Skip to content

JoachimGoedhart/VolcaNoseR

master
Switch branches/tags
Code

Latest commit

 

Git stats

Files

Permalink
Failed to load latest commit information.

VolcaNoseR

A Shiny App for making Volcano plots

Running the App

The web-tool runs from a shiny server, and can be accessed at:

o https://huygens.science.uva.nl/VolcaNoseR/

o https://goedhart.shinyapps.io/VolcaNoseR/, while bandwidth lasts

Alternatively, the app can run from R/Rstudio and this is perhaps the best option for loading large files. See instructions below

Preparations

Note that the app depends on several R packages that need to be installed (shiny, ggplot2, dplyr, magrittr, ggrepel, DT, shinycssloaders, RCurl, readxl).

Run this command in R/Rstudio to download and install all the packages (only needs to be done once):

install.packages("shiny", "ggplot2", "dplyr", "magrittr", "ggrepel", "DT", "shinycssloaders", "RCurl", "readxl")

o The first option is running it directly from Github. In the command line (in R or Rstudio) type:

shiny::runGitHub('VolcaNoseR', 'JoachimGoedhart')

o The second option is download the app and to use it offline:

-download the app.R and csv files (Data-Vulcano-plot.csv and elife-45916-Cdc42QL_data.csv) with example data.

-Run RStudio and load app.R

-Select 'Run All' (shortcut is command-option-R on a Mac) or click on "Run App" (upper right button on the window)

This should launch a web browser with the Shiny app.

Credits

There are several Shiny apps for Volcano plots that have served as a source of inspiration:

-VolcanoR

-Volcanoshiny

-VolcanoPlot_shiny_app

VolcaNoseR is created and maintained by Joachim Goedhart (@joachimgoedhart)

Example output

Standard output generated with the example data:

alt text

Output with user selected annotation of data:

alt text