UpSet Plot

[Jessica]

Hello,

When trying to use the UpSet plot app (https://gnps-fbmn-upset.herokuapp.com/) I wanted to create an upset plot with a subset of my data from a FBMN job; I have selected a metadata column but for the purposes of the figure that I am making, I want to select only a subset of the terms within that column. As of now, even when I only select a subset of the terms, I still see all terms included in the UpSet plot. If anyone knows how to generate an upset plot from a subset of my data, please advise!

Thank you!

Jessica

[Vanessa Phelan]

Hi Jessica-

The UpSet plot feature on GNPS has minimum function. I suggest using the UpSetR Shiny app (https://gehlenborglab.shinyapps.io/upsetr/) or, for highest quality figures, generation of UpSet plots in R  (https://cran.r-project.org/web/packages/UpSetR/index.html#:~:text=UpSetR%3A%20A%20More%20Scalable%20Alternative,10.1093%2Fbioinformatics%2Fbtx364%3E.). I've only made UpSet plots from classical molecular networking data, as we use mzmine for feature finding and gap-filling generally results in only non-zero values . But I assume the process is similar. The easiest method is to export the table from the cytoscape file, remove any extraneous columns, and change it from an abundance table to a binary (1/0 presence/absence) table for use in either the Shiny app or in R.  It sounds more complicated than it is. The Shiny app has some csv data you can download to see the appropriate format for upload. Give it a try. If you're having issues, shoot me a message and either myself or one of my students will walk you through it.

Best wishes,

Vanessa