If I paste() a huge DNAbin alignment (by accident) (as in: 250MB object
size with 15 sequences) R Studio hangs and can not be closed or
aborted (Esc key). I have to Crtl+Strg+Del force quit the process.
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R-sig-phylo mailing list -
Dear Vojtech,
my code snippet works, and the other solutions were also correct. The
problem is with your alignment. Your 3rd sequence only contains N's,
therefore whatever approach you use, all coloumns are filtered out if
you filter all coloumns containing N.
Please open your alignment in a
Hello V.
Because you speak of columns I assume you are handling an alignment,
right? If you handle an alignment all sequences have the same length and
you can do as.matrix
Like this?
library(magrittr)
#maximum number of n's
thresh <- 0.005 #0.5%
seq <- as.matrix(seq)
temp <- seq %>%
Dear list members,
I was wondering if somebody already tried (or knows somebody who did)
using R to access CIPRES using the RESTful API? I think it's a great
solution for people with limited resources.
https://www.phylo.org/restusers/docs/guide.html#SampleCode
Best wishes,
Andreas
Hello Kirston,
try this:
x <- read.fas("example.fasta")
y <- x[grep("1011",rownames(x)),]
Greetings,
Andreas
Am 2016-09-05 08:07, schrieb Kirston Barton:
Hi,
I have my data in a fasta file and am importing it into R using
read.dna, which creates a DNAbin matrix object. I would like to subset
Hello Chris,
you could check out ggtree, especially "Advanced Tree Annotation" from
Bioconductor.
It accepts many ggplot objects and lets you put them on the nodes plus
many more cool things.
Cheers,
Andreas
Am 2016-05-11 20:43, schrieb Chris Buddenhagen:
Is there a way to quickly associate a
