A Shiny App for making Volcano plots
The web-tool runs from a shiny server, and can be accessed at:
o https://huygens.science.uva.nl/VolcaNoseR/
o https://huygens.science.uva.nl/VolcaNoseR2/
o https://amsterdamstudygroup.shinyapps.io/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
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", "tidyverse", "ggrepel", "DT", "shinycssloaders", "RCurl", "readxl", "ggiraph", "htmlwidgets")
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.
There are several Shiny apps for Volcano plots that have served as a source of inspiration:
VolcaNoseR is created and maintained by Joachim Goedhart (@joachimgoedhart)
Standard output generated with the example data:
Output with user selected annotation of data:
