tag:blogger.com,1999:blog-8499895524521663926.post760150545971023258..comments2024-03-27T07:13:39.236-04:00Comments on Phylogenetic Tools for Comparative Biology: New phytools version with some phylogeny & geographic mapping optionsLiam Revellhttp://www.blogger.com/profile/04314686830842384151noreply@blogger.comBlogger4125tag:blogger.com,1999:blog-8499895524521663926.post-28176997056313993962017-03-23T17:13:10.266-04:002017-03-23T17:13:10.266-04:00Thank you so much for this !
It seems that this fu...Thank you so much for this !<br />It seems that this function doesn't work with any kind of tree.<br />I tried this one, with success:<br /><br />(Copte:8.0,((Compostelle:2.0,(Byzance:1.0,Latin:1.0):1.0):3.0,(Roumanie:2.0,Russie:2.0,Bucovine:2.0):3.0):3.0,(Geez:1.0,Arabe:1.0):7.0);<br /><br />But this one failed, and I had a message "Error in xy.coords(x, y) : 'x' and 'y' lengths differ":<br /><br />(Copte:8.0,((Compostelle:2.0,(Byzance:1.0,Latin:1.0):1.0):3.0,(Roumanie:2.0,Russie:2.0,Bucovine:2.0):3.0):3.0,(Geez:1.0,Arabe:1.0):7.0);<br /><br />Is there a way to change this ?<br /><br />And is there a possibility to rotate the tree above the map?<br /><br />Ex.: <br /><br />I used this set of coordinates (named "coords.csv"):<br /><br />X lat long<br />Copte 31.2 29.90<br />Geez 9.0 38.70<br />Arabe 30.0 31.00<br />Compostelle 42.8 -8.50<br />Byzance 41.0 28.90<br />Latin 51.5 0.07<br />Roumanie 47.0 25.50<br />Russie 55.7 37.60<br />Bucovine 48.0 26.00<br /><br />Then I wrote:<br /><br />coords <-read.csv("coords.csv", header = TRUE, sep= ";")<br />row.names(coords)=coords$X<br />coords=coords[,c(2,3)]<br />phy <- "((Copte:2.0,(Geez:1.0,Arabe:1.0):1.0):2.0,((Bucovine:2.0,(Roumanie:1.0,Russie:1.0):1.0):1.0,(Compostelle:2.0,(Byzance:1.0,Latin:1.0):1.0):1.0):1.0);"<br />tree <-read.newick(text=phy)<br />plot(tree,use.edge.length=FALSE, edge.width=4,edge.color="brown", label.offset=0.15)<br />obj<-phylo.to.map(tree,coords, fsize=0.9, psize=2, asp=1.2,split=c(0.3,0.5), mar=c(2.1,8.1,2.1,2.1), ylim=c(-10,75), xlim=c(-30,90))<br /><br />The result is OK, but I'd prefer to rotate the tree in order to have the left branch (Copte, Geez, Arabe) on the right site.<br /><br />Is this possible ?<br /><br />Thank you for your time !<br />My best,<br /><br />JLLQ<br /><br />Anonymoushttps://www.blogger.com/profile/02442043626415355430noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-81116092705029025212015-07-13T22:06:03.686-04:002015-07-13T22:06:03.686-04:00Hi Lina. I just wrote a post about this here. Let ...Hi Lina. I just wrote a post about this <a href="http://blog.phytools.org/2015/07/adding-gridlines-to-phylotomap-plot.html" rel="nofollow">here</a>. Let me know if this is what you had in mind. - LiamLiam Revellhttps://www.blogger.com/profile/04314686830842384151noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-82295333850938707252015-07-13T11:37:37.673-04:002015-07-13T11:37:37.673-04:00Liam, is it possible to add latitude and longitude...Liam, is it possible to add latitude and longitude tick marks with this function phylo.to.map? <br /><br />Thanks, LinaLinahttps://www.blogger.com/profile/10138760905795994162noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-63073981526195784412013-10-31T18:46:27.861-04:002013-10-31T18:46:27.861-04:00Would it be possible to Plot the base map at an an...Would it be possible to Plot the base map at an angle, as if you were viewing the map from space, and plot a cladogram where the tips are anchored to the map?Anonymousnoreply@blogger.com