# Help with concat

**URL:** <https://discourse.scverse.org/t/help-with-concat/676>\
**Category:** anndata\
**Created:** [August 12, 2022, 1:58am UTC](https://discourse.scverse.org/t/help-with-concat/676 "2022-08-12T01:58:06Z")\
**Posts on this page:** 3\
**Page:** 1

<div class="post-metadata">

**Author:** ![johnkerl](https://yyz1.discourse-cdn.com/flex035/user_avatar/discourse.scverse.org/johnkerl/32/340_2.png) [@johnkerl](https://discourse.scverse.org/u/johnkerl)\
**Post date:** [August 12, 2022, 1:58am UTC](https://discourse.scverse.org/t/help-with-concat/676/1 "2022-08-12T01:58:06Z")

</div>

The obs-wise merge is not doing what I would expect – curious how to get the desired result.

Script:

```auto
#!/usr/bin/env python

import pandas as pd
import numpy as np
import anndata as ad

# ----------------------------------------------------------------
def show_adata(adata, name):
    print()
    print("----", name)
    print("X:")
    print(adata.X)
    print("obs:")
    print(adata.obs)
    print("var:")
    print(adata.var)

# ----------------------------------------------------------------
X1 = np.asarray([[1,2,3],[4,5,6]], dtype=np.float32)
obs1 = pd.DataFrame(
    index=np.asarray(['cell1', 'cell2']),
    data={
        "oa": np.asarray([10,20]),
        "ob": np.asarray(["a","b"]),
    },
)
var1 = pd.DataFrame(
    index=np.asarray(['gene1', 'gene2', 'gene3']),
    data={
        "va": np.asarray([30,40,50]),
        "vb": np.asarray([True, False, True]),
        "vc": np.asarray(["c","d","e"]),
    },
)
adata1 = ad.AnnData(X=X1, obs=obs1, var=var1)
show_adata(adata1, "ADATA1")

X2 = np.asarray([[7,8],[9,10]], dtype=np.float32)
obs2 = pd.DataFrame(
    index=np.asarray(['cell3', 'cell4']),
    data={
        "oa": np.asarray([60,70]),
        "ob": np.asarray(["f","g"]),
    },
)
var2 = pd.DataFrame(
    index=np.asarray(['gene1', 'gene4']),
    data={
        "va": np.asarray([80,90]),
        "vb": np.asarray([True, False]),
        "vc": np.asarray(["h","i"]),
    },
)
adata2 = ad.AnnData(X=X2, obs=obs2, var=var2)
show_adata(adata2, "ADATA2")

adatac = ad.concat([adata1, adata2], axis=0, join="outer", merge="first")
show_adata(adatac, "ADATAC")

```

Output:

```auto

---- ADATA1
X:
[[1. 2. 3.]
 [4. 5. 6.]]
obs:
       oa ob
cell1 10 a
cell2 20 b
var:
       va vb vc
gene1 30 True c
gene2 40 False d
gene3 50 True e

---- ADATA2
X:
[[7. 8.]
 [9. 10.]]
obs:
       oa ob
cell3 60 f
cell4 70 g
var:
       va vb vc
gene1 80 True h
gene4 90 False i

---- ADATAC
X:
[[1. 2. 3. nan]
 [4. 5. 6. nan]
 [7. nan nan 8.]
 [9. nan nan 10.]]
obs:
       oa ob
cell1 10 a
cell2 20 b
cell3 60 f
cell4 70 g
var:
         va vb vc
gene1 30.0 True c
gene2 40.0 False d
gene3 50.0 True e
gene4 NaN NaN NaN

```

I want to have:

```auto
var:
         va vb vc
gene1 30.0 True c
gene2 40.0 False d
gene3 50.0 True e
gene4 90.0. False. i

```

---

<div class="post-metadata">

**Author:** ![johnkerl](https://yyz1.discourse-cdn.com/flex035/user_avatar/discourse.scverse.org/johnkerl/32/340_2.png) [@johnkerl](https://discourse.scverse.org/u/johnkerl)\
**Post date:** [August 17, 2022, 5:29pm UTC](https://discourse.scverse.org/t/help-with-concat/676/2 "2022-08-17T17:29:48Z")

</div>

A colleague set me up! 😃

For the record, the solution was to change from:

```auto
adatac = ad.concat([adata1, adata2], axis=0, join="outer", merge="first")

```

to handle the var merge on its own, as in:

```auto
# merge obs & X (and var, but we discard that)
adatac = ad.concat([adata1, adata2], axis=0, join="outer", merge="first")
# merge var
merged_var = pd.concat([adata1.var, adata2.var], join="outer")
adatac.var = merged_var[~merged_var.index.duplicated()]

```

---

<div class="post-metadata">

**Author:** ![tavareshugo](https://yyz1.discourse-cdn.com/flex035/user_avatar/discourse.scverse.org/tavareshugo/32/1031_2.png) [@tavareshugo](https://discourse.scverse.org/u/tavareshugo)\
**Post date:** [May 1, 2024, 4:41pm UTC](https://discourse.scverse.org/t/help-with-concat/676/3 "2024-05-01T16:41:49Z")

</div>

I was looking for a solution to the same issue and while your solution partially works, I don’t think it ensures the order of the genes is correct.

In case others find this thread, my modified suggestion is:

```python
# merge obs & X
adatac = ad.concat([adata1, adata2], axis=0, join="outer", merge="first")
# merge var
merged_var = pd.concat([adata1.var, adata2.var], join="outer")
merged_var = merged_var[~merged_var.index.duplicated()]
adatac.var = merged_var.loc[adatac.var_names]

```

The last line of code ensures that the gene order of the `merged_var` DataFrame is the same as the gene names in the original AnnData object.