...
.. .. .. .. ..$ assay : chr "RNA"
.. .. .. .. ..$ k.param : num 20
.. .. .. .. ..$ return.neighbor: logi FALSE
.. .. .. .. ..$ compute.SNN : logi TRUE
.. .. .. .. ..$ prune.SNN : num 0.0667
.. .. .. .. ..$ nn.method : chr "annoy"
.. .. .. .. ..$ n.trees : num 50
.. .. .. .. ..$ annoy.metric : chr "euclidean"
.. .. .. .. ..$ nn.eps : num 0
.. .. .. .. ..$ verbose : logi TRUE
.. .. .. .. ..$ do.plot : logi FALSE
.. .. .. .. ..$ graph.name : chr [1:2] "RNA_nn" "RNA_snn"
.. .. .. .. ..$ l2.norm : logi FALSE
.. .. .. .. ..$ cache.index : logi FALSE
.. ..$ FindClusters :Formal class 'SeuratCommand' [package "SeuratObject"] with 5 slots
.. .. .. ..@ name : chr "FindClusters"
.. .. .. ..@ time.stamp : POSIXct[1:1], format: "2024-12-12 09:02:59"
.. .. .. ..@ assay.used : chr "RNA"
.. .. .. ..@ call.string: chr "FindClusters(., resolution = c(0.13))"
.. .. .. ..@ params :List of 11
.. .. .. .. ..$ graph.name : chr "RNA_snn"
.. .. .. .. ..$ cluster.name : chr "RNA_snn_res.0.13"
.. .. .. .. ..$ modularity.fxn : num 1
.. .. .. .. ..$ resolution : num 0.13
.. .. .. .. ..$ method : chr "matrix"
.. .. .. .. ..$ algorithm : num 1
.. .. .. .. ..$ n.start : num 10
.. .. .. .. ..$ n.iter : num 10
.. .. .. .. ..$ random.seed : num 0
.. .. .. .. ..$ group.singletons: logi TRUE
.. .. .. .. ..$ verbose : logi TRUE
..@ tools : list()
@Hinna0818
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I have met the same problem above.
thanks for answering that

@renyzh5-2
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it works when i run with 'show_plot = F'.

HCC_sub <- RunSlingshot(srt = PC_HCC, group.by = "clusters", reduction = "tsne",show_plot = F)

DynamicPlot(
srt = HCC_sub, lineages = c("Lineage1", "Lineage2"), group.by = "clusters",
features = c("TMEM176B"),
compare_lineages = TRUE, compare_features = FALSE
)

image

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@Hinna0818 @renyzh5-2