API#
Import scirpy together with scanpy as
import scanpy as sc
import scirpy as ir
For consistency, the scirpy API tries to follow the scanpy API as closely as possible.
Input/Output: io
#
Note
scirpy’s data structure has been updated in v0.13.0.
Previously, receptor data was expanded into columns of adata.obs
, now they are stored as an awkward array in adata.obsm["airr"]
.
Moreover, we now use MuData
to handle paired transcriptomics and AIRR data.
AnnData
objects created with older versions of scirpy can be upgraded with scirpy.io.upgrade_schema()
to be compatible with the latest version of scirpy.
Please check out
the release notes for details about the changes and
the documentation about Scirpy’s data structure
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Update older versions of a scirpy anndata object to the latest schema. |
The following functions allow to import V(D)J information from various formats.
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Read MuData object from HDF5 file |
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Read |
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Read AIRR data from 10x Genomics cell-ranger output. |
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Read data from TraCeR ([SLonnbergP+16]). |
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Read IR data from the BD Rhapsody Analysis Pipeline. |
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Read data from AIRR rearrangement format. |
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Scirpy can export data to the following formats:
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To convert own formats into the scirpy Storing AIRR rearrangement data in AnnData, we recommend building
a list of AirrCell
objects first, and then converting them into
an AnnData
object using from_airr_cells()
.
For more details, check the Data loading tutorial.
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Data structure for a Cell with immune receptors. |
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Convert an adata object with IR information back to a list of |
Preprocessing: pp
#
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Selects primary/secondary VJ/VDJ cells per chain according to the Immune receptor (IR) model. |
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Merge two AnnData objects with IR information (e.g. BCR with TCR). |
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Computes a sequence-distance metric between all unique VJ CDR3 sequences and between all unique VDJ CDR3 sequences. |
Get: get
#
The get
module allows retrieving AIRR data stored in adata.obsm["airr"]
as a per-cell DataFrame
or Series
.
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Retrieve AIRR variables for each cell, given a specific chain. |
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Contextmanager that temporarily adds columns to obs. |
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Contextmanager that temporarily adds AIRR information to obs. |
Tools: tl
#
Tools add an interpretable annotation to the AnnData
object
which usually can be visualized by a corresponding plotting function.
Generic#
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Summarizes the number/fraction of cells of a certain category by a certain group. |
Quality control#
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Perform quality control based on the receptor-chain pairing configuration. |
Define and visualize clonotypes#
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Define clonotypes based on CDR3 nucleic acid sequence identity. |
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Define clonotype clusters. |
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Finds evidence for Convergent evolution of clonotypes. |
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Computes the layout of the clonotype network. |
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Get an |
Analyse clonal diversity#
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Adds a column to |
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Summarizes clonal expansion by a grouping variable. |
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Computes the alpha diversity of clonotypes within a group. |
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Compute distance between cell groups based on clonotype overlap. |
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Identifies clonotypes or clonotype clusters consisting of cells that are more transcriptionally related than expected by chance by computing the Clonotype modularity. |
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Aims to find clonotypes that are the most enriched or depleted in a category. |
Query reference databases#
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Query a referece database for matching immune cell receptors. |
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Annotate cells based on the result of |
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Returns the inner join of |
V(D)J gene usage#
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Summarizes the distribution of CDR3 region lengths. |
Plotting: pl
#
Generic#
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A customized wrapper to the |
Tools#
Every of these plotting functions has a corresponding tool in the scirpy.tl
section. Depending on the computational load, tools are either invoked on-the-fly
when calling the plotting function or need to be precomputed and stored in
AnnData
previously.
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Plot the alpha diversity per group. |
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Visualize clonal expansion. |
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Plots the number of cells per group, split up by a categorical variable. |
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Show the distribution of CDR3 region lengths. |
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Creates a ribbon plot of the most abundant VDJ combinations. |
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Visualizes overlap betwen a pair of samples on a scatter plot or |
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Plots the Clonotype modularity score against the associated log10 p-value. |
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Plot the Clonotype network. |
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Aims to find clonotypes that are the most enriched or depleted in a category. |
Base plotting functions: pl.base
#
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Basic plotting function built on top of bar plot in Pandas. |
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Basic plotting function built on top of line plot in Pandas. |
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Basic plotting function built on top of bar plot in Pandas. |
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Basic plotting function for drawing KDE-smoothed curves. |
Plot styling: pl.styling
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Apply a predefined style to an axis object. |
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Style an axes object. |
Datasets: datasets
#
Example datasets#
Reference databases#
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Download VDJdb and process it into an AnnData object. |
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Download IEBD v3 and process it into an AnnData object. |
A reference database is also just a Scirpy-formatted AnnData object. This means you can follow the instructions in the data loading tutorial to build a custom reference database.
Utility functions: util
#
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Transparent access to airr modality in both AnnData and MuData objects. |
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Compute a graph layout by layouting all connected components individually. |
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Compute the Fruchterman-Reingold layout respecting node sizes. |
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Get an igraph object from an adjacency or distance matrix. |
IR distance utilities: ir_dist
#
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Calculate a sequence x sequence distance matrix. |
distance metrics#
Abstract base class for a CDR3-sequence distance calculator. |
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Abstract base class for a DistanceCalculator that computes distances in parallel. |
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Calculates the Identity-distance between CDR3 sequences. |
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Calculates the Levenshtein edit-distance between sequences. |
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Calculates the Hamming distance between sequences of identical length. |
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Calculates distance between sequences based on pairwise sequence alignment. |
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Calculates distance between sequences based on pairwise sequence alignment. |