4  Inspect the demo results

The public demo uses outputs/ as its results store. Other checkouts may use a different folder, recorded under store in _targets.yaml. The R commands below use that configuration automatically.

The store contains serialized R objects in objects/, file artifacts in files/, and requested review figures in plots/.

4.1 Objects

Most intermediate and final result objects are saved automatically by targets under outputs/objects during a pipeline run. Read them with targets::tar_read() from a repository-root R session after the demo has completed.

R
cell_metadata <- targets::tar_read(
  metadata_w_cell_types_tibble.WNN.immune_human_2x
)
dim(cell_metadata)
head(cell_metadata)

demo_object <- targets::tar_read(multimodal_Seurat_object.immune_human_2x)
demo_object

The metadata table describes the retained nuclei and their annotations. WNN means weighted nearest neighbors: the integrated representation uses information from both RNA and ATAC. The Seurat/Signac object is a convenient export for further exploration; the pipeline also retains its matrices in BPCells format on disk.

4.2 Files

File targets also load with targets::tar_read(), but their value is a path rather than an in-memory result.

R
targets::tar_read(cellranger_barcodes_tsv.healthy_PBMC_human)
targets::tar_read(aggregated_GEX_BPCells_matrix_dir.GEX.immune_human_2x)
targets::tar_read(consensus_peak_BPCells_matrix_dir.ATAC.immune_human_2x)

For example, aggregated_GEX_BPCells_matrix_dir.GEX.immune_human_2x is placed under:

outputs/files/immune_human_2x/GEX/

Other files are grouped under outputs/files/<scope>/, where the scope is a GEM well, an internal pre-aggregation QC group, or an aggregation.

4.3 Plots

Open the main pipeline gallery to see example QC, RNA, ATAC, and WNN plots. These are saved documentation snapshots, so you can browse them without running the demo. They do not show the state of your own analysis.

Requested plots use the same scope-based layout under outputs/plots/.

The final-object demo command does not build all these plots. See Request an additional result for how to build a named gallery target, or follow the numbered QC reviews for the broader diagnostics.

4.4 Next steps