adding tables to adata.obs and subsetting #150

StasMakarchuk · 2025-01-09T16:55:30Z

Added possibility to add custom csv table to adata.obs (for example cell types or clustering outputs). Make sure that csv file contatins column with correct cell identifiers and specify this column name
Subsetting of xenium and spaceranger datasets - both in anndata and in image label file. We keep original cell ids, so subsetted set of cell ids (numbers) may have "gaps", like 1,2,3,5,9,....

added possibility to add columns in adata.obs and subsetting in visium and xenium

make sure spot id becomes column, and indeces are integer numbers starting with 1

prete · 2025-01-09T19:15:11Z

envs/build-docker-imgs.sh

@@ -1,5 +1,5 @@
 #! /bin/sh
-VERSION=0.5.2
+VERSION=0.5.3


I think this goes as 0.5.4, because 0.5.3 is the current version 🤔

prete · 2025-01-09T19:15:15Z

envs/Dockerfile

@@ -1,5 +1,5 @@
 FROM python:3.10
-ARG BIOFORMATS2RAW="0.4.0"
+ARG BIOFORMATS2RAW="0.7.0"


Could I ask to sneak in an additional version bump and make this 0.9.4 ?

and also update conda environment.yaml

prete · 2025-01-09T19:15:37Z

main.nf

@@ -5,7 +5,7 @@ import groovy.json.*
 nextflow.enable.dsl=2

 verbose_log = true
-version = "0.5.2"
+version = "0.5.3"


Same as above, I think it should be 0.5.4

prete · 2025-01-09T19:17:15Z

bin/process_spaceranger.py

+<<<<<<< HEAD
+        filter_obs_column (str): name of the column which will be used to perform data filtering
+        filter_obs_values (list): list of strings that has to pass the filter inside the column specified
+
+=======
+>>>>>>> f4cd6259b647c7919c15260dc0aa73e6fb161e11


This looks like a unresolved conflict?

prete · 2025-01-09T19:18:44Z

bin/process_xenium.py

    # starting on v1.3 cell_id looks like "aaabinlp-1"
    # pd.Categorical.codes converts them to int this is done manually at this step
    # instead of reindex_anndata so we control what matches the label image
+    #just to make sure the column with name as index name column is not exists in adata.obs


column does not exist in adata.obs

prete · 2025-01-09T19:26:39Z

sphinx/installation.rst


-   2023-05-18 09:30:16 (9.12 MB/s) - ‘v0.5.2.tar.gz’ saved [2835534]
+   2023-05-18 09:30:16 (9.12 MB/s) - ‘v0.5.3.tar.gz’ saved [2835534]


prete · 2025-01-09T19:26:44Z

sphinx/installation.rst

@@ -44,7 +44,7 @@ Using `curl`
 .. code-block:: shell
   :caption: Input

-   curl -L -o v0.5.2.tar.gz https://github.com/haniffalab/webatlas-pipeline/archive/refs/tags/v0.5.2.tar.gz
+   curl -L -o v0.5.3.tar.gz https://github.com/haniffalab/webatlas-pipeline/archive/refs/tags/v0.5.3.tar.gz


prete · 2025-01-09T19:26:49Z

sphinx/installation.rst

-   tar -xzvf ./v0.5.2.tar.gz
-   cd webatlas-pipeline-0.5.2
+   tar -xzvf ./v0.5.3.tar.gz
+   cd webatlas-pipeline-0.5.3


prete · 2025-01-09T19:26:57Z

sphinx/installation.rst

+   webatlas-pipeline-0.5.3/
+   webatlas-pipeline-0.5.3/.github/


prete · 2025-01-09T19:27:02Z

sphinx/installation.rst

+   webatlas-pipeline-0.5.3/tests/input/simple_config.json
+   webatlas-pipeline-0.5.3/tests/test_class.py


StasMakarchuk added 24 commits November 8, 2024 15:44

Add files via upload

801eff9

added possibility to add columns in adata.obs and subsetting in visium and xenium

Update process_h5ad.py

dcc1627

Update process_spaceranger.py

13cf164

Create conf_xenium_subset.yaml

756d18e

Create visium_conf_subset.yaml

f0cb990

Update process_spaceranger.py

d6bd13c

make sure spot id becomes column, and indeces are integer numbers starting with 1

Update process_spaceranger.py

2a7613b

Update generate_image.py

20c3ec0

Update process_xenium.py

5a515bd

fixed bug with index

c92adb4

Update Dockerfile

d03db9c

Update build-docker-imgs.sh

8b985a1

Update main.nf

33c94c0

Update multimodal.nf

de8aa42

Update nextflow.config

5058d00

Update visium.rst

4a2c757

Update xenium.rst

b2987e9

Update installation.rst

f4cd625

Update process_h5ad.py

f613d74

Update process_spaceranger.py

28a0fd9

Update process_xenium.py

7be9454

Update process_xenium.py

ee0ea24

Update process_spaceranger.py

32edf8a

Update configuration.rst

1da9bbe

prete requested changes Jan 9, 2025

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adding tables to adata.obs and subsetting #150

adding tables to adata.obs and subsetting #150

StasMakarchuk commented Jan 9, 2025

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		2023-05-18 09:30:16 (9.12 MB/s) - ‘v0.5.2.tar.gz’ saved [2835534]
		2023-05-18 09:30:16 (9.12 MB/s) - ‘v0.5.3.tar.gz’ saved [2835534]

		webatlas-pipeline-0.5.3/tests/input/simple_config.json
		webatlas-pipeline-0.5.3/tests/test_class.py

adding tables to adata.obs and subsetting #150

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adding tables to adata.obs and subsetting #150

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