{"repo":"cxli233/customized_upset_plots","free":true,"listed":false,"github":"https://github.com/cxli233/customized_upset_plots","clone":"git clone https://github.com/cxli233/customized_upset_plots.git","description":"Make customized upset plots: from raw data to plots","language":null,"stars":62,"topics":["data-visualization","r"],"license":"CC0-1.0","category":"analytics","readme_excerpt":"Customized Upset Plots This repository contains scripts to produce customized upset plots, an alternative to Venn diagrams. Author: Chenxin Li, Ph.D., Assistant Professor at Department of Plant Biology, Michigan State University. Contact: lichen27@msu.edu @chenxinli2.bsky.social‬ The Scripts/ directory contains .Rmd files that generate the graphics shown below. It requires R, RStudio, and the rmarkdown package. R: R Download RStudio: RStudio Download rmarkdown can be installed using the intall packages interface in RStudio Use bar lengths to present set or subset sizes In Venn diagrams, we use area to represent set or subset sizes. However, I have found it much easier to discern different lengths than different area. This is a workflow for set/intersect visualization using UpSet plots. The upstream segment of the workflow (intersect size determination) is based on the re-implementation of UpSetR by ComplexHeatmap. List, data frame, and plot handling was provided by the tidyverse. Lastly, construction of composite plots is provided by patchwork. In traditional upset plots, intersects/subsets are indicated by dots. When two dots are connected by a line, it represents the distinct intersect between the two sets. Set and intersect sizes are then represented by bars. The workflow produces customized upset plot where intersects/subsets are indicated by a heatmap. The customized upset plot has 4 parts: The upper left shows the total set sizes. The upper right is legend/color scheme.","default_branch":null,"files":null,"tree":[],"storefront":"/r/cxli233","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/cxli233/customized_upset_plots/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}