Ingesting spatial data
Similar to the cell suspension workflow, spatial_qc
ingests Vizgen
and/or Visium
data and saves the data into MuData
objects.
A primary difference to the cell suspension ingestion
workflow is that we are not concatenating the input data into a single matrix, but keeping the samples as separate MuData
objects, each with a spatial
layer. This ensures that the processing does not introduce any technical batch effect when tissue slides are very different in cell composition. In a future release, we will use SpatialData as a data format and framework to process multi-slides experiments.
Steps
Data is ingested into
MuData
objects with the modalityspatial
. The workflow generates one MuData per dataset.Raw
MuData
objects are saved into./tmp
QC metrics are computed using
scanpy
functionalities:Basic QC metrics are computed using
sc.pp.calculate_qc_metrics
(Optional) Compute cell-cycle scores using
sc.tl.score_genes_cell_cycle
. For that, the default gene list can be used or a path to a tsv file can be specified.(Optional) Custom genes actions. Default gene list can be used or a path to a csv file can be specified.
Calculate proportions of gene groups, e.g. mitochondrial genes
Score genes using
sc.tl.score_genes
MuData
objects with calculated QC metrics are saved inqc.data
Metadata (
.obs
) is saved into the current directory as tsv files
Specified QC metrics are plotted in violin and spatial embedding plots
For
Vizgen
data, additional histograms are plotted
Steps to run
Generate sample submission file. You can find more information about the generation here
(Optional) Generate QC gene lists as described in gene list format
Activate conda environment
conda activate pipeline_env
Generate yaml and log file
panpipes qc_spatial config
Specify the parameter setting in the pipeline.yml file
Run complete QC workflow with
panpipes qc_spatial make full --local
Use outputs to decide filtering thresholds
Note that the actual filtering occurs in the first step of the
preprocess_spatial
workflow
The Ingesting 10X Visium data with Panpipes and Ingesting MERFISH data with Panpipes tutorials guide you through the ingestion step by step.