plot a 3D figure about the threshold and gene number

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Maoting Chen

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Jun 14, 2021, 4:00:27 AMJun 14
to majiq_voila
Hi,

I know in the voila we can change the threshold of the dPSI and confidence and get the genes that above the setted thresholds. However, I am wondering if we can plot a 3D figure of the gene number ~ dPSI + confidence, let's say, x - dPSI threshold, y - confidence, z - corresponding gene number. I think it can be helpful for us to find the suitable thresholds. 

Looking forward to your reply.

Thanks,
Maoting

Maoting Chen

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Jun 29, 2021, 6:11:57 AMJun 29
to majiq_voila
Hi,

Just to add on to my question. 
In Voila view html file, we can adjust  the threshold of the dPSI and confidence and get the corresponding number of entries (LVS). So what I am really wondering is that how those enteries are validated to fulfill the threshold requirement? The following is my guessing: 
From the tsv file generated from voila tsv, each entry/LSV has the columns 'mean_dpsi_per_lsv_junction', 'probability_changing', and 'probability_non_changing'. For one entry/LSV, if its 'mean_dpsi_per_lsv_junction' has at least one value larger than dPSI threshold and its 'probability changing' also has at least one value larger than confidence, is it counted?
I used R to compute a tsv file using my own data and setted threshold, but the result is not consistent with the number counted from voila. 

Really appreciate it if I can get some explanations. Or is there any public source code that I can access to?
Looking forward to your reply.

Thanks,
Maoting

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