asntech / intervene-shiny

An interactive Shiny App for UpSet plots, Venn diagrams and Pairwise heatmaps

Intervene

An interactive Shiny App for UpSet plots, Venn diagrams and Pairwise heatmaps

Intervene Shiny App provides an interactive interface for intersection and effective visualization of gene or genomic region sets. Currently, Shiny app does not acccept genomic regions as input, but the text files generated by Interve's command line interface can be easily uploaded to further explore and customize the plots in an interactive way. Intervene has three modules:

• venn to generate Venn diagrams of up-to 6 sets,
• upset to generate UpSet plots of more than 3 sets and
• pairwise to compute and visualize pariwise intersections as clustered heatmap.

Install the required packages

Install the following packages:

install.packages(c("shiny","shinydashboard", "devtools", "d3heatmap", "plotly", "gplots", "ggplot2", "gridExtra", "plyr", "UpSetR", "colourpicker", "corrplot", "BBmisc", "readr", "DT"));
source("https://bioconductor.org/biocLite.R"); biocLite(c("RBGL","graph"));
library(devtools); install_github("js229/Vennerable");

Online availability

Intervene Shiny App is freely available at

https://asntech.shinyapps.io/intervene

OR

https://intervene.shinyapps.io/intervene

Support

If you have questions, or found any bug in the program, please write to us at aziz.khan[at]ncmm.uio.no

Cite

If you use Intervene please cite us:

Khan A, Mathelier A. Intervene: a tool for intersection and visualization of multiple gene or genomic region sets. BMC Bioinformatics. 2017;18:287. doi: 10.1186/s12859-017-1708-7

intervene-shiny's Issues

Error executing Intervene Upset Plots

Hi,
I´m using R 4.0.2 and upon using intervene, it tries to install upsetR in library 3.6, How can I point it to R 4.0.2 on macOS ?

Error in library.dynam(lib, package, package.lib) :
shared object ‘rlang.dylib’ not found
Calls: ... loadNamespace -> namespaceImport -> loadNamespace -> library.dynam
Execution halted
ERROR: lazy loading failed for package ‘UpSetR’

• removing ‘/Users/ankushs/Library/R/3.6/library/UpSetR’
• restoring previous ‘/Users/ankushs/Library/R/3.6/library/UpSetR’

The downloaded source packages are in
‘/private/var/folders/st/7_q6h2897zv73w3x6g85m6y80000gn/T/RtmpMmzk2W/downloaded_packages’
Warning message:
In install.packages("UpSetR", repos = "http://cran.us.r-project.org") :
installation of package ‘UpSetR’ had non-zero exit status
Error: package or namespace load failed for ‘UpSetR’ in library.dynam(lib, package, package.lib):
shared object ‘rlang.dylib’ not found
Execution halted

Thanks

[Feature request] Option to download list of intersecting elements

Hi @asntech,

I am big fan of this tool -thank you!

Recently I started missing a feature which is very important for my colleagues: the ability to download the overlapping (and exclusive) list of genes. Say in a two away venn / upset download the genes which are common to A and B, but also the ones which found only in one or the other.

Something along these lines:

• upset https://stackoverflow.com/questions/65027133/extract-intersection-list-from-upset-object
• venn https://stackoverflow.com/questions/23559371/get-the-list-of-items-in-venn-diagram