ggbio | Grid and ggplot2 based visualization for biological data | Data Visualization library

by tengfei R Version: Current License: No License

X-Ray Key Features Code Snippets(2)Community Discussions(3)Vulnerabilities Install Support

kandi X-RAY | ggbio Summary

ggbio is a R library typically used in Analytics, Data Visualization, D3 applications. ggbio has no bugs, it has no vulnerabilities and it has low support. You can download it from GitHub.

Grid and ggplot2 based visualization for biological data

Support

Quality

Security

License

Reuse

Support

ggbio has a low active ecosystem.

It has 75 star(s) with 16 fork(s). There are 9 watchers for this library.

It had no major release in the last 6 months.

There are 61 open issues and 67 have been closed. On average issues are closed in 115 days. There are 3 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of ggbio is current.

Quality

ggbio has no bugs reported.

Security

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

License

ggbio 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

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

Installation instructions are not available. Examples and code snippets are available.

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ggbio Key Features

No Key Features are available at this moment for ggbio.

ggbio Examples and Code Snippets

Explanation

Java

Lines of Code : 119

License : No License

Copy

public interface Potion {
  void drink();
}

@Slf4j
public class HealingPotion implements Potion {
  @Override
  public void drink() {
    LOGGER.info("You feel healed. (Potion={})", System.identityHashCode(this));
  }
}

@Slf4j
public class HolyWate

Explanation

Java

Lines of Code : 12

License : No License

Copy

{
    "Version": "2012-10-17",
    "Statement": [
        {
            "Sid": "PublicReadGetObject",
            "Effect": "Allow",
            "Principal": "*",
            "Action": "s3:GetObject",
            "Resource": "arn:aws:s3:::my-static-w

Community Discussions

Trending Discussions on ggbio

GenomicRanges: C stack usage ... is too close to the limit

Annotate karyogram with Granges track

Karyogram and SNP with ggplot2 (geom_path, geom_bar, ggbio)

QUESTION

GenomicRanges: C stack usage ... is too close to the limit

Asked 2017-Jul-24 at 20:16

I'm loading a built-in ideogram from the biovizBase package:

...

ANSWER

Answered 2017-Jul-20 at 23:15

The stack memory of each process is limited not only by available memory but also by OS (by default no more than a few MiBs).

I didn't understand whether ulimit -s unlimited did the trick or not. what does "it's not clear how to accomplish this from without RStudio" mean?

Source https://stackoverflow.com/questions/45225966

QUESTION

Annotate karyogram with Granges track

Asked 2017-May-19 at 08:38

I want to create a karyogram/ideogram of human hg19 that contains in addition a track with numeric data, e.g. p-values, as an point plot.

...

ANSWER

Answered 2017-May-19 at 08:38

Finally it turned out to be not very difficult if one found the proper URL.

http://www.tengfei.name/ggbio/docs/man/layout_karyogram-method.html points to a line plot above each chromosome's karyogram.

the x-coordinate from the GRanges object to be used would be start
ylim defines the size of the point-subplots
size needs to be reduced a little as default point size would produce a nearly unreadable plot

Source https://stackoverflow.com/questions/44003072

QUESTION

Karyogram and SNP with ggplot2 (geom_path, geom_bar, ggbio)

Asked 2017-Mar-28 at 12:57

I want to plot a karyogram with SNP markers.
It works with function segments but I want to use ggplot2 package to display an elegant graphic.

ggbio:
I checked the package ggbio with the function layout_karyogram but the chromosomes are plotted in a vertical position. I didn't find a way to rotate the graph with the name below each chromosome and to write the name of my SNP next to their segment.

geom_bar:
Then I tried geom_bar from the package ggplot2:

...

ANSWER

Answered 2017-Mar-28 at 12:57

I would go for geom_segment. The x start/end of the SNP segments are hardcoded (as.integer(chr) -+ 0.05), but otherwise the code is fairly straightforward.

Source https://stackoverflow.com/questions/43065723

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

Vulnerabilities

No vulnerabilities reported

Install ggbio

You can download it from GitHub.

Support

For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .

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