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.
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.
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.
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)
)
}
)
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
- 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
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/
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