Re: [R-sig-phylo] ape and pvclust
Kyle Dexter (NSF International Fellow at Royal Botanic Garden Edinburgh/University of Leeds) contacted me earlier about this. He wrote function that convert pvclust object into phylo class. He describes, main aim of doing this was to have the support values as node labels and to then be able to take advantage of the flexibility of plot.phylo. This might be your solution too. Viren -Original Message- From: Gilles Benjamin Leduc [mailto:g...@hi.is] Sent: Saturday, December 01, 2012 5:20 PM To: Viky Koralkova Cc: Amin, Viren; r-sig-phylo@r-project.org Subject: Re: [R-sig-phylo] ape and pvclust what about that? From my object 'Honkenya' pvclust(t(Honkenya),method.dist=euclidean)-pvc Bootstrap (r = 0.5)... Done. Bootstrap (r = 0.6)... Done. Bootstrap (r = 0.7)... Done. Bootstrap (r = 0.8)... Done. Bootstrap (r = 0.9)... Done. Bootstrap (r = 1.0)... Done. Bootstrap (r = 1.1)... Done. Bootstrap (r = 1.2)... Done. Bootstrap (r = 1.29)... Done. Bootstrap (r = 1.4)... Done. plot(pvc) pvc$edges$bp [1] 0.4951716613 0.2032013398 0.2910987395 0.9340127352 0.4035529728 0.5447190865 0.3572038743 0.1536864252 0.5270015188 0.3267035814 0.2743854728 0.0987248868 [13] 0.0801774299 0.9866418181 0.1273635273 0.0132019869 0.0236836210 0.6223535990 0.792765 0.2657101863 0.1336651349 0.3610068209 0.7781688199 0.6712364369 [25] 0.0009243720 0.00 0.0362376487 0.3169056116 0.3491294774 0.509255 0.5982804189 0.00 0.5202499234 0.1234962648 0.2571189332 0.1141604874 [37] 0.3883167944 0.2216256880 0.0011849073 0.1187124005 0.0764747960 0.6674296374 0.2722804549 0.4843545471 0.2586820600 0.5059421088 0.1929187828 0.0823025587 [49] 0.0046726208 0.0134633228 0.1006816368 0.2071893876 0.0832511906 0.0929060120 0.1283216438 0.2237870450 0.2619809269 0.4451794099 0.2339210818 0.2490667465 [61] 0.2723912381 0.0057375311 0.1604730040 0.0040761968 0.2269091991 0.2399147247 0.2473521312 0.1418729972 0.1843708163 0.2714629663 0.1478053934 0.1597415034 [73] 0.3059365036 0.1158633632 0.1812697700 0.2831258999 0.0254612363 0.0208276528 0.3147245340 0.0458701909 0.3267795070 0.0091590594 0.1568188781 0.2087502653 [85] 0.2953284646 0.1325699491 0.1988358859 0.2031920519 0.0873642913 0.2057051900 0.0702308386 0.0121120462 0.3171176000 0.2431403668 0.1696482283 0.0463135614 [97] 0.0410591556 0.0089793538 0.2819056591 0.0217874431 0.0641458107 0.2415355942 0.2583278858 0.2713952814 0.1527077134 0.3390957893 0.1399284945 0.0894367607 [109] 0.1036380788 0.1917546389 0.0906929023 0.1213947286 0.2194779359 0.0631706142 0.0019294341 0.0133228895 0.0279335604 0.0903032666 0.0355018160 0.1089914330 [121] 0.0046618192 0.0284010717 0.0070834519 0.0511161926 0.0662917387 0.1724581117 0.1347067634 0.1336960426 0.1230102818 0.1284032863 0.0254373309 0.0738759960 [133] 0.1104924280 0.00 0.0340173294 0.1129225678 0.0185724085 0.0172544777 0.0028657728 0.0126264750 0.00 0.0140718341 0.1400726639 0.0202570783 [145] 0.0948808223 0.2036646342 0.1522527939 0.2774225085 0.1702825341 0.1073638865 0.1619658176 0.0039251756 0.1496349094 0.0441916665 0.2144840068 0.2353987935 [157] 0.00 0.00 0.0428268650 0.0330031630 0.0175946161 0.0012466098 0.0016499755 0.0102129364 0.0154151397 0.0476662858 0.0032655085 0.0674716521 [169] 0.0863001829 0.0256263176 0.0317071397 0.1966243868 0.0914319305 0.1860376342 0.0717596304 0.0999875696 0.0063240304 0.0453137203 0.0171133466 0.0203221879 [181] 0.0017667241 0.0229074658 0.0036822950 0.00 0.001000 0.0008927039 0.00 0.00 0.0013384996 0.0190243120 0.1285879171 0.0294484548 [193] 0.0597251976 0.1265782243 0.1786614255 0.0143452066 0.0078556628 0.1008874311 0.0057736709 0.0116851012 0.0066407134 0.0383533991 0.0301806171 0.0177810262 [205] 0.00 0.0035262198 0.0103899002 0.0018301184 0.00 0.00 0.0211685525 0.0318513758 0.0044838058 0.1680381127 0.0489839738 0.00 [217] 0.00 0.00 0.00 0.0010195116 0.0535590136 0.0014523209 0.0030986192 0.0047224292 0.00 0.00 0.0017581113 0.00 [229] 0.00 0.0457057413 0.0071184049 0.0016677997 0.0009219831 0.0146409561 0.0891777309 0.1512069612 0.0520111793 0.00 0.00 0.00 [241] 0.001000 0.00 0.0051189360 0.0010487877 0.0029715409 0.00 0.00 0.0202307316 0.00 0.0100379505 0.0471348578 0.00 [253] 0.00 0.0096065703 0.0009689567 0.0021562140 0.00 0.00 0.00 0.0009598627 0.00 0.00 0.00 0.00 [265] 0.00 0.00 0.0014706419 0.0109697764 0.1554938941 0.00 0.1391729074 0.00 0.0011000793 0.00 0.00 0.00 [277] 0.00 0.0058950160 0.00 0.00 0.00 0.00 0.00 0.0840119138 0.0045494995 0.00 0.00 0.00 [289] 0.00 0.00 0.2035015039 0.0814756181 0.0009868164 0.00
[R-sig-phylo] ape and pvclust
Mathias, I am also currently trying on plotting au/bp values from pvclust to tree plot from ape package. Were you able to figure this out? If you did, I would really appreciate if you can provide me tips. Thanks Viren [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] ape and pvclust
Hi Mathias and Antigoni, It seems worth writing a method function as.phylo.pvclust since other users are also interested in such functionality. If anybody has some code, that'd be a good start. Cheers, Emmanuel -Original Message- From: Antigoni Kaliontzopoulou antig...@mail.icav.up.pt Sender: r-sig-phylo-boun...@r-project.org Date: Sat, 19 Nov 2011 10:26:02 To: r-sig-phylo@r-project.org Subject: Re: [R-sig-phylo] ape and pvclust Hi Mathias, a fast way to see/check the order of nodes in the tree (before assigning any values to the nodes) is: plot(mytree) nodelabels() The labels you need to show will then have to be a vector with its elements in the order of the numbering of nodes you see in the tree. Normally nodes in ape tree objects are numbered from root to tips and from bottom to top (although a practical test will be more illustrative). You would probably also have to play with the parameters of nodelabels() for formatting. Hope this helps Antigoni On 11/19/2011 02:07 AM, Walter, Mathias wrote: Hi, I wonder if it's possible to plot the au and bp values computed by pvclust on the nodes of an pyhlo tree of the ape package. It should look like here: http://treethinkers.blogspot.com/2008/10/labeling-trees-posterior-probability.html I tried to transfer the computed values put they are not assigned to the right node. Does anybody know how to do this? -- Kind regards, Mathias ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Antigoni Kaliontzopoulou CIBIO, Centro de Investigacao em Biodiversidade e Recursos Geneticos Campus Agrario de Vairao, 4485-661 Vairao PORTUGAL Department of Ecology, Evolution, and Organismal Biology Iowa State University, Ames, Iowa 50011, USA tel: +351 91 3086188 mail to: antig...@mail.icav.up.pt ant...@gmail.com ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
[R-sig-phylo] ape and pvclust
Hi, I wonder if it's possible to plot the au and bp values computed by pvclust on the nodes of an pyhlo tree of the ape package. It should look like here: http://treethinkers.blogspot.com/2008/10/labeling-trees-posterior-probability.html I tried to transfer the computed values put they are not assigned to the right node. Does anybody know how to do this? -- Kind regards, Mathias ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] ape and pvclust
Hi Mathias, a fast way to see/check the order of nodes in the tree (before assigning any values to the nodes) is: plot(mytree) nodelabels() The labels you need to show will then have to be a vector with its elements in the order of the numbering of nodes you see in the tree. Normally nodes in ape tree objects are numbered from root to tips and from bottom to top (although a practical test will be more illustrative). You would probably also have to play with the parameters of nodelabels() for formatting. Hope this helps Antigoni On 11/19/2011 02:07 AM, Walter, Mathias wrote: Hi, I wonder if it's possible to plot the au and bp values computed by pvclust on the nodes of an pyhlo tree of the ape package. It should look like here: http://treethinkers.blogspot.com/2008/10/labeling-trees-posterior-probability.html I tried to transfer the computed values put they are not assigned to the right node. Does anybody know how to do this? -- Kind regards, Mathias ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Antigoni Kaliontzopoulou CIBIO, Centro de Investigacao em Biodiversidade e Recursos Geneticos Campus Agrario de Vairao, 4485-661 Vairao PORTUGAL Department of Ecology, Evolution, and Organismal Biology Iowa State University, Ames, Iowa 50011, USA tel: +351 91 3086188 mail to: antig...@mail.icav.up.pt ant...@gmail.com ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
