Concatenation

Concatenation#

With concat(), AnnData objects can be combined via a composition of two operations: concatenation and merging.

  • Concatenation is when we keep all sub elements of each object, and stack these elements in an ordered way.

  • Merging is combining a set of collections into one resulting collection which contains elements from the objects.

Note

This function borrows from similar functions in pandas and xarray. Argument which are used to control concatenation are modeled after pandas.concat() while strategies for merging are inspired by xarray.merge()’s compat argument.

Concatenation#

Let’s start off with an example:

>>> import scanpy as sc, anndata as ad, numpy as np, pandas as pd
>>> from scipy import sparse
>>> from anndata import AnnData
>>> pbmc = sc.datasets.pbmc68k_reduced()
>>> pbmc
AnnData object with n_obs × n_vars = 700 × 765
    obs: 'bulk_labels', 'n_genes', 'percent_mito', 'n_counts', 'S_score', 'G2M_score', 'phase', 'louvain'
    var: 'n_counts', 'means', 'dispersions', 'dispersions_norm', 'highly_variable'
    uns: 'bulk_labels_colors', 'louvain', 'louvain_colors', 'neighbors', 'pca', 'rank_genes_groups'
    obsm: 'X_pca', 'X_umap'
    varm: 'PCs'
    obsp: 'distances', 'connectivities'

If we split this object up by clusters of observations, then stack those subsets we’ll obtain the same values – just ordered differently.

>>> groups = pbmc.obs.groupby("louvain", observed=True).indices
>>> pbmc_concat = ad.concat([pbmc[inds] for inds in groups.values()], merge="same")
>>> assert np.array_equal(pbmc.X, pbmc_concat[pbmc.obs_names].X)
>>> pbmc_concat
AnnData object with n_obs × n_vars = 700 × 765
    obs: 'bulk_labels', 'n_genes', 'percent_mito', 'n_counts', 'S_score', 'G2M_score', 'phase', 'louvain'
    var: 'n_counts', 'means', 'dispersions', 'dispersions_norm', 'highly_variable'
    obsm: 'X_pca', 'X_umap'
    varm: 'PCs'

Note that we concatenated along the observations by default, and that most elements aligned to the observations were concatenated as well. A notable exception is obsp, which can be re-enabled with the pairwise keyword argument. This is because it’s not obvious that combining graphs or distance matrices padded with 0s is particularly useful, and may be unintuitive.

Inner and outer joins#

When the variables present in the objects to be concatenated aren’t exactly the same, you can choose to take either the intersection or union of these variables. This is otherwise called taking the "inner" (intersection) or "outer" (union) join. For example, given two anndata objects with differing variables:

>>> a = AnnData(sparse.eye(3, format="csr"), var=pd.DataFrame(index=list("abc")))
>>> b = AnnData(sparse.eye(2, format="csr"), var=pd.DataFrame(index=list("ba")))
>>> ad.concat([a, b], join="inner").X.toarray()
array([[1., 0.],
       [0., 1.],
       [0., 0.],
       [0., 1.],
       [1., 0.]])
>>> ad.concat([a, b], join="outer").X.toarray()
array([[1., 0., 0.],
       [0., 1., 0.],
       [0., 0., 1.],
       [0., 1., 0.],
       [1., 0., 0.]])

The join argument is used for any element which has both (1) an axis being concatenated and (2) an axis not being concatenated. When concatenating along the obs dimension, this means elements of .X, obs, .layers, and .obsm will be affected by the choice of join.

To demonstrate this, let’s say we’re trying to combine a droplet based experiment with a spatial one. When building a joint anndata object, we would still like to store the coordinates for the spatial samples.

>>> coords = np.hstack([np.repeat(np.arange(10), 10), np.tile(np.arange(10), 10)]).T
>>> spatial = AnnData(
...     sparse.random(5000, 10000, format="csr"),
...     obsm={"coords": np.random.randn(5000, 2)}
... )
>>> droplet = AnnData(sparse.random(5000, 10000, format="csr"))
>>> combined = ad.concat([spatial, droplet], join="outer")
>>> sc.pl.embedding(combined, "coords")

Annotating data source (label, keys, and index_unique)#

Often, you’d like to be able to tell which values came from which object. This can be accomplished with the label, keys, and index_unique keyword arguments.

For an example, we’ll show how you can keep track of the original dataset by passing a Mapping of dataset names to AnnData objects to concat:

>>> adatas = {
...     "a": ad.AnnData(
...         sparse.random(3, 50, format="csr", density=0.1),
...         obs=pd.DataFrame(index=[f"a-{i}" for i in range(3)])
...     ),
...     "b": ad.AnnData(
...         sparse.random(5, 50, format="csr", density=0.1),
...         obs=pd.DataFrame(index=[f"b-{i}" for i in range(5)])
...     ),
... }
>>> ad.concat(adatas, label="dataset").obs
    dataset
a-0       a
a-1       a
a-2       a
b-0       b
b-1       b
b-2       b
b-3       b
b-4       b

Here, a categorical column (with the name specified by label) was added to the result. As an alternative to passing a Mapping, you can also specify dataset names with the keys argument.

In some cases, your objects may share names along the axes being concatenated. These values can be made unique by appending the relevant key using the index_unique argument:

>>> adatas = {
...     "a": ad.AnnData(
...         sparse.random(3, 10, format="csr", density=0.1),
...         obs=pd.DataFrame(index=[f"cell-{i}" for i in range(3)])
...     ),
...     "b": ad.AnnData(
...         sparse.random(5, 10, format="csr", density=0.1),
...         obs=pd.DataFrame(index=[f"cell-{i}" for i in range(5)])
...     ),
... }
>>> ad.concat(adatas).obs  
Observation names are not unique. To make them unique, call `.obs_names_make_unique`.
Empty DataFrame
Columns: []
Index: [cell-0, cell-1, cell-2, cell-0, cell-1, cell-2, cell-3, cell-4]
>>> ad.concat(adatas, index_unique="_").obs
Empty DataFrame
Columns: []
Index: [cell-0_a, cell-1_a, cell-2_a, cell-0_b, cell-1_b, cell-2_b, cell-3_b, cell-4_b]

Merging#

Combining elements not aligned to the axis of concatenation is controlled through the merge arguments. We provide a few strategies for merging elements aligned to the alternative axes:

  • None: No elements aligned to alternative axes are present in the result object.

  • "same": Elements that are the same in each of the objects.

  • "unique": Elements for which there is only one possible value.

  • "first": The first element seen in each from each position.

  • "only": Elements that show up in only one of the objects.

We’ll show how this works with elements aligned to the alternative axis, and then how merging works with .uns. First, our example case:

>>> import scanpy as sc
>>> blobs = sc.datasets.blobs(n_variables=30, n_centers=5)
>>> sc.pp.pca(blobs)
>>> blobs
AnnData object with n_obs × n_vars = 640 × 30
    obs: 'blobs'
    uns: 'pca'
    obsm: 'X_pca'
    varm: 'PCs'

Now we will split this object by the categorical "blobs" and recombine it to illustrate different merge strategies.

>>> adatas = []
>>> for group, idx in blobs.obs.groupby("blobs").indices.items():
...     sub_adata = blobs[idx].copy()
...     sub_adata.obsm["qc"], sub_adata.varm[f"{group}_qc"] = sc.pp.calculate_qc_metrics(
...         sub_adata, percent_top=(), inplace=False, log1p=False
...     )
...     adatas.append(sub_adata)
>>> adatas[0]
AnnData object with n_obs × n_vars = 128 × 30
    obs: 'blobs'
    uns: 'pca'
    obsm: 'X_pca', 'qc'
    varm: 'PCs', '0_qc'

adatas is now a list of datasets with disjoint sets of observations and a common set of variables. Each object has had QC metrics computed, with observation-wise metrics stored under "qc" in .obsm, and variable-wise metrics stored with a unique key for each subset. Taking a look at how this affects concatenation:

>>> ad.concat(adatas)
AnnData object with n_obs × n_vars = 640 × 30
    obs: 'blobs'
    obsm: 'X_pca', 'qc'
>>> ad.concat(adatas, merge="same")
AnnData object with n_obs × n_vars = 640 × 30
    obs: 'blobs'
    obsm: 'X_pca', 'qc'
    varm: 'PCs'
>>> ad.concat(adatas, merge="unique")
AnnData object with n_obs × n_vars = 640 × 30
    obs: 'blobs'
    obsm: 'X_pca', 'qc'
    varm: 'PCs', '0_qc', '1_qc', '2_qc', '3_qc', '4_qc'

Note that comparisons are made after indices are aligned. That is, if the objects only share a subset of indices on the alternative axis, it’s only required that values for those indices match when using a strategy like "same".

>>> a = AnnData(
...     sparse.eye(3, format="csr"),
...     var=pd.DataFrame({"nums": [1, 2, 3]}, index=list("abc"))
... )
>>> b = AnnData(
...     sparse.eye(2, format="csr"),
...     var=pd.DataFrame({"nums": [2, 1]}, index=list("ba"))
... )
>>> ad.concat([a, b], merge="same").var
   nums
a     1
b     2

Merging .uns#

We use the same set of strategies for merging uns as we do for entries aligned to an axis, but these strategies are applied recursively. This is a little abstract, so we’ll look at some examples of this. Here’s our setup:

>>> from anndata import AnnData
>>> import numpy as np
>>> a = AnnData(np.zeros((10, 10)), uns={"a": 1, "b": 2, "c": {"c.a": 3, "c.b": 4}})
>>> b = AnnData(np.zeros((10, 10)), uns={"a": 1, "b": 3, "c": {"c.b": 4}})
>>> c = AnnData(np.zeros((10, 10)), uns={"a": 1, "b": 4, "c": {"c.a": 3, "c.b": 4, "c.c": 5}})

For quick reference, these are the results from each of the merge strategies. These are discussed in more depth below:

uns_merge

Result

None

{}

"same"

{"a": 1, "c": {"c.b": 4}}

"unique"

{"a": 1, "c": {"c.a": 3, "c.b": 4, "c.c": 5}}

"only"

{"c": {"c.c": 5}}

"first"

{"a": 1, "b": 2, "c": {"c.a": 3, "c.b": 4, "c.c": 5}}

The default returns a fairly obvious result:

>>> ad.concat([a, b, c]).uns == {}
True

But let’s take a look at the others in a bit more depth. Here, we’ll be wrapping the output data in a dict for simplicity of the return value.

>>> dict(ad.concat([a, b, c], uns_merge="same").uns)
{'a': 1, 'c': {'c.b': 4}}

Here only the values for uns["a"] and uns["c"]["c.b"] were exactly the same, so only they were kept. uns["b"] has a number of values and neither uns["c"]["c.a"] or uns["c"]["c.b"] appears in each uns.

A key feature to note is that comparisons are aware of the nested structure of uns and will be applied at any depth. This is why uns["c"]["c.b"] was kept.

Merging uns in this way can be useful when there is some shared data between the objects being concatenated. For example, if each was put through the same pipeline with the same parameters, those parameters used would still be present in the resulting object.

Now let’s look at the behaviour of unique:

>>> dict(ad.concat([a, b, c], uns_merge="unique").uns)
{'a': 1, 'c': {'c.a': 3, 'c.b': 4, 'c.c': 5}}

The results here are a super-set of those from "same". Note that there was only one possible value at each position in the resulting mapping. That is, there were not alternative values present for uns["c"]["c.c"] even though it appeared only once.

This can be useful when the object’s were both run through the same pipeline but contain specific metadata per object. An example of this would be a spatial dataset, where the images are stored in uns.

>>> dict(ad.concat([a, b, c], uns_merge="only").uns)
{'c': {'c.c': 5}}

uns["c"]["c.c"] is the only value that is kept, since it is the only one which was specified in only one uns.

>>> dict(ad.concat([a, b, c], uns_merge="first").uns)
{'a': 1, 'b': 2, 'c': {'c.a': 3, 'c.b': 4, 'c.c': 5}}

In this case, the result has the union of the keys from all the starting dictionaries. The value is taken from the first object to have a value at this key.