Why UpSet
Everyday I face the problems that need to understand the relationships between sets. Ven diagram always a great job if the number of sets is limited (like up to 4)but it gets clumsy when the number of sets increases. A Venn diagram with multiple sets is difficult to interpret and easy to be lost. So UpSet is another "visualization technique for the quantitative analysis of sets, their intersections, and aggregates of intersections".
How to use UpSet
The source code of Python implementation of UpSet can be downloaded from HERE while R version is HERE. The web version of UpSet can be used from HERE or HERE. Obviously web versions are easy to use for any project but unfortunately, our taste doesn't match always. I just modified two main functions which draw the main plots. New functions give more flexibility to the plot such as
- can automatically calculate the number of unique colours for each comparison.
- colours of numbers can be changed and it doesn't have to be the same as bar color.
- fonts are also changeable.
Prerequisite
We need following R libraries to run the script
- UpSetR
- ggplot2
- grid
- RColorBrewer
- extrafont
Downloads
All files can be downloaded from here
UpsetR_modified
UpsetR_modified - This repository contains the R script the make plot using UpsetR library. Two functions were modified to make the package more flexible.
Extract Part of a FASTA Sequences with Position by python script HERE
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