Dear all,
I am trying to create a consensus skyline plot using the "ape"
package(newbie).
I have a nexus file that looks like the one from above containing many
trees. (my_file.trees)
#NEXUS
begin trees; [Treefile generated by sim_coal.exe (Laurent Excoffier)]
tree true_tree_1 = [&U] (((13.1:6, 43.1:5):12, 28.1:14):284, (((((21.1:0,
(20.1:1, 4.1:0):0):1, ((37.1:0, (23.1:0, 29.1:0):0):0, 15.1:0):3):7,
(36.1:3, (40.1:0, 26.1:1):2):1):2, ((16.1:0, 33.1:0):3, (10.1:0,
18.1:0):2):8):46, ((((6.1:1, (11.1:0, 34.1:0):0):2, 2.1:1):19, (((38.1:4,
(35.1:4, ((8.1:0, 42.1:0):1, 22.1:0):3):2):0, ((5.1:2, (27.1:0,
39.1:0):0):0, (17.1:0, 30.1:0):1):4):8, ((31.1:0, ((41.1:0, (7.1:0,
25.1:1):0):0, 3.1:0):3):0, (12.1:0, (14.1:0, 1.1:0):0):0):13):10):14,
(((24.1:0, 9.1:0):0, 32.1:0):1, 19.1:0):25):20):206);
tree true_tree_2 = [&U] ((((37.1:4, ((36.1:0, 25.1:0):0, 39.1:0):2):0,
33.1:1):2, (1.1:0, 43.1:0):1):81, (((((21.1:1, (38.1:1, 14.1:1):0):3,
(((29.1:0, 35.1:0):1, 4.1:1):1, ((41.1:1, (24.1:0, ((8.1:0, 32.1:0):0,
7.1:0):0):1):0, (10.1:2, (6.1:1, (26.1:1, (15.1:0,
16.1:0):0):0):0):2):0):4):1, (28.1:1, (3.1:1, 13.1:0):0):7):12, (((22.1:5,
(((2.1:1, 34.1:1):0, 19.1:0):3, (18.1:0, 42.1:0):3):0):0, 17.1:0):3,
(27.1:14, (((30.1:0, 23.1:0):1, 31.1:0):1, 5.1:2):5):3):5):9, ((11.1:0,
9.1:1):0, (12.1:0, (20.1:0, 40.1:1):1):3):23):67);
I haven't managed to read this file content using the *read.tree* function
..
Error in if (tp[3] != "") obj$node.label <- tp[3] :
missing value where TRUE/FALSE needed
Does anyone know first of all, why I cannot read this file (not even with
read.nexus function)? And secondly how can one generate an "average"
skyline
plot from several trees?
Thank you in advance!
Cheers!
[[alternative HTML version deleted]]
Bhoom Suktitipat
2011-Jun-20 03:54 UTC
[R] Skyline plots from several trees in newick format
Does read.nexus work for you? Bhoom On Sun, Jun 19, 2011 at 5:04 PM, Andra Tolbus <andralia.tolbus@gmail.com>wrote:> Dear all, > > I am trying to create a consensus skyline plot using the "ape" > package(newbie). > I have a nexus file that looks like the one from above containing many > trees. (my_file.trees) > > #NEXUS > begin trees; [Treefile generated by sim_coal.exe (Laurent Excoffier)] > > tree true_tree_1 = [&U] (((13.1:6, 43.1:5):12, 28.1:14):284, (((((21.1:0, > (20.1:1, 4.1:0):0):1, ((37.1:0, (23.1:0, 29.1:0):0):0, 15.1:0):3):7, > (36.1:3, (40.1:0, 26.1:1):2):1):2, ((16.1:0, 33.1:0):3, (10.1:0, > 18.1:0):2):8):46, ((((6.1:1, (11.1:0, 34.1:0):0):2, 2.1:1):19, (((38.1:4, > (35.1:4, ((8.1:0, 42.1:0):1, 22.1:0):3):2):0, ((5.1:2, (27.1:0, > 39.1:0):0):0, (17.1:0, 30.1:0):1):4):8, ((31.1:0, ((41.1:0, (7.1:0, > 25.1:1):0):0, 3.1:0):3):0, (12.1:0, (14.1:0, 1.1:0):0):0):13):10):14, > (((24.1:0, 9.1:0):0, 32.1:0):1, 19.1:0):25):20):206); > tree true_tree_2 = [&U] ((((37.1:4, ((36.1:0, 25.1:0):0, 39.1:0):2):0, > 33.1:1):2, (1.1:0, 43.1:0):1):81, (((((21.1:1, (38.1:1, 14.1:1):0):3, > (((29.1:0, 35.1:0):1, 4.1:1):1, ((41.1:1, (24.1:0, ((8.1:0, 32.1:0):0, > 7.1:0):0):1):0, (10.1:2, (6.1:1, (26.1:1, (15.1:0, > 16.1:0):0):0):0):2):0):4):1, (28.1:1, (3.1:1, 13.1:0):0):7):12, (((22.1:5, > (((2.1:1, 34.1:1):0, 19.1:0):3, (18.1:0, 42.1:0):3):0):0, 17.1:0):3, > (27.1:14, (((30.1:0, 23.1:0):1, 31.1:0):1, 5.1:2):5):3):5):9, ((11.1:0, > 9.1:1):0, (12.1:0, (20.1:0, 40.1:1):1):3):23):67); > > I haven't managed to read this file content using the *read.tree* function > .. > > Error in if (tp[3] != "") obj$node.label <- tp[3] : > missing value where TRUE/FALSE needed > > Does anyone know first of all, why I cannot read this file (not even with > read.nexus function)? And secondly how can one generate an "average" > skyline > plot from several trees? > > Thank you in advance! > Cheers! > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >[[alternative HTML version deleted]]