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 0.3333792765 0.2657101863 0.1336651349 0.3610068209 0.7781688199 0.6712364369 [25] 0.0009243720 0.0000000000 0.0362376487 0.3169056116 0.3491294774 0.5222209255 0.5982804189 0.0000000000 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 0.0000000000 0.0340173294 0.1129225678 0.0185724085 0.0172544777 0.0028657728 0.0126264750 0.0000000000 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] 0.0000000000 0.0000000000 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 0.0000000000 0.0010000000 0.0008927039 0.0000000000 0.0000000000 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] 0.0000000000 0.0035262198 0.0103899002 0.0018301184 0.0000000000 0.0000000000 0.0211685525 0.0318513758 0.0044838058 0.1680381127 0.0489839738 0.0000000000 [217] 0.0000000000 0.0000000000 0.0000000000 0.0010195116 0.0535590136 0.0014523209 0.0030986192 0.0047224292 0.0000000000 0.0000000000 0.0017581113 0.0000000000 [229] 0.0000000000 0.0457057413 0.0071184049 0.0016677997 0.0009219831 0.0146409561 0.0891777309 0.1512069612 0.0520111793 0.0000000000 0.0000000000 0.0000000000 [241] 0.0010000000 0.0000000000 0.0051189360 0.0010487877 0.0029715409 0.0000000000 0.0000000000 0.0202307316 0.0000000000 0.0100379505 0.0471348578 0.0000000000 [253] 0.0000000000 0.0096065703 0.0009689567 0.0021562140 0.0000000000 0.0000000000 0.0000000000 0.0009598627 0.0000000000 0.0000000000 0.0000000000 0.0000000000 [265] 0.0000000000 0.0000000000 0.0014706419 0.0109697764 0.1554938941 0.0000000000 0.1391729074 0.0000000000 0.0011000793 0.0000000000 0.0000000000 0.0000000000 [277] 0.0000000000 0.0058950160 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0840119138 0.0045494995 0.0000000000 0.0000000000 0.0000000000 [289] 0.0000000000 0.0000000000 0.2035015039 0.0814756181 0.0009868164 0.0000000000 0.0000000000 0.0000000000 0.0171647448 0.0000000000 0.0000000000 0.0000000000 [301] 0.0313124347 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.1152870461 0.2520664359 0.0059600071 0.0000000000 0.1664861087 0.0000000000 [313] 0.0000000000 0.0000000000 0.0380268345 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0047902015 0.0000000000 0.0000000000 [325] 0.0000000000 0.0267263105 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.1463688076 0.3859630102 1.0000000000 > dist=vegdist(Honkenya, method="euclidian", binary=TRUE, diag=FALSE, upper=FALSE, na.rm = FALSE) > dendro=hclust(dist,"average") > plot(as.phylo(dendro),type="u") > nodelabels(round(100*pvc$edges$bp)) I tried this but it is very hard to see if it match... what do you think? pvclust is easy to use, but it can not be converted to phylo objet, and does not propose Jacard index :s Benjamin > Hi Armin and Mathias, > > I am not familiar with program Mathias uses, tho I think I can at > least show you directions to go. > Explore possibilities of ape functions nodelabels(), tiplabels() and > edgelabels(). They draw labels (text, symbols, numbers) to nodes, tips > and branches, respectively. Their use with nice examples is described > in Emmanuel Paradis's book Analysis of Phylogenetics and Evolution > with R > (http://www.springer.com/life+sciences/evolutionary+%26+developmental+biology/book/978-1-4614-1742-2). > > > Cheers, > Ivana > > 2012/11/14 Amin, Viren <va...@bcm.edu>: >> 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 > > _______________________________________________ > R-sig-phylo mailing list > R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo >
as.phylo.pvclust.R
Description: as.phylo.pvclust.R
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