biomformat | Biom file format support in R/Bioconductor , vers | Genomics library

by joey711 R Version: Current License: No License

X-Ray Key Features Code Snippets Community Discussions(2)Vulnerabilities Install Support

kandi X-RAY | biomformat Summary

biomformat is a R library typically used in Artificial Intelligence, Genomics applications. biomformat has no bugs, it has no vulnerabilities and it has low support. You can download it from GitHub.

This is an R package for interfacing with both the JSON and HDF5 versions of the biom file format. This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, as well as limited support for writing a biom-object back to a biom-format file.

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Quality

Security

License

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Support

biomformat has a low active ecosystem.

It has 5 star(s) with 4 fork(s). There are 1 watchers for this library.

It had no major release in the last 6 months.

There are 7 open issues and 1 have been closed. On average issues are closed in 31 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of biomformat is current.

Quality

biomformat has no bugs reported.

Security

biomformat has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

License

biomformat does not have a standard license declared.

Check the repository for any license declaration and review the terms closely.

Without a license, all rights are reserved, and you cannot use the library in your applications.

Reuse

biomformat releases are not available. You will need to build from source code and install.

Installation instructions, examples and code snippets are available.

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biomformat Key Features

No Key Features are available at this moment for biomformat.

biomformat Examples and Code Snippets

No Code Snippets are available at this moment for biomformat.

Community Discussions

Trending Discussions on biomformat

Unset existing scale_fill_discrete in ggplot2 or suppress message for new scale

Removing lines from barplot in R

QUESTION

Unset existing scale_fill_discrete in ggplot2 or suppress message for new scale

Asked 2020-May-12 at 10:43

I am currently trying to knit an R markdown document to html (or pdf) where in a certain chunk I generate multiple plots. I specify the captions through the fig.cap argument in the chunk options with a vector of the same length as the number of plots. However, for this to work the chunk option message has to be TRUE. The issue starts when a ggplot2 object is generated by a function in the chunk and I want to apply a new fill with viridis::scale_fill_viridis. Which is fine, but inevitably throws a message/warning that there is already a fill applied to the ggplot2 object and that the viridis will replace it (Scale for 'fill' is already present. Adding another scale for 'fill', which will replace the existing scale). I do not want to get this into the output of my markdown html. Using suppressMessages apparently also suppresses the html (and pdf!) captions. So my question is: is there a way to "unset" the existing scales attribute to avoid this message being generated? Short from that my only other option would be to dive into the code that generated the object in the first place. Or: is there a way that knitr preserves captions when the chunk option messages=F?

A minimal working example would be the following code in an R markdown document:

...

ANSWER

Answered 2017-Sep-01 at 15:07

Take a look at a ggplot object, here p:

str(p)

There's a lot of sub-structure. Take a look at p$scales. It's a ScalesList. The following might help you:

i <- which(sapply(p$scales$scales, function(x) 'fill' %in% x$aesthetics)) p$scales$scales[[i]] <- NULL

Source https://stackoverflow.com/questions/45998396

QUESTION

Removing lines from barplot in R

Asked 2018-Jan-18 at 08:32

I have created a barplot for metagenomic data using RStudio

...

ANSWER

Answered 2018-Jan-18 at 07:12

plot_bar from the phyloseq package uses ggplot for plotting. You can look at the code for plot_bar by typing plot_bar in the console, which yields:

Source https://stackoverflow.com/questions/48314292

Community Discussions, Code Snippets contain sources that include Stack Exchange Network

Vulnerabilities

No vulnerabilities reported

Install biomformat

To install the latest stable release of the biomformat package enter the following in an R session (after official release). Before official release, or to install the latest development version, enter the following into an R session.

Support

Please post feature or support requests and bugs at the Issues Tracker for the biomformat package on GitHub. Issues related to the format itself and not the R interface should be posted on the issues tracker for the biom-format team. Note that this is a separate (but friendly!) project from the biom-format team, and the software license is different between this package and much of the rest of the biom-format software, which has switched to BSD. This package is scheduled for inclusion in the next stable release of the Bioconductor project (BioC). BioC is also where the rhdf5 package lives. The original release of this package was made available through CRAN, as the "biom" package, supporting version 1.x (JSON) only. The current plan is to let "biom" remain on CRAN in maintenance-only mode until "biomformat" is released on Bioconductor. At which point "biom" will be considered deprecated, and eventually removed.

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