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MsVolcano - Dynamic Volcano Plotting

Comparative genome- and proteome-wide screens yield large amounts of data. To efficiently present such datasets and to simplify the identification of hits, the results are often presented in a type of scatterplot known as a volcano plot, which shows a measure of effect size versus a measure of significance. The data points with the largest effect size and a statistical significance beyond a user-defined threshold are considered as hits. Such hits are usually annotated in the plot by a label with their name.

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Volcano plots can represent ten thousands of data points, of which typically only a handful is annotated. The information of data that is not annotated is hardly or not accessible. To simplify access to the data and enable its re-use, we have developed an open source and online web tool with R/Shiny.

The web app is named Volca Nose R and it can be used to create, explore, label and share volcano plots (https://huygens.nl/Volca Nose R). When the data is stored in an online data repository, the web app can retrieve that data together with user-defined settings to generate a customized, interactive volcano plot. Users can interact with the data, adjust the plot and share their modified plot together with the underlying data.

Therefore, Volca Nose R increases the transparency and re-use of large comparative genome- and proteome-wide datasets. The volcano plot visualizes complex datasets generated by genomic screening or proteomic approaches. It is essentially a scatter plot, in which the coordinates of data points are defined by effect size and statistical significance. Although volcano plots are based on rich datasets, only a handful of data points are usually labeled with a gene or protein name. This enables the visual identification of hits and simplifies the interpretation of the complex dataset.

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Nevertheless, the data points that are not annotated may be of equal interest. Therefore, it is highly desirable to have easy access to the information of all data points from such large datasets. Volcano plots are typically generated using commercial software or with software that requires the user to write scripts.

A viable alternative is provided by dedicated free web apps that allow users to generate plots through a graphical user interface (GUI). Several web apps are available, but these do not generate interactive plots and only have limited options for customization and annotation.   Moreover, there is currently no easy and straightforward way of sharing the volcano plot together with the data.  

Therefore, we decided to generate a web-based online tool for generating and sharing volcano plots, similar to other plotting apps that we previously generated. Here, we report an open source web app for generating, exploring, labeling and sharing volcano plots.

The web app is created with R/Shiny and is dubbed Volca Nose R. The Volca Nose R webtool is available at: https://huygens.nl/Volca Nose R or at (as long as the bandwidth limit is not reached): https://goedhart.shinyapps.io/Volca Nose R/. The code was written using R (https:// and Rstudio (https:// To run the app, several freely available packages are required: shiny, ggplot2, magrittr, dplyr, ggrepel, shinycssloaders, DT, RCurl and readxl.

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The code of version 1.0.3 reported in this manuscript is archived at Zenodo.org: https://doi.org/10.5281/zenodo.4002791. Up-to-date code and new releases will be made available on Git Hub, together with information on running the app locally: https://github.com/Joachim Goedhart/Volca Nose R. The Git Hub page of Volca Nose R is the preferred way to communicate issues and request features (https://github.com/Joachim Goedhart/Volca Nose R/issues). Alternatively, the users can contact the developers by email or Twitter. Contact information is found on the “About” page of the app. The accepted file formats are text (with extension CSV or TXT) and spreadsheets (with extension XLS or XLSX). Different delimiters are acceptable for the text format, including the Comma Separate Values (CSV) format. Upload of Excel workbooks with multiple sheets is also supported.

Alternatively, a CSV file from an online data repository can be used through a URL. A limitation of the app on the Huygens server (https://huygens.nl/Volca Nose R) is the file size of ~ 1 Mb.