tree manipulation
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@anthony-ferrari-3991
Last seen 10.2 years ago
Hi all, Does exist a package that allows one to recursively apply a custom function to nodes in a binary tree (from hclust) from leaves to the root ? A kind of "tree_apply" ? Ideally, after that, we could easily retrieve the value of the function at each node and the leaves IDs under that node. Thank you. AF [[alternative HTML version deleted]]
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@wolfgang-huber-3550
Last seen 3 months ago
EMBL European Molecular Biology Laborat…
On 11/05/10 14:49, Anthony Ferrari wrote: > Hi all, > > Does exist a package that allows one to recursively apply a custom function > to nodes in a binary tree (from hclust) from leaves to the root ? > A kind of "tree_apply" ? > Ideally, after that, we could easily retrieve the value of the function at > each node and the leaves IDs under that node. > > Thank you. > > AF > > Dear Anthony, /* this would be better for R-help.... */ perhaps there is already a solution out there, but the task is so simple that you may not need a package. For trees that are represented as lists of lists, something like the below code example would work. For the representation used by hclust, you could write a similar function that loops over the rows of the "merge" matrix (see the hclust man page). tree = list(a = list( A=1, B=2), b = list( A=list(x=3, y=4, z=5), B=list(x=6, y=7), C=8), c = 9) traverse = function(x, f) if (is.list(x)) lapply(x, traverse, f=f) else f(x) traverse(tree, f=function(x) x+1) Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber
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Try: ?dendrapply Thomas On Wed, May 12, 2010 at 12:34:11AM +0200, Wolfgang Huber wrote: > On 11/05/10 14:49, Anthony Ferrari wrote: > >Hi all, > > > >Does exist a package that allows one to recursively apply a custom > >function > >to nodes in a binary tree (from hclust) from leaves to the root ? > >A kind of "tree_apply" ? > >Ideally, after that, we could easily retrieve the value of the function at > >each node and the leaves IDs under that node. > > > >Thank you. > > > >AF > > > > > > Dear Anthony, > > /* this would be better for R-help.... */ > > perhaps there is already a solution out there, but the task is so simple > that you may not need a package. > > For trees that are represented as lists of lists, something like the > below code example would work. > > For the representation used by hclust, you could write a similar > function that loops over the rows of the "merge" matrix (see the hclust > man page). > > > tree = list(a = list( A=1, B=2), > b = list( A=list(x=3, y=4, z=5), > B=list(x=6, y=7), > C=8), > c = 9) > > traverse = function(x, f) > if (is.list(x)) lapply(x, traverse, f=f) else f(x) > > traverse(tree, f=function(x) x+1) > > > > > Wolfgang Huber > EMBL > http://www.embl.de/research/units/genome_biology/huber > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
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Thanks Wolfgang and Thomas. Indeed, looping recursively over the rows of the merge matrix is simple. On 12 May 2010 01:56, Thomas Girke <thomas.girke@ucr.edu> wrote: > Try: > > ?dendrapply > > Thomas > > On Wed, May 12, 2010 at 12:34:11AM +0200, Wolfgang Huber wrote: > > On 11/05/10 14:49, Anthony Ferrari wrote: > > >Hi all, > > > > > >Does exist a package that allows one to recursively apply a custom > > >function > > >to nodes in a binary tree (from hclust) from leaves to the root ? > > >A kind of "tree_apply" ? > > >Ideally, after that, we could easily retrieve the value of the function > at > > >each node and the leaves IDs under that node. > > > > > >Thank you. > > > > > >AF > > > > > > > > > > Dear Anthony, > > > > /* this would be better for R-help.... */ > > > > perhaps there is already a solution out there, but the task is so simple > > that you may not need a package. > > > > For trees that are represented as lists of lists, something like the > > below code example would work. > > > > For the representation used by hclust, you could write a similar > > function that loops over the rows of the "merge" matrix (see the hclust > > man page). > > > > > > tree = list(a = list( A=1, B=2), > > b = list( A=list(x=3, y=4, z=5), > > B=list(x=6, y=7), > > C=8), > > c = 9) > > > > traverse = function(x, f) > > if (is.list(x)) lapply(x, traverse, f=f) else f(x) > > > > traverse(tree, f=function(x) x+1) > > > > > > > > > > Wolfgang Huber > > EMBL > > http://www.embl.de/research/units/genome_biology/huber > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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