HINT-ATAC differential: uniform y-axis for different plots

[konsta-kukkonen]

Thank you for the great tool.

I have a multi variable design in my experiment (treatments with several concentrations of a substance and multiple cell lines). For this reason I want to make several plots (samples of the same cell line, but with the different treatments in one plot), but to be able to compare the footprints across the plots (and to facilitate this I want to adjust the Y-axes so that it's the same for every plot. I tried modifying the source code (https://github.com/CostaLab/reg-gen/blob/master/rgt/HINT/DifferentialAnalysis.py), but after some testing I realized that this is probably not the code that creates the actual lineplots when running rgt-hint differential. I suspect that the correct code would be found in Plotting.py, but I'm not sure where to start. For example, like for the code found in DifferentialAnalysis.py, there is no obvious function I want to input my data to and then run it so that is processes the data like in the command line tool. Can you give any pointers to how this manual pipeline should look like?

User defined adjustment of the y-axis in addition to the x-axis could be a new feature maybe in the future iterations of the tool? I assume not many people need it if they make only one plot, but for this special case it's very much needed, and I would guess, it wouldn't be that difficult to implement either.

Ps. I also tried inputting all the 16 conditions into same analysis, and split the plot manually in GraphPad but that lead to dampening of any differences between the treatments into noise. If you have any other comments or suggestions of easier approach, those are also welcome.

Best,
-Konsta