Import scirpy as
import scanpy as sc import scirpy as ir
Scirpy is an extension to Scanpy and adheres to its workflow principles:
We decided to handle a few minor points differently to Scanpy:
Plotting functions with inexpensive computations (e.g.
scirpy.pl.clonal_expansion()) call the corresponding tool (
scirpy.tl.clonal_expansion()) on-the-fly and don’t store the results in the
All plotting functions, by default, return a
Axesobject, or a list of such.
For instructions how to load data into scirpy, see Loading adaptive Immune Receptor (IR)-sequencing data with Scirpy.
Scirpy leverages the AnnData data structure
which combines a gene expression matrix (
.X), gene-level annotations (
cell-level annotations (
.obs) into a single object.
AnnData forms the basis for the
Scanpy analysis workflow
for single-cell transcriptomics data.
Scirpy adds the following IR-related columns to
IR_VJ_2_<attr>: columns related to the primary and secondary VJ-chain of a receptor (
IR_VDJ_2_<attr>: columns related to the primary and secondary VDJ-chain of a receptor (
Truefor all cells with an adaptive immune receptor
extra_chains: Contains non-productive chains (if not filtered out), and extra chains that do not fit into the 2
VDJchain model encoded as JSON. Scirpy does not use this information except for writing it back to AIRR format using
Truefor all cells with more than two productive
VJcells or two or more productive
<attr> can be any field of the AIRR Rearrangement Schema.
For Scirpy the following fields are relevant:
locus: The IMGT locus name of the chain (
j_call: The gene symbols of the respective genes
junction: The amino acid and nucleotide sequences of the CDR3 regions