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Prepare Seurat objects for the SCExplorer

Source: R/app.R
PrepareSCExplorer.Rd

This function prepares one or multiple Seurat objects for the SCExplorer app. It takes a Seurat object or a list of Seurat objects as input and outputs two hdf5 files: one for the data and one for the metadata.

Usage

PrepareSCExplorer(
  object,
  base_dir = "SCExplorer",
  data_file = "data.hdf5",
  meta_file = "meta.hdf5",
  assays = "RNA",
  layers = c("counts", "data"),
  ignore_nlevel = 100,
  write_tools = FALSE,
  write_misc = FALSE,
  compression_level = 6,
  overwrite = FALSE
)

Arguments

object

A Seurat object or a list of Seurat objects.

base_dir

The base directory where the SCExplorer hdf5 files will be written. Default is "SCExplorer".

data_file

Path to the output data file. If not provided, the file will be named "data.hdf5" in the current directory.

meta_file

Path to the output meta file. If not provided, the file will be named "meta.hdf5" in the current directory.

assays

The assays to include in the data file. Default is "RNA".

layers

The layers to include in the data file. Default is "data".

ignore_nlevel

The number of levels above which a metadata field will be ignored. Default is 100.

write_tools

Whether to write the tools information to the meta file. Default is FALSE.

write_misc

Whether to write the miscellaneous information to the meta file. Default is FALSE.

compression_level

Compression level for the HDF5 dataset. Default is 6.

overwrite

Whether to overwrite existing data in the data file. Default is TRUE.

See also

CreateDataFile, CreateMetaFile, FetchH5, RunSCExplorer

Examples

data(pancreas_sub)
pancreas_sub <- standard_scop(pancreas_sub)
#> ℹ [2026-05-14 06:45:19] Start standard processing workflow...
#> ℹ [2026-05-14 06:45:20] Checking a list of <Seurat>...
#> ! [2026-05-14 06:45:20] Data 1/1 of the `srt_list` is "unknown"
#> ℹ [2026-05-14 06:45:20] Perform `NormalizeData()` with `normalization.method = 'LogNormalize'` on 1/1 of `srt_list`...
#> ℹ [2026-05-14 06:45:23] Perform `Seurat::FindVariableFeatures()` on 1/1 of `srt_list`...
#> ℹ [2026-05-14 06:45:23] Use the separate HVF from `srt_list`
#> ℹ [2026-05-14 06:45:23] Number of available HVF: 2000
#> ℹ [2026-05-14 06:45:23] Finished check
#> ℹ [2026-05-14 06:45:23] Perform `Seurat::ScaleData()`
#> ℹ [2026-05-14 06:45:24] Perform pca linear dimension reduction
#> ℹ [2026-05-14 06:45:24] Use stored estimated dimensions 1:20 for Standardpca
#> ℹ [2026-05-14 06:45:24] Perform `Seurat::FindClusters()` with `cluster_algorithm = 'louvain'` and `cluster_resolution = 0.6`
#> ℹ [2026-05-14 06:45:25] Reorder clusters...
#> ℹ [2026-05-14 06:45:25] Skip `log1p()` because `layer = data` is not "counts"
#> ℹ [2026-05-14 06:45:25] Perform umap nonlinear dimension reduction
#> ℹ [2026-05-14 06:45:25] Perform umap nonlinear dimension reduction using Standardpca (1:20)
#> ℹ [2026-05-14 06:45:30] Perform umap nonlinear dimension reduction using Standardpca (1:20)
#> ✔ [2026-05-14 06:45:35] Standard processing workflow completed
PrepareSCExplorer(pancreas_sub, base_dir = "./SCExplorer")
#> ℹ [2026-05-14 06:45:35] Set the project name of each <Seurat> to their dataset name
#> ℹ [2026-05-14 06:45:35] Prepare data for object: "SeuratProject"
#> ℹ [2026-05-14 06:45:35] Write the expression matrix to: /home/runner/work/scop/scop/docs/reference/SCExplorer/data.hdf5
#> ℹ [2026-05-14 06:45:35] Group "/SeuratProject/RNA/counts" already exists in /home/runner/work/scop/scop/docs/reference/SCExplorer/data.hdf5
#> ℹ [2026-05-14 06:45:35] Group "/SeuratProject/RNA/data" already exists in /home/runner/work/scop/scop/docs/reference/SCExplorer/data.hdf5
#> ℹ [2026-05-14 06:45:35] Write the meta information to: /home/runner/work/scop/scop/docs/reference/SCExplorer/meta.hdf5
#> ℹ [2026-05-14 06:45:35] Group "/SeuratProject/metadata/orig.ident" already exists in /home/runner/work/scop/scop/docs/reference/SCExplorer/meta.hdf5
#> ℹ [2026-05-14 06:45:35] Group "/SeuratProject/metadata/nCount_RNA" already exists in /home/runner/work/scop/scop/docs/reference/SCExplorer/meta.hdf5
#> ℹ [2026-05-14 06:45:35] Group "/SeuratProject/metadata/nFeature_RNA" already exists in /home/runner/work/scop/scop/docs/reference/SCExplorer/meta.hdf5
#> ℹ [2026-05-14 06:45:35] Group "/SeuratProject/metadata/S_score" already exists in /home/runner/work/scop/scop/docs/reference/SCExplorer/meta.hdf5
#> ℹ [2026-05-14 06:45:35] Group "/SeuratProject/metadata/G2M_score" already exists in /home/runner/work/scop/scop/docs/reference/SCExplorer/meta.hdf5
#> ℹ [2026-05-14 06:45:35] Group "/SeuratProject/metadata/nCount_spliced" already exists in /home/runner/work/scop/scop/docs/reference/SCExplorer/meta.hdf5
#> ℹ [2026-05-14 06:45:35] Group "/SeuratProject/metadata/nFeature_spliced" already exists in /home/runner/work/scop/scop/docs/reference/SCExplorer/meta.hdf5
#> ℹ [2026-05-14 06:45:35] Group "/SeuratProject/metadata/nCount_unspliced" already exists in /home/runner/work/scop/scop/docs/reference/SCExplorer/meta.hdf5
#> ℹ [2026-05-14 06:45:35] Group "/SeuratProject/metadata/nFeature_unspliced" already exists in /home/runner/work/scop/scop/docs/reference/SCExplorer/meta.hdf5
#> ℹ [2026-05-14 06:45:35] Group "/SeuratProject/metadata/CellType" already exists in /home/runner/work/scop/scop/docs/reference/SCExplorer/meta.hdf5
#> ℹ [2026-05-14 06:45:35] Group "/SeuratProject/metadata/SubCellType" already exists in /home/runner/work/scop/scop/docs/reference/SCExplorer/meta.hdf5
#> ℹ [2026-05-14 06:45:35] Group "/SeuratProject/metadata/Phase" already exists in /home/runner/work/scop/scop/docs/reference/SCExplorer/meta.hdf5
#> ℹ [2026-05-14 06:45:35] Group "/SeuratProject/metadata/Standardpca_SNN_res.0.6" already exists in /home/runner/work/scop/scop/docs/reference/SCExplorer/meta.hdf5
#> ℹ [2026-05-14 06:45:35] Group "/SeuratProject/metadata/ident" already exists in /home/runner/work/scop/scop/docs/reference/SCExplorer/meta.hdf5
#> ℹ [2026-05-14 06:45:35] Group "/SeuratProject/metadata/Standardpcaclusters" already exists in /home/runner/work/scop/scop/docs/reference/SCExplorer/meta.hdf5
#> ℹ [2026-05-14 06:45:35] Group "/SeuratProject/metadata/Standardclusters" already exists in /home/runner/work/scop/scop/docs/reference/SCExplorer/meta.hdf5
#> ℹ [2026-05-14 06:45:35] Group "/SeuratProject/metadata.stat" already exists in /home/runner/work/scop/scop/docs/reference/SCExplorer/meta.hdf5
#> ℹ [2026-05-14 06:45:35] Group "/SeuratProject/reductions/Standardpca" already exists in /home/runner/work/scop/scop/docs/reference/SCExplorer/meta.hdf5
#> ℹ [2026-05-14 06:45:35] Group "/SeuratProject/reductions/StandardpcaUMAP2D" already exists in /home/runner/work/scop/scop/docs/reference/SCExplorer/meta.hdf5
#> ℹ [2026-05-14 06:45:36] Group "/SeuratProject/reductions/StandardpcaUMAP3D" already exists in /home/runner/work/scop/scop/docs/reference/SCExplorer/meta.hdf5
#> ℹ [2026-05-14 06:45:36] Group "/SeuratProject/reductions/StandardUMAP2D" already exists in /home/runner/work/scop/scop/docs/reference/SCExplorer/meta.hdf5
#> ℹ [2026-05-14 06:45:36] Group "/SeuratProject/reductions/StandardUMAP3D" already exists in /home/runner/work/scop/scop/docs/reference/SCExplorer/meta.hdf5
#> ℹ [2026-05-14 06:45:36] Group /SeuratProject/reductions.stat already exists in the /home/runner/work/scop/scop/docs/reference/SCExplorer/meta.hdf5