can't plot either Consensus Tree or NLDR plot

[drelo]

Dear Huang et al,

I am following the tutorial example and when I try to plot the consensus tree nothing appears and when I try to plot the NLDR only the image below appears, but the button Plot Tree doesn't work. All the NLDR results I obtained are in the attached zip.

(I am using Ubuntu 16.04 I can provide additional details as requested, please let me know how can I fix this. Thanks)

results.zip

[drelo]

Hi again, here are the files obtained before the NLDR Thanks for your help

beforeR.zip

[whuang08]

Hi, I just fixed the problem about plotting a consensus tree. The new version should work. I did not see problems when I plot a 2D NLDR result. Did you check the "weighted trees" box when you load trees? If not, then all the edges in all the trees have weights 1, which is clear not what we want. It follows that the distances between the same topology trees are 0. Therefore, the NLDR plot will only have a few points.

[drelo]

Yes, I used 'weighted trees' I just downloaded and tried the new version the consensus plot now works fine but the NLDR doesn't work it just return an image similar to the previous one.

Attaching the files

LAST.zip

[whuang08]

Can you tell me all the exact step to plot an NLDR picture? I just tried again and still don't see the problem. I would like to reproduce the problem so that I can debug. Thanks.

[drelo]

I loaded the tress, computed bipartition matrix, compute consensus, plot it, compute T to T distances, go to the next tab, select dimension 3 and step size 100, click Run NLDR , pick a folder ( I choose one containing the Linux... extracted folder, called TREESCAPER), and the click plot results which shows this Sorry if this sounds confusing, probably I am doing something wrong.

[whuang08]

So you change the step size in the "plot parameter", right? So what is the number of cluster? My setting is:

[drelo]

Sorry to bother you again, I did it without the 'step' setting, cluster is 1, I checked and I have everything as in your pic of the dialog. It still gives me the same image.

[whuang08]

Can you also send me the weighted RF-distance file? The following is the NLDR parameters that I used, which are also the default values.

[drelo]

Sure, Here is the weighted RF distance file!

Linux_TreeScaper_v1_unrooted_weighted_RF-distance.txt

[whuang08]

En. It is a zero matrix, which does not make sense.

[drelo]

But the raw tees are the ones in the example file, there might be something odd in the calculation of the distances. I just used another machine and did a new installation from scratch and I got the same results (the figure with only 1 point)

Here are the results loading the pre computed distances (unweigthed RF) from the tutorial files Output folder. But

[whuang08]

I agree with that there may be something odd in the distances. However, I am not able to reproduce the bug in my computer. I can correctly compute weighted RF distance matrix. I will find a new Ubuntu computer and see if I can reproduce the bug.

[drelo]

Thanks for your help! let me know if I can assist by sending or processing any file.

[whuang08]

Weird. I find a new computer which uses Ubuntu 16.04.01. It is the same as the one you have, isn't it? I still can not reproduce the problem :( BTW, did you use Unweighted RF-distance or Weighted distance? The picture in your previous message seems to be the result by Unweighted RF-distance.

[drelo]

Yes, I have 16.04.

I loaded the unweighted distances from the

Following the tutorial I tried weighted RF

Here is a GIF of what I did

[whuang08]

Thank you for the GIF. It is very helpful, though I don't see any problems. Can you send me the "log.txt" file in the TreeScaper's directory after you finish all the steps?

[drelo]

Sure, please find it attached

El lun., 26 de feb. de 2018 a la(s) 19:32, Wen Huang < notifications@github.com> escribió:

Thank you for the GIF. It is very helpful, though I don't see any problems. Can you send me the "log.txt" file in the TreeScaper's directory after you finish all the steps?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/whuang08/TreeScaper/issues/17#issuecomment-368674750, or mute the thread https://github.com/notifications/unsubscribe-auth/AJ2minrsF6fJx3tmeNX0PuN59gyuA8vAks5tYzD0gaJpZM4SSDn5 .

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Successfully read 100 trees.

Unique bipartition number: 19 Translation of taxa: taxon_1 , 1 taxon_2 , 2 taxon_3 , 3 taxon_4 , 4 taxon_5 , 5 taxon_6 , 6 taxon_7 , 7 taxon_8 , 8 taxon_9 , 9 taxon_10 , 10 taxon_11 , 11 taxon_12 , 12 taxon_13 , 13 taxon_14 , 14 taxon_15 , 15 taxon_16 , 16 bipartition 1 : 0011111111111111, appear times: 100 bipartition 2 : 0000000000000011, appear times: 67 bipartition 3 : 0000000000001100, appear times: 100 bipartition 4 : 0000111100000000, appear times: 36 bipartition 5 : 0011000000000000, appear times: 100 bipartition 6 : 0000000000001111, appear times: 61 bipartition 7 : 0000100011111111, appear times: 64 bipartition 8 : 0000000000110000, appear times: 100 bipartition 9 : 0000000011000000, appear times: 100 bipartition 10 : 0000100000000010, appear times: 33 bipartition 11 : 0000110000000000, appear times: 26 bipartition 12 : 0000000011110000, appear times: 100 bipartition 13 : 0000100000000011, appear times: 37 bipartition 14 : 0000001100000000, appear times: 100 bipartition 15 : 0000011100000000, appear times: 74 bipartition 16 : 0000000011111100, appear times: 2 bipartition 17 : 0000100000001111, appear times: 37 bipartition 18 : 0000000011111111, appear times: 63 bipartition 19 : 0000111111111111, appear times: 100 Successfully computed bipartition matrix.

Obtain 13 bipartitions in the consensus tree!

Successfully computed the majority consensus tree!

Successfully computed Weighted Robinson Foulds distance.

Running NLDR... Start program: /home/andrelo/Desktop/TREESCAPER/Linux_TreeScaper_v1.0.0_Binary_2018-02-24/1000bp1L_RF_3D_CCA_STOCHASTIC Compute start time:1493807 epochs : 0 epochs : 1 epochs : 2 epochs : 3 epochs : 4 epochs : 5 epochs : 6 epochs : 7 epochs : 8 epochs : 9 epochs : 10 epochs : 11 epochs : 12 epochs : 13 epochs : 14 epochs : 15 epochs : 16 epochs : 17 epochs : 18 epochs : 19 epochs : 20 epochs : 21 epochs : 22 epochs : 23 epochs : 24 epochs : 25 epochs : 26 epochs : 27 epochs : 28 epochs : 29 epochs : 30 epochs : 31 epochs : 32 epochs : 33 epochs : 34 epochs : 35 epochs : 36 epochs : 37 epochs : 38 epochs : 39 epochs : 40 epochs : 41 epochs : 42 epochs : 43 epochs : 44 epochs : 45 epochs : 46 epochs : 47 epochs : 48 epochs : 49 epochs : 50 epochs : 51 epochs : 52 epochs : 53 epochs : 54 epochs : 55 epochs : 56 epochs : 57 epochs : 58 epochs : 59 epochs : 60 epochs : 61 epochs : 62 epochs : 63 epochs : 64 epochs : 65 epochs : 66 epochs : 67 epochs : 68 epochs : 69 epochs : 70 epochs : 71 epochs : 72 epochs : 73 epochs : 74 epochs : 75 epochs : 76 epochs : 77 epochs : 78 epochs : 79 epochs : 80 epochs : 81 epochs : 82 epochs : 83 epochs : 84 epochs : 85 epochs : 86 epochs : 87 epochs : 88 epochs : 89 epochs : 90 epochs : 91 epochs : 92 epochs : 93 epochs : 94 epochs : 95 epochs : 96 epochs : 97 epochs : 98 epochs : 99 stress value : 1.88895e-29 Compute end time:1670495 Compute time cost:176688 Analysis start time:1670502 Analysis end time:1682661 Analysis time cost:12159 Please see the help for details of the introduction of output files.

To plot the trees, press SHIFT + R and circle points from the figure. Then, click the 'Plot Trees' button.

[drelo]

Here it is, Thanks

log.txt

[whuang08]

Thank you for the file. I still don't see any problems~~~Can you also send me the bipartition matrix? It would be much easier to debug if I can reproduce the bug on my machine...

[drelo]

Yeah, here are the files

1000bp1L_unrooted_weighted_listFormat_bipartition.txt Linux_TreeScaper_v1_unrooted_weighted_RF-distance.txt 1000bp1L_unrooted_weighted_Consensus_tree_Newick.txt

[whuang08]

The bipartition matrix is not correct. Let me check.

[whuang08]

Can you also output the Weighted treeset in the memory by clicking "Weighted treeset" in the bottom left window on TreeScaper?

[drelo]

I guess this is it

1000bp1L_unrooted_weighted_Newick.txt

[whuang08]

Thanks. This output file shows that the trees are unweighted...

[drelo]

Maybe the button at the beginning ' isn't ' working because I highlighted or selected this at the beginning. I just double checked the weighted box (see pic) and run everything again, here all all the files in a zip

TREESCAPER.zip

[whuang08]

Can you also send me 1000bp1L.nex file that you are using? Another possible reason is that all the weights become zeros when TreeScaper reads trees.

[drelo]

Sure

1000bp1L.txt

[whuang08]

I believe the bug comes from the mistaken weights when reading trees. All the weights become zero for an unknown reason. In this case, the weighted RF distance between any trees is always zero. When output trees to a file, a safeguard in TreeScaper turns all the zero weights to one. That is why all trees look like unweighted trees. However, I have not figured out why all the weights become zero on your machine.

[drelo]

It happens on two machines (a Desktop and a laptop) but I don't understand what is causing it.

[whuang08]

I will find a new computer tomorrow. Hopefully I can reproduce the bug. Thank you very much for the helps.

[whuang08]

I tested the Linux version on another Ubuntu 16.04 computer. However, I still can not reproduce the bug. @jembrown @jrash @mmarchand11 If you have chance, please see if you can reproduce the bug?