Is that possible to add option of barplot number annotation for oncoplots

[Alexander17Z]

Hello guys,

The library you made is really awesome and ready to use. But I really wonder is it possible to add a parameter for controlling the number of genes on plot_genes or other plotting functions, which I am manually doing now.

Best regards

[sbslee]

@Alexander17Z,

I'm glad to hear that you find pypgx helpful. As for your question, most of the methods of pymaf.MafFrame, including pymaf.MafFrame.plot_genes, have an argument to control the number of the displayed genes (e.g., count). See this documentation as an example.

[Alexander17Z]

Thank you for replying to my issue! I may not have explained my question very well. Actually, I meant the number annotation on barplot circle by red now. Because I previously tried the classic ax.container method for the returned ax object

for i, bar in enumerate(ax.containers[0]): # Get the x position of the bar x = bar.get_x() + bar.get_width() / 2 # Calculate the total height (sum) of the stacked bars at this position total = sum([c[i].get_height() for c in ax.containers]) # Place the annotation ax.text(x, total + 0.25, f'{total}', fontsize=12)

But this looks pretty weird, so I had to annotate them manually using for loop as the bar width is 1 according to my observation, which is OK for me but not that great. So I would like to ask, is it possible to add this parameter for controlling the number annotation of barplots?

Best regards

[sbslee]

Hi @Alexander17Z,

Thank you for your clarification, and my apologies for the delayed response. I now understand what you're asking. However, to be honest, I currently don't have the capacity to work on this feature. That said, I hope this doesn't stop you from adding it!

I encourage you to check out the source code for the pymaf.MafFrame.plot_genes method and see if you can modify it to display the number of genes. I'd be more than happy to review your code if you submit a pull request.