Option to aggregate individual MistyData objects from multiple samples

[whitneyt1]

Hello!

Thank you for this package. I'm looking to run this pipeline on 36 Visium reactions and mistyR has the option to run MISTy on multiple individual samples and aggregate results (via collect_results) to plot the differences (plot_contrast_heatmap), as recommended in my MISTy question.

Am I able to replicate this in the python package?

Thanks!

[dbdimitrov]

Hi @whitneyt1,

You could indeed aggregate the results by passing e.g. mean as a function to aggregate_fun of the visualizations for misty. You would need to pass a concatenated dataframe of misty results across samples. Though, plotting contrasts with these functions is not available yet (which seems to be the use case that you describe in the issue that you've linked).

I hope this helps.
Daniel

[whitneyt1]

Great thank you. So, if I use the RandomForestModel on each individual sample, I can combine these reactions using the aggregate_fun argument within plotting functions, i can manually compare. Thank you!!!

[dbdimitrov]

Hi @whitneyt1,

Yes, exactly. You could also see matplotlib versions of these plots with a condition here:
https://github.com/saezlab/lianaplus_manuscript/blob/main/notebooks/sma/sma_plot.ipynb

Hope this helps.

[whitneyt1]

Thank you! I appreciate it!