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      • R语言-UpSetR高级韦恩图制作

      R语言-UpSetR高级韦恩图制作

      • 发布者 Sam 蔡
      • 分类 未分类
      • 日期 2019年10月27日
      • 评论 0评论

      UpSetR Travis-CI Build Status

      Technique

      UpSetR generates static UpSet plots. The UpSet technique visualizes set intersections in a matrix layout and introduces aggregates based on groupings and queries. The matrix layout enables the effective representation of associated data, such as the number of elements in the aggregates and intersections, as well as additional summary statistics derived from subset or element attributes.

      For further details about the original technique see the UpSet website. You can also check out the UpSetR shiny app. Here is the source code for the shiny wrapper.

      A Python package called py-upset to create UpSet plots has been created by GitHub user ImSoErgodic.

      Citation

      If you use UpSetR in a paper, please cite:

      Jake R Conway, Alexander Lex, Nils Gehlenborg UpSetR: An R Package for the Visualization of Intersecting Sets and their Properties doi: https://doi.org/10.1093/bioinformatics/btx364

      The original technique and the interactive visualization tool implementing the approach are described here:

      Alexander Lex, Nils Gehlenborg, Hendrik Strobelt, Romain Vuillemot, Hanspeter Pfister,
      UpSet: Visualization of Intersecting Sets,
      IEEE Transactions on Visualization and Computer Graphics (InfoVis ’14), vol. 20, no. 12, pp. 1983–1992, 2014.
      doi: https://doi.org/10.1109/TVCG.2014.2346248

      Sample Data

      Sample data sets for UpSetR are included in the package and can be loaded like this:

      movies <- read.csv( "http://www.weinformatics.cn/wp-content/uploads/2019/10/movies.csv", header=T, sep=";" )
      mutations <- read.csv( "http://www.weinformatics.cn/wp-content/uploads/2019/10/mutations.csv", header=T, sep = ",")
      

      The movie data set created by the GroupLens Lab and curated by Bilal Alsallakh and the mutations data set was originally created by the TCGA Consortium and represents mutations for the 100 most mutated genes in a glioblastoma multiforme cohort.

      Examples

      In addition to the examples shown here, we have included a range of UpSetR plots in the paper about the R package, which can be found in a separate GitHub repository.

      Vignettes

      There are currently four vignettes that explain how to use the features included in the UpSetR package:

      • Basic Usage
      • Queries
      • Attribute Plots
      • Set Metadata

      Demo

      A view of the UpSet plot with additional plots based on elements in the intersections.

      Image

      upset(movies,attribute.plots=list(gridrows=60,plots=list(list(plot=scatter_plot, x="ReleaseDate", y="AvgRating"),
      list(plot=scatter_plot, x="ReleaseDate", y="Watches"),list(plot=scatter_plot, x="Watches", y="AvgRating"),
      list(plot=histogram, x="ReleaseDate")), ncols = 2))
      

      A view of UpSetR mimicking the plot published by Lex & Gehlenborg http://www.nature.com/nmeth/journal/v11/n8/abs/nmeth.3033.html

      image

      upset(mutations, sets = c("PTEN", "TP53", "EGFR", "PIK3R1", "RB1"), sets.bar.color = "#56B4E9",
      order.by = "freq", empty.intersections = "on")
      

      An example using two set queries (war movies and noir movies) along with attribute plots comparing the average rating (top) and average rating vs the number of times the movies have been watched (bottom).

      image

      upset(movies, attribute.plots=list(gridrows = 100, ncols = 1, 
      plots = list(list(plot=histogram, x="AvgRating",queries=T),
      list(plot = scatter_plot, y = "AvgRating", x = "Watches", queries = T))), 
      sets = c("Action", "Adventure", "Children", "War", "Noir"),
      queries = list(list(query = intersects, params = list("War"), active = T),
      list(query = intersects, params = list("Noir"))))
      

      Download

      Install the latest released version from CRAN

      BiocManager::install("UpSetR")
      

      Download the latest development code of UpSetR from GitHub using devtools with

      BiocManager::install("hms-dbmi/UpSetR")
      

      更多参加: https://www.jianshu.com/p/324aae3d5ea4

      请关注“恒诺新知”微信公众号,感谢“R语言“,”数据那些事儿“,”老俊俊的生信笔记“,”冷🈚️思“,“珞珈R”,“生信星球”的支持!

      • 分享:
      Sam 蔡
      Sam 蔡

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