An error occurred when running the pt.pl.coda.boxplots function.

[Zstark11]

Describe the bug When using the pt.pl.coda.boxplots function, an AttributeError occurs: AttributeError: module 'pertpy.plot' has no attribute 'coda', which prevents the function from executing successfully.

To Reproduce Steps to reproduce the behavior:

1. Python runtime environment and version：I have tried versions Python 3.9, 3.10, and 3.12. The pertpy version is 0.9.4, and I have also tried downgrading it to versions 0.8.0 through 0.5.0. The omicverse version is 1.6.6.

2. Run the following code:

   import omicverse as ov
   import scanpy as sc
   import scvelo as scv
   import pertpy as pt
   ov.utils.ov_plot_set()
   adata=ov.read(r'D:\Python单细胞\test-haber\haber_count.h5ad')
   adata
   adata.obs['condition'].cat.categories
   ##
   sccoda_model = pt.tl.Sccoda()
   sccoda_data = sccoda_model.load(
   adata,
   type="cell_level",
   generate_sample_level=True,
   cell_type_identifier="cell_label",
   sample_identifier="batch",
   covariate_obs=["condition"],
   )
   sccoda_data
   ##
   pt.pl.coda.boxplots(
   sccoda_data,
   modality_key="coda",
   feature_name="condition",
   figsize=(12, 5),
   add_dots=True,
   args_swarmplot={"palette": ["red"]},
   )
   plt.show()

3. See error: AttributeError: module 'pertpy.plot' has no attribute 'coda'。 Regarding the installation of pertpy, following pip install 'pertpy [coda]' still yields an error AttributeError: module 'pertupy. plot' has no attribute 'coda'

[Zstark11]

The problem has been resolved. For the latest version 0.9.4 of Pertpy, the drawing function needs to be changed. For example, pt. pl. coda. boxplots need to be changed to sccoda_model.plot_boxplots. I hope this can help everyone.

[Dexterssssss]

@Zstark11 It worked. Thank you for sharing.