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 > _______________________________________________ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
