hms-dbmi / upsetr-paper

Data and scripts for UpSetR paper.

UpSetR Paper Figures

The scripts and data in this directory were used to generate the figures in the UpSetR paper:

Jake R Conway, Alexander Lex, Nils Gehlenborg UpSetR: An R Package for the Visualization of Intersecting Sets and their Properties bioRxiv 120600 doi: https://doi.org/10.1101/120600

Pulling Project Mutation Data From ICGC

To pull mutation data from various projects on the ICGC data portal use the ICGC_API_pull.R script. Since the ICGC REST API has a pagination of 100 results, this script may take several minutes to run. It is also important to note that this API is actively being updated, so data is constantly being added and removed. To avoid running this script we've provided a text file (icgcData.txt) containing all of the data pulled on 3/18/2016, which is the data used to generate the UpSetR plots in the paper.

Generating ICGC plots

The ICGCpaperFigures.R script can be used to generate the ICGC UpSetR plots using the data in icgcData.txt.

Banana Venn

The bananaPlot.R script can be used to generate the UpSetR version of the "Banana Venn" plot (D’Hont, A., et al., 2012).

SNP Caller

The SNPcallerPlot.R script can be used to generate the UpSetR version of the SNP caller Euler diagram presented in Xu et al., 2012.