TypeError: pyGSEA.plot_enrichment() got an unexpected keyword argument 'bbox_to_anchor_used'，along with other suggestions

[GhostInTheShellwjc]

In fact,the params bbox_to_anchor_used，node_diameter have been deleted in func pyGSEA.plot_enrichment,and it should be deleted in the tutorial "Different Expression Analysis with DEseq2".Maybe the tutorial should be updated since many funcs have been updated and added since omicverse 1.6.3 and 1.6.5. BTW,I really hope that a new function which can draw selected type of Enrichment Plot (such as barplot,cnetplot,emapplot,upsetplot and treeplot in clusterprofiler in R),together with a new param which can classify the up genes and down genes accroding to the results of Deseq2 and draw the up genes and down genes in different colors,could be added in module ov.bulk.
platform:Jupyter in vscode on Windows 11
version:omicverse 1.6.8

[HendricksJudy]

Sir, we will try to understand your report. It seemed to miss some context for us to investigate this issue.

[GhostInTheShellwjc]

I'm very sorry for the confusion my information has caused you. I can provide some more detailed information. In the omicverse tutorial "Different Expression Analysis with DEseq2," the gsea_obj.plot_enrichment function in [19] no longer includes the bbox_to_anchor_used and node_diameter parameters, but they are still mentioned in the tutorial. This may be due to the tutorial being outdated，and this may cause confusion and inconvenience for those who are beginners in using the omicverse package. Therefore, I kindly request an update to the tutorial version to reflect the current function parameters. BTW, I have also encountered some inconveniences while using omicverse in my daily work, and I hope some new features can be added. For specifics, please see my first point in this issue. I would greatly appreciate it if you could consider my suggestions. Thank you very much!

[HendricksJudy]

Thanks for your additional contextual information. Our team is going to work on this issue soon.

[GhostInTheShellwjc]

@HendricksJudy If possible, could you please also take a look at issues #216 and #218? Thank you very much. BTW, when running deep learning algorithms on Jupyter in VSCode, it is currently necessary to addos.environ['KMP_DUPLICATE_LIB_OK'] = 'True'to prevent Jupyter from crashing. I hope this can be added automatically when importing omicverse or a note can be made in the tutorial to prevent crashes.