Justin Sing

@copilot can you try address reviewer comments again

@copilot can you try address reviewer comments again

@jcharkow I think it should be good to go. Once the CI finishes we can merge

Sorry, I don't have any experience with Agilent IM data either. MSConvert might behave/store the IM differently for Agilent IM data. Might be useful to reach out the them to...

I would suggest maybe adopting `facet_col`/`facet_row` similar to how plotly does it. https://plotly.com/python/facet-plots/

> Hi [@timosachsenberg](https://github.com/timosachsenberg) , > > I'm facing a ModuleNotFoundError in app.py while trying to run pyopenms_viz using Streamlit. The error is related to plotMSExperiment, but after checking the repo,...

@Imama-Kainat @Leandro1302 , we currently mutate the intensity data (either `y` for 1D plots or `z` for 2D plots) for two cases: 1) when we want to plot the intensity...

This can be done by specifying the `y_kind` / `x_kind` ``` df.plot(kind="peakmap", x="feature_mz", y="feature_rt", z="feature_intensity", xlabel = "m/z", ylabel = "rt", y_kind = "chromatogram", x_kind = "spectrum", aggregate_duplicates=True, add_marginals=True, **kwargs)...

Testing for visualizations is definitely annoying and tricky... I feel like we run into issues with bokeh updates, we had to switch from v2 to v3, and seem to be...

Thanks for reporting. The plotly spectrum example in the [docs](https://pyopenms-viz.readthedocs.io/en/latest/gallery/ms_bokeh/plot_spectrum_dia_ms_bokeh.html) seems to be working fine as expected. Can you provide a bit more information (reprex) to how you produced the...