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https://github.com/freezecoder/mutsneedle
R package for viewing mutation needle lollipop plot widgets
https://github.com/freezecoder/mutsneedle
Last synced: 27 days ago
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R package for viewing mutation needle lollipop plot widgets
- Host: GitHub
- URL: https://github.com/freezecoder/mutsneedle
- Owner: freezecoder
- Created: 2018-01-30T18:39:14.000Z (almost 7 years ago)
- Default Branch: master
- Last Pushed: 2018-04-18T18:00:31.000Z (over 6 years ago)
- Last Synced: 2024-08-04T03:05:39.655Z (4 months ago)
- Language: JavaScript
- Size: 428 KB
- Stars: 11
- Watchers: 3
- Forks: 1
- Open Issues: 3
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
- awesome-shiny-extensions - mutsneedle - Interactive mutation lollipop diagrams. (Visualization / Biological Data)
README
# Mutsneedle: An R package to generating interactive lolipop plots
Mutsneedle is an R version of the MutsNeedlePlot package developed by Michael Schroeder https://github.com/mpschr
In many bioinformatics/genomics task involving mutation inspection it is quite useful to explore the significant of certain alterations to a protein sequence.
Installation
==============
Firstly download and Install the package using devtools
```
library(devtools)
library(htmlwidgets)
install_github("freezecoder/mutsneedle")
```
It may not be necessary to include htmlwidgets with mutsneedle but this has not been tested.
Usage
==============
The mutsneedle function expects a data frame of mutation information for a particular gene. It can also accept domain/region information to annotate the lolipop plot.
```
mutsneedle(mutdata=exampleData(),domains=exampleRegionData())
```
The mutdata input is an R data frame with the colums:
* coord - A string coordinate e.g. "11" , "1-10" are both valid
* category - String describing the category of the mutation
* value - numeric value
Other columns may be present in the dataframe but they will be ignored.
You may also insert a gene and transcript ID into the plot using the 'gene' and 'transcript' args to the mutsneedle function.
Usage in a Shiny App
=====================
The app is quite easy to call in Shiny thanks to the wonderful htmlwidgets package
```
library(shiny)
library(mutsneedle)
library(htmlwidgets)
shinyApp(
ui = mutsneedleOutput("id",width=800,height=500),
server = function(input, output) {
output$id <- renderMutsneedle(
data <- exampleMutationData()
regiondata <- exampleRegionData()
mutsneedle(mutdata=data,domains=regiondata)
)
}
)
```
More info Mutations Needle Plot (muts-needle-plot)
=================================================
A needle-plot (aka stem-plot or lollipop-plot) plots each data point as a big dot and adds a vertical line that makes it appear like a needle.
This software is **citable**! Different citation styles available at *http://dx.doi.org/*+DOI
Availability
-----------------------
* **Live examples** at the BioJS-registry:
* **Installable JavaScript library** at npm-registry:
* **Source code** at GitHub:
Examples (snippets)
----------------------
This library is can be found as npm-library in the BioJS registry.
Thus examples can bee seen at the biojs.net registry:
Issues
----------
Please report issues at:
Authors
--------
Original credit goes to Michael Schroeder and his group for the javascript version.
The R/HTMLWidgets credit is done by
**Zayed Albertyn**
+