tree.scale_bar() returns undefined, maybe an edge case?

[guidorice]

Hi Miguel, we have noticed that in some of our trees, the tnt.tree is unable to calculate the distance. For the tree below, tree.scale_bar(100, 'pixels'); returns undefined.

This only happens with some of our trees- and I suspect it has something to do with zero- length branches, but I cannot see what is going wrong in the code. Please let me know if you have any ideas or fixes.

Here is the newick

(((arath.AT5G60640.1:0.32911,(solly.Solyc06g075210.2.1:0.42215,solly.Solyc11g069400.1.1:0.13359):0.16168):0.06772,((((lotja.Lj3g3v3085830.1:0.11216,((aradu.Aradu.IRK0C.1:0.01585,aradu.Aradu.XJ6TW.1:0.01412):0.00053,(araip.Araip.9K298.1:0.00213,aradu.Aradu.1291C.1:0.09688):0.00186):0.22815):0.02341,(cajca.C.cajan_21520:0.06963,((phavu.Phvul.011G079000.1:0.03461,vigra.Vradi02g05810.1:0.04503):0.04038,(glyma.Glyma.11G146800.1:0.03475,glyma.Glyma.12G067700.1:0.0674):0.02313):0.01473):0.03652):0.02815,(cicar.Ca_14570:0.06004,medtr.Medtr4g059450.1:0.07727):0.038):0.09289,((((glyma.Glyma.12G172800.1:0.05337,glyma.Glyma.13G326200.1:0.04236):0.04403,(cajca.C.cajan_34019:0.07586,(phavu.Phvul.005G135600.1:0.05345,vigra.Vradi04g02780.1:0.04608):0.05396):0.0156):0.04602,(lotja.Lj0g3v0149129.2:0.09957,(cicar.Ca_02530:0.07903,medtr.Medtr2g094180.1:0.11076):0.07025):0.03662):0.01674,(aradu.Aradu.8P6BN.1:0.00171,araip.Araip.SB6R7.1:0.01115):0.11834):0.04132):0.06071):0,(vitvi.GSVIVT01025184001:0.11134,(prupe.ppa003432m:0.21011,(((arath.AT3G54960.1:0.42194,(orysa.LOC_Os02g01010.1:0.1347,(zeama.GRMZM2G033829_P01:0.09654,zeama.GRMZM2G134889_P01:0.06871):0.11319):0.37777):0.08035,(ambtr.evm_27.model.AmTr_v1.0_scaffold00175.37:0.34236,solly.Solyc04g049450.2.1:0.26635):0.03042):0.01848,vitvi.GSVIVT01016282001:0.25257):0.02943):0.03241):0.00833):0;

Also note the tree displays fine with scale(true), it's just the scale_bar() calculation that fails.

[emepyc]

Yes, the scale was set based on the first branch length, if it is zero it returned NaN.
I have fixed this now in v0.1.8. Please update and let me know if that works properly now.

[guidorice]

@emepyc I updated to latest in npm, and it's working now. Thanks so much! We are going-live with the tnt.tree and the biojs msa component this week, I will post a note on Gitter if you want to take look.

[guidorice]

Oops just noticed one minor thing, I think you left some console.log() in the tree.js file.
edit: apparently just in the build/tnt.tree.js.

[emepyc]

Yay! sorry, just fixed it (v0.1.9)

[guidorice]

Thanks :)

[emepyc]

btw, I'd love to take a look at your implementation once you have something live! :-)
Thanks for your feedback and your bug reports