gjuggler / ggphylo Goto Github PK
View Code? Open in Web Editor NEWPhylogenetic plots for R and ggplot
Phylogenetic plots for R and ggplot
Any expectation for further development of this package? I was unable to download for R version 3.3.2, and installation failed for devtools::install_github("gjuggler/ggphylo")
Hi there
I'm having difficulty using ggphylo. First, when I tried building and installing the package, I got an error during the construction of vignettes:
could not find function "is.linear"
I was able to get past this by bypassing the vignettes, but once I tried actually running some simple code, I got the same error. Is it possible that there is a dependency that isn't being specified properly?
We're running R 2.14.2 (64 bit Linux), for what it's worth.
Please let me know if you have any suggestions, and thank you for your time.
Chris
When I try to install ggphylo I get the following
githubinstall('gjuggler/ggphylo')
[...]
* installing *source* package 'ggphylo' ...
** R
** inst
** preparing package for lazy loading
Error in eval(expr, envir, enclos) :
could not find function "eval"
Error : unable to load R code in package 'ggphylo'
ERROR: lazy loading failed for package 'ggphylo'
* removing 'C:/Users/Francisco/Documents/R/win-library/3.3/ggphylo'
Error: Command failed (1)
Hey @gjuggler,
I've run into a conflict using ggphylo
with the R package Shiny.
Your S3 method tags
function(object, ...) {
UseMethod("tags")
}
is also in Shiny. I am using these together in a Shiny app. I wonder if you think it's possible to change tags
to something else? Like ggtags
or something else that won't conflict.
This issue stems from the Roxygen convention that the first LaTeX-paragraph of the roxygen header become the title. The package's function index expects relatively short sentences/phrases here, or the rendering looks pretty bad in the index. I think the title ends-up being a run-on when you read the documentation in a GUI as well.
The fix:
Easy. Put a space between the short phrase you want to keep as the title, and the rest of the paragraph(s) that you want to use for additional details. The first paragraph after the title in the roxygen header becomes the summary, and any additional paragraphs beyond that get dropped into "additional details" or whatever it's called.
Many of the smaller functions in this package might be considered "internal", and useful to others in only a small minority of special cases. In these cases, there is no need for the @export
tag in the rox-header, and even better to add an explicit
#' @keywords internal
tag to the header. The documentation will still be built, but it won't show up in the normal package index. This will help the largest fraction of the intende audience find the main functions we really want them to use. Not-exporting these internal functions helps others import our package without having to worry about name-clashes with other packages. A motivated user will still have access to our functions, and these internal functions can still be directly accessed via
pkgname:::funname()
In general this should feel less like a convention and more like a helpful organizing principle to make it easier on the users.
HI,
When attempting to install ggphylo using install_github('ggphylo', 'gjuggler')
I received the error message:
Error: processing vignette 'ggphylo.Rnw' failed with diagnostics:
chunk 7 (label = phylo5)
Error in coord_polar(expand = F, theta = "y") :
unused argument(s) (expand = F)
Execution halted
Does anyone know what might be the issue?
Thanks,
:)
Maybe you have already done this. If not, it would be great to have the option of plotting bipartite networks, sort of like bipartite::plotweb
, e.g., try
data(Safariland)
plotweb(Safariland, high.lablength=3, low.lablength=0, arrow="down")
How do we access the node and tip labels to change their size, font, or to remove them?
Hi, I would like to use ggphylo to run a R tutorial but I could not find the package in the Cran repository archive in order to download the binary file. Is there a way to get ggphylo in R 3.3.3?
thanks a lot
A declarative, efficient, and flexible JavaScript library for building user interfaces.
๐ Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. ๐๐๐
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google โค๏ธ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.