[R-sig-phylo] reverse order plotting of newick tree/phylo object
Dear R-sig-phylo, I am looking for a method to plot an unrooted tre/phylo object e in the reverse order (of the tip labels). Like all the nodes would have rotated. Any of you has an idea? Kind regards, Thierry Thierry Janssens Postdoctoral researcher Delft University of Technology Bionanoscience Kavli Institute of Nanoscience Lorentzweg 1 2628LJ Delft the Netherlands Tel: +31 15 2781175 Fax:+31 15 2781202 e-mail: t.k.s.janss...@tudelft.nl mailto:t.k.s.janss...@tudelft.nl [[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] reverse order plotting of newick tree/phylo object
Hi Thierry, There might be a more elegant way to do this, but you can just apply the ape function rotate() to each node number of the tree (excluding tips). I.e. tr2-tree for(i in length(tr2$tip)+1:tr2$Nnode) tr2-rotate(tr2,i) plot(tr2) [rotate() may also be able to take a vector of nodes, but I was not able to get this to work.] - Liam -- Liam J. Revell University of Massachusetts Boston web: http://faculty.umb.edu/liam.revell/ email: liam.rev...@umb.edu blog: http://phytools.blogspot.com On 3/17/2011 10:51 AM, Thierry Janssens - TNW wrote: Dear R-sig-phylo, I am looking for a method to plot an unrooted tre/phylo object e in the reverse order (of the tip labels). Like all the nodes would have rotated. Any of you has an idea? Kind regards, Thierry Thierry Janssens Postdoctoral researcher Delft University of Technology Bionanoscience Kavli Institute of Nanoscience Lorentzweg 1 2628LJ Delft the Netherlands Tel: +31 15 2781175 Fax:+31 15 2781202 e-mail: t.k.s.janss...@tudelft.nlmailto:t.k.s.janss...@tudelft.nl [[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
Re: [R-sig-phylo] reverse order plotting of newick tree/phylo object
Hi Liam, Thanks for the help. It works partially, one clade remains at the bottom of the plot, but since it is an unrooted tree there is no node to rotate anymore. But can you explain to me what is the rationale behind this? There are only 47 nodes and 54 tips. How can the nodes from 55 to 47 than be rotated? Kind regards, Thierry Thierry Janssens Postdoctoral researcher Delft University of Technology Bionanoscience Kavli Institute of Nanoscience Lorentzweg 1 2628LJ Delft the Netherlands Tel: +31 15 2781175 Fax:+31 15 2781202 e-mail: t.k.s.janss...@tudelft.nl -Original Message- From: Liam J. Revell [mailto:liam.rev...@umb.edu] Sent: donderdag 17 maart 2011 16:11 To: Thierry Janssens - TNW Cc: r-sig-phylo@r-project.org Subject: Re: [R-sig-phylo] reverse order plotting of newick tree/phylo object Hi Thierry, There might be a more elegant way to do this, but you can just apply the ape function rotate() to each node number of the tree (excluding tips). I.e. tr2-tree for(i in length(tr2$tip)+1:tr2$Nnode) tr2-rotate(tr2,i) plot(tr2) [rotate() may also be able to take a vector of nodes, but I was not able to get this to work.] - Liam -- Liam J. Revell University of Massachusetts Boston web: http://faculty.umb.edu/liam.revell/ email: liam.rev...@umb.edu blog: http://phytools.blogspot.com On 3/17/2011 10:51 AM, Thierry Janssens - TNW wrote: Dear R-sig-phylo, I am looking for a method to plot an unrooted tre/phylo object e in the reverse order (of the tip labels). Like all the nodes would have rotated. Any of you has an idea? Kind regards, Thierry Thierry Janssens Postdoctoral researcher Delft University of Technology Bionanoscience Kavli Institute of Nanoscience Lorentzweg 1 2628LJ Delft the Netherlands Tel: +31 15 2781175 Fax:+31 15 2781202 e-mail: t.k.s.janss...@tudelft.nlmailto:t.k.s.janss...@tudelft.nl [[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
Re: [R-sig-phylo] reverse order plotting of newick tree/phylo object
But can you explain to me what is the rationale behind this? There are only 47 nodes and 54 tips. How can the nodes from 55 to 47 than be rotated? Liam's code is rotating nodes 55+(1:47), rather than 55 to 47. The internal node indexing in ape's phylo class starts with number of tips plus 1. Thus, using rotate on nodes starting with length(phy$tip.label) + 1 means it is starting with node 56 (the root node) and going through length(phy$tip.label) + phy$Nnode, e.g.,, all internal nodes. You can see that 55+(1:47) gives a vector of node numbers that is not the same as 55 to 47. If it isn't working right - maybe it is that you have polytomies? I think you should have n-1 internal nodes (53 in your case). Try multi2di (from ape) for polytomy resolution and see if it works as desired. ~Dan Rabosky Kind regards, Thierry Thierry Janssens Postdoctoral researcher Delft University of Technology Bionanoscience Kavli Institute of Nanoscience Lorentzweg 1 2628LJ Delft the Netherlands Tel: +31 15 2781175 Fax:+31 15 2781202 e-mail: t.k.s.janss...@tudelft.nl -Original Message- From: Liam J. Revell [mailto:liam.rev...@umb.edu] Sent: donderdag 17 maart 2011 16:11 To: Thierry Janssens - TNW Cc: r-sig-phylo@r-project.org Subject: Re: [R-sig-phylo] reverse order plotting of newick tree/phylo object Hi Thierry, There might be a more elegant way to do this, but you can just apply the ape function rotate() to each node number of the tree (excluding tips). I.e. tr2-tree for(i in length(tr2$tip)+1:tr2$Nnode) tr2-rotate(tr2,i) plot(tr2) [rotate() may also be able to take a vector of nodes, but I was not able to get this to work.] - Liam -- Liam J. Revell University of Massachusetts Boston web: http://faculty.umb.edu/liam.revell/ email: liam.rev...@umb.edu blog: http://phytools.blogspot.com On 3/17/2011 10:51 AM, Thierry Janssens - TNW wrote: Dear R-sig-phylo, I am looking for a method to plot an unrooted tre/phylo object e in the reverse order (of the tip labels). Like all the nodes would have rotated. Any of you has an idea? Kind regards, Thierry Thierry Janssens Postdoctoral researcher Delft University of Technology Bionanoscience Kavli Institute of Nanoscience Lorentzweg 1 2628LJ Delft the Netherlands Tel: +31 15 2781175 Fax:+31 15 2781202 e-mail: t.k.s.janss...@tudelft.nlmailto:t.k.s.janss...@tudelft.nl [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] reverse order plotting of newick tree/phylo object
Dan is right on - and I also suspect that the issue of the non-rotating node is probably due to a polytomy at that node. Thanks for the insight Dan. - Liam -- Liam J. Revell University of Massachusetts Boston web: http://faculty.umb.edu/liam.revell/ email: liam.rev...@umb.edu blog: http://phytools.blogspot.com On 3/17/2011 12:26 PM, Dan Rabosky wrote: But can you explain to me what is the rationale behind this? There are only 47 nodes and 54 tips. How can the nodes from 55 to 47 than be rotated? Liam's code is rotating nodes 55+(1:47), rather than 55 to 47. The internal node indexing in ape's phylo class starts with number of tips plus 1. Thus, using rotate on nodes starting with length(phy$tip.label) + 1 means it is starting with node 56 (the root node) and going through length(phy$tip.label) + phy$Nnode, e.g.,, all internal nodes. You can see that 55+(1:47) gives a vector of node numbers that is not the same as 55 to 47. If it isn't working right - maybe it is that you have polytomies? I think you should have n-1 internal nodes (53 in your case). Try multi2di (from ape) for polytomy resolution and see if it works as desired. ~Dan Rabosky Kind regards, Thierry Thierry Janssens Postdoctoral researcher Delft University of Technology Bionanoscience Kavli Institute of Nanoscience Lorentzweg 1 2628LJ Delft the Netherlands Tel: +31 15 2781175 Fax:+31 15 2781202 e-mail: t.k.s.janss...@tudelft.nl -Original Message- From: Liam J. Revell [mailto:liam.rev...@umb.edu] Sent: donderdag 17 maart 2011 16:11 To: Thierry Janssens - TNW Cc: r-sig-phylo@r-project.org Subject: Re: [R-sig-phylo] reverse order plotting of newick tree/phylo object Hi Thierry, There might be a more elegant way to do this, but you can just apply the ape function rotate() to each node number of the tree (excluding tips). I.e. tr2-tree for(i in length(tr2$tip)+1:tr2$Nnode) tr2-rotate(tr2,i) plot(tr2) [rotate() may also be able to take a vector of nodes, but I was not able to get this to work.] - Liam -- Liam J. Revell University of Massachusetts Boston web: http://faculty.umb.edu/liam.revell/ email: liam.rev...@umb.edu blog: http://phytools.blogspot.com On 3/17/2011 10:51 AM, Thierry Janssens - TNW wrote: Dear R-sig-phylo, I am looking for a method to plot an unrooted tre/phylo object e in the reverse order (of the tip labels). Like all the nodes would have rotated. Any of you has an idea? Kind regards, Thierry Thierry Janssens Postdoctoral researcher Delft University of Technology Bionanoscience Kavli Institute of Nanoscience Lorentzweg 1 2628LJ Delft the Netherlands Tel: +31 15 2781175 Fax:+31 15 2781202 e-mail: t.k.s.janss...@tudelft.nlmailto:t.k.s.janss...@tudelft.nl [[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 [[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
