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: http://biojs.io/d/muts-needle-plot
- Installable JavaScript library at npm-registry: https://www.npmjs.org/package/muts-needle-plot
- Source code at GitHub: https://github.com/bbglab/muts-needle-plot
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: http://biojs.net/
Issues
Please report issues at: https://github.com/freezecoder/mutsneedle/issues Authors
Original credit goes to Michael Schroeder and his group for the javascript version.
The R/HTMLWidgets credit is done by
Zayed Albertyn