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phyloacc / PhyloAcc

PhyloAcc a software to detect the changes of conservation of a genomic region
GNU General Public License v3.0
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What is the branch length and color plotted by plotZPost? #25

Closed binlu1981 closed 2 years ago

binlu1981 commented 3 years ago

Hi @xyz111131 ,

I looked the R script and found the code mytree$edge.length <- mytree$edge.length*(posterior_z[1,] + posterior_z[2,] * ratio1 + posterior_z[3,]* ratio2) Why posterior probability * n_rate or c_rate here? Also what the color mean? Dose it represents posterior probability 3? And should I selected candidates that have higher posterior_3 and logBF1 ?

Best regards Bin

xyz111131 commented 3 years ago

Hi Bin,

the edge length represents expected substitution rate, the right hand side is like a conditional expectation formula. The color means the posterior mean of Z. If the posterior probability 3 is higher, then it will be more red. Yes you could select candidates with higher posterior_3 and logBF1, and you might also add logBF2>0.

Best,

binlu1981 commented 3 years ago

Got it! Thanks for quick replay.

binlu1981 commented 3 years ago

Hi @xyz111131 ,

One more question. Should I set significant threshold of posterior probability to 0.95?

xyz111131 commented 3 years ago

Posterior probability > 0.95 should be fine.