Iterate through list to make a graph per term

[spatts14]

It is possible to iterate through a list and save the plots individually?

e.g list = ["term1", "term2", "term3"]

for term in list: gc.pl.filtration_curves.compare_conditions( adata=adata, node_labels=term, # Set node_labels to the current term metric_key=metric_key, palette="Set2", save=f"figures/{term}_filtration_curves.pdf" )

Thanks!

[merelkuijs]

Yes, that is possible. The only change you need to make is to put "term" between square brackets:

gc.pl.filtration_curves.compare_conditions(
        adata=adata,
        node_labels=[term], # Set node_labels to the current term
        metric_key=metric_key,
        palette="Set2",
        save=f"figures/{term}_filtration_curves.pdf"
)

[spatts14]

Ill try that thanks!

[mayarali]

@spatts14, can you please confirm that this solved your issue? If so, we'll close this issue.

[spatts14]

Hi sorry!

I got this error:

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
Cell In[13], [line 2](vscode-notebook-cell:?execution_count=13&line=2)
      [1](vscode-notebook-cell:?execution_count=13&line=1) for term in cell_type_names:
----> [2](vscode-notebook-cell:?execution_count=13&line=2)     gc.pl.filtration_curves.compare_conditions(
      [3](vscode-notebook-cell:?execution_count=13&line=3)         adata=adata,
      [4](vscode-notebook-cell:?execution_count=13&line=4)         node_labels=[term], # Set node_labels to the current term
      [5](vscode-notebook-cell:?execution_count=13&line=5)         metric_key=metric_key,
      [6](vscode-notebook-cell:?execution_count=13&line=6)         palette="Set2",
      [7](vscode-notebook-cell:?execution_count=13&line=7)         save=f"figures/{term}_filtration_curves.pdf"
      [8](vscode-notebook-cell:?execution_count=13&line=8) )

File [/opt/anaconda3/envs/graphcompass/lib/python3.11/site-packages/graphcompass/pl/_filtration_curves.py:91](https://file+.vscode-resource.vscode-cdn.net/opt/anaconda3/envs/graphcompass/lib/python3.11/site-packages/graphcompass/pl/_filtration_curves.py:91), in compare_conditions(adata, node_labels, metric_key, return_ax, figsize, dpi, palette, right, save, **kwargs)
     [89](https://file+.vscode-resource.vscode-cdn.net/opt/anaconda3/envs/graphcompass/lib/python3.11/site-packages/graphcompass/pl/_filtration_curves.py:89) for i, key in enumerate(node_labels):
     [90](https://file+.vscode-resource.vscode-cdn.net/opt/anaconda3/envs/graphcompass/lib/python3.11/site-packages/graphcompass/pl/_filtration_curves.py:90)     try:
---> [91](https://file+.vscode-resource.vscode-cdn.net/opt/anaconda3/envs/graphcompass/lib/python3.11/site-packages/graphcompass/pl/_filtration_curves.py:91)         axes[i].step(
     [92](https://file+.vscode-resource.vscode-cdn.net/opt/anaconda3/envs/graphcompass/lib/python3.11/site-packages/graphcompass/pl/_filtration_curves.py:92)             df.weight,
     [93](https://file+.vscode-resource.vscode-cdn.net/opt/anaconda3/envs/graphcompass/lib/python3.11/site-packages/graphcompass/pl/_filtration_curves.py:93)             df[key],
     [94](https://file+.vscode-resource.vscode-cdn.net/opt/anaconda3/envs/graphcompass/lib/python3.11/site-packages/graphcompass/pl/_filtration_curves.py:94)             where='pre',
     [95](https://file+.vscode-resource.vscode-cdn.net/opt/anaconda3/envs/graphcompass/lib/python3.11/site-packages/graphcompass/pl/_filtration_curves.py:95)             label=label[0],
     [96](https://file+.vscode-resource.vscode-cdn.net/opt/anaconda3/envs/graphcompass/lib/python3.11/site-packages/graphcompass/pl/_filtration_curves.py:96)             color=category_color_map[label[0]],
     [97](https://file+.vscode-resource.vscode-cdn.net/opt/anaconda3/envs/graphcompass/lib/python3.11/site-packages/graphcompass/pl/_filtration_curves.py:97)             alpha=0.15
     [98](https://file+.vscode-resource.vscode-cdn.net/opt/anaconda3/envs/graphcompass/lib/python3.11/site-packages/graphcompass/pl/_filtration_curves.py:98)         )
     [99](https://file+.vscode-resource.vscode-cdn.net/opt/anaconda3/envs/graphcompass/lib/python3.11/site-packages/graphcompass/pl/_filtration_curves.py:99)     except KeyError:
    [100](https://file+.vscode-resource.vscode-cdn.net/opt/anaconda3/envs/graphcompass/lib/python3.11/site-packages/graphcompass/pl/_filtration_curves.py:100)         continue

TypeError: 'Axes' object is not subscriptable

[merelkuijs]

Hi again!

I've pushed changes to resolve the bug you're seeing. We will include the updated code in the next release. If you want to make the plots immediately, you can install the updated code from the development branch:

git clone https://github.com/theislab/graphcompass.git
cd graphcompass
pip install -e .['development']

[spatts14]

Thank you!

[merelkuijs]

GraphCompass 0.2.4 is now available on PyPi. You can get the updated version using pip install --upgrade graphcompass.