Four years later, I am now able to answer this question. Circos plots are popular for displaying huge amounts of data in a relatively small visual space. The flexibility of this package is based on the usage of low-level graphics functions such that self-defined high-level graphics can be easily implemented by users for specific purposes. The documentation on circlize was extremely helpful to get me started! Below is the code I wrote for now, so I can remember what I have done in case I want to utilize circlize packages. I stumbled across this beautiful art on Washington Post article, and I wanted to try making the similar art using "digits in pi" myself using R and things I've learned recently. arrow circos. Continue reading Circlizing Numbers → She makes the sound the sea makes to calm me down (Dissolve Me, Alt-J) Searching how to do draw chord diagrams in the Internet with ggplot2 I found a very-easy-to-use package called circlize which does exactly that. Today's graphical system of R is directly derived from the one of S. Again create your own function, my_kable_styling() to standardize the resulting output of these libraries. ), develop GUI (shiny) and many more. As I did before, I used circlize package, which implements in R the features of Circos, a software to create stunning circular visualizations. The adjacency matrix displays all origins in rows, and all destinations in columns. Data visualization system for high-dimensional data. A list of package vignettes built from knitr on CRAN - readme. UpSetR: an R package for the visualization of intersecting sets and their properties Jake R Conway Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA. chordDiagram function, R package circlize. To help, tools to effectively visualize integrated multidimensional data are important for understanding and describing the relationship between genomic variations and cancers. 1/ 2002-10-15 15:06 - 1. R Packages: shiny, ggplot2, plotly, tidyverse,reshape, circlize World Development Indicators (WDI) is an extensive and holistic database compiled by World Bank focusing on countries development across the globe. ggdend function. 0 Depends: R (>= 3. Upon submission, your changes will be run on the appropriate platforms to give the reviewer an opportunity to confirm that the changes result in a successful build. Line data was prepared by ordering the data frame in descending order. points` # - `circos. I did a quick search before this post and didn’t find anything that stuck out more than this package, so I’ll stick with it. u/rharrington31. The plot is built using circlize R package. 0 Depends: R (>= 2. By gjabel I figured out how to replicate these plots in R using the circlize package. How to plot heatmap without connection height in circlize R package? Ask Question Asked 1 month ago. fr on the connections between Euro 2016 players and the country of birth using the circlize package in R. Dedicated windows binaries already have all R packages bundled, and the options summarized above should be considered only when troubleshooting R script execution issues. Although legends cannot be automatically generated by circlize, by using functionality from other R packages, it is just a few more lines to really implement it. The strengths and weaknesses of each visualization technique have been assessed, and a final workflow of visualization produced that combines the use of standard. packages or BiocManager::install functions. In particular, I have made four changes:. This package is a simplified implementation of the Tanaka method. There are a number of groups that maintain particularly important or difficult packages. We would like to show you a description here but the site won't allow us. The goal of this package is to interface a tidy data frame with this powerful tool. ? Another question, is there a way to change the color or the axis? Thanks! On Monday, December 15, 2014 1:39 PM, "Gu, Zuguang" wrote: Hi, In current version, `labels. However, later I discovered another site where you can download. genomicLabels circos. The package closely follows the paper by Tardio and Pardo-de-Santayana (2008). The flexibility of the package is based on the usage of low-level graphics functions such that self-defined high-level graphics can be easily implemented by users for specific purposes. This package aims to implement circular layout in R. 3 colorRamp2. In this project, we will invent flowers using this fact. The flexibility of this package is based on the usage of low-level graphics functions such that self-defined high-level graphics can be easily implemented by users for specific purposes. Debian Quality Assurance. However, later I discovered another site where you can download. This doesn’t just help your wallet - it means that a huge community of R programmers will constantly develop an distribute new R functionality and packages at a speed that leaves all those other packages in the dust! Unlike Fight Club, the first rule of R is “Do talk about R!” The size of the R programming community is staggering. The first problem concerning the notes messages is not really a problem. An R package to interact with the Project Vote Smart API for scientific research : 2014-09-23 : Rvcg: Manipulations of triangular meshes (smoothing, quadric edge collapse decimation, im- and export of various mesh file-formats, cleaning, etc. phylo function). genomicHeatmap circos. However, later I discovered another site where you can download. Scores of studies in molecular ecology and population genetics utilize methods to estimate ancestral or contemporary migration routes between populations, such as MIGRATE-N, IM/IMa2, IMMANC, BayesAss, etc. , 2014) Niu K, Komatsoulis GA, Meerzaman D. A couple of months back, after the paper was already in the submission process, I figured out how to replicate these plots in R using the circlize package. Our goal is to help R learners learn in real-world contexts. Also called “relief contours method”, “illuminated contour method” or “shaded contour lines method”, the Tanaka method enhances the representation of topography on a map using shaded contour lines. This is the repository for the Shiny application presented in "shinyCircos: an R/Shiny application for interactive creation of Circos plot" (Yu et al. For each genomic category, multiple dimensional data which are represented as tracks describe different features from different aspects. Description Details Examples. Some of the advantages are: Row and/or columns colour annotations are easy to integrate just specifying one parameter (column names). The flexibility of this package is based. This package is one of several organism-level packages which are re-built every 6 months. # Current there are following low-level graphic functions: # - `circos. Four years later, I am now able to answer this question. Updating the whole local set of packages goes like so. 2/ 2002-12-19 15:36 - 1. When R is installed, you get from it two base packages, 'graphics' and 'grid', which produce graphics that are exported with the grDevices package. This post explores creating Circos-style genomic data plots in R using R package circlize. The chordDiagram() function of the circlize package makes it a breeze to build chord diagrams from adjacency matrix in R. Use it along with kableExtra and formattable to create attractive text tables with color. Hi All, I have attached the three different datasets for Rn6 genome (rat) and I needed to use circos plot by *circlize package in R*. taoyan：R语言中文社区专栏作者，伪码农，R语言爱好者，爱开源。 个人博客: https://ytlogos. The adjacency matrix displays all origins in rows, and all destinations in columns. circlize包 这个包有两个文档，一个是介绍基本原理的绘制简单圈圈图的，也是本次要介绍的。 另外一份文档专门介绍基因组数据绘制圈圈图Genomic Circos Plot，我自己还没看完，下次再介绍。. 1BestCsharp blog 4,822,867 views. Upon submission, your changes will be run on the appropriate platforms to give the reviewer an opportunity to confirm that the changes result in a successful build. GPG/PGP keys of package maintainers can be downloaded from here. package bioconductor-complexheatmap ¶ Versions. If you have other chord diagram recommendations or requests, let me. I am wondering if anybody can guide me towards the correct package and / or code to create an output like this on R. Additional information about FFTs, and the FFTrees package can be found at Phillips, Neth, Woike & Gaissmaier, 2017. drawing points and lines). I chose R, because it is one of the most popular free statistical software packages around. The header at the top lists the available environments and the left column describes the name and summary of the library. The goal of this package is to interface a tidy data frame with this powerful tool. ggbio is a package build on top of ggplot2() to visualize easily genomic data. However, it would be a good challenge if we can replicate this visual in R using the Circlize Package. To demonstrate, I have put two demo files in my migest R package. Use it along with kableExtra and formattable to create attractive text tables with color. genomicLabels circos. However one drawback arises that circlize is completely blind to users' data so that one important thing is missing for the visualization which is the legend. Circlize comes with functions to render Circular layout which is an efficient way for the visualization of huge amounts of information. Gu, Thank you very much for the answer. Question: Is There Any R Or R / Bioconductor Package That Can Make Circular Plots Like Perl / Circos. The flexibility of this package is based on the usage of low-level graphics functions such that self-defined high-level graphics can be easily implemented by users for specific purposes. Bhatnagar, Yang, Khundrakpam, Evans, Blanchette, Bouchard, Greenwood (2017). Thumbs up for Circlize,. io Find an R package R language docs Run R in your browser R Notebooks. 2-1) Emacs mode for statistical programming and data analysis ess (18. For instance: Python programming with applications to bioinformatics - Introductory Python course; You may also look. Do not load pheatmap library. There are two packages that purport to do it, circlize and plotrix. Searching how to do draw chord diagrams in the Internet with ggplot2 I found a very-easy-to-use package called circlize which does exactly that. 0), xtable, pbapply Suggests. circlize package is built in the R base graphic system which is not straightforward to define a length with absolute units (e. With the circlize package, putting together a Chord Diagram is simple. Each cell is filled with a numeric value specifying the flow strength. It provides a range of new functionality that can be added to the plot object in order to customize how it should change with time. Here this package provides an implementation of circular layout generation in R as well as an enhancement of available software. In R, the circlize package is the best option to build it. Please anyone help me > in writing the code and making the plot. Any help will be highly > appreciated. Guy gives other several examples (with R code) of creating such " circular migration flow plots " on his blog. Line data was prepared by ordering the data frame in descending order. I have seen lots of G-G diagrams, though (mainly for motorcycle performance stuff ). An R package to perform LPUE standardization and stock assessment of the English Channel cuttlefish stock using a two-stage biomass model cvAUC Cross-Validated Area Under the ROC Curve Confidence Intervals. [R] Correlation heatmap with "corrplot" package [R] Vertex Contraction with "igraph" package [R] Multilayer Network with "RCytoscape" package [R] Circular Graph with "circlize" package; Recent Comments Archives. View source: R/circlize. I have a dataframe containing cars with four columns. Here the circlize package provides an implementation of circular layout generation in R as well as an enhancement of available software. It provides a range of new functionality that can be added to the plot object in order to customize how it should change with time. Also check out the chorddiag package on github. This type of plot is also sometimes called fan tree plot (although the name fan-plot is also used for a different plot in time series analysis), radial tree plot, polar tree plot, circular tree plot, and probably other names as well. In each chapter, we load the necessary packages with the library() or require() function when we use the. 21; 조선일보 크롤링 R코드 스케치 2017. [email protected] I put a feature request for this on the ggplot2 github issues. For seminal papers on FFTs, consult Martignon, Katsikopoulos & Woike, 2008 and Martignon, Vitouch, Takezawa & Forster, 2003. It provides highly dynamic and interactive graphics such as tours, as well as familiar graphics such as the scatterplot, barchart and parallel coordinates plots. Software Packages in "buster", Subsection gnu-r elpa-ess (18. Project Participants. genomicDensity circos. Register; Log in; Entries feed; Comments feed; WordPress. You can use the powerful R programming language to create visuals in the Power BI service. Moreover, it presents the results in a standardised way (pdf report). A list of package vignettes built from knitr on CRAN - readme. Some of them are great and you should definitely use them for well established types of figures. These functions generate and output plots using the ggplot2 and other R packages for aesthetics including: ggthemes , ComplexHeatmap , circlize , RColorBrewer and theme. Aside from R base graphics, a ggplot2 dendrogram may be created using the as. Please anyone help me > in writing the code and making the plot. circlize package: different font size for axis labels. Here the circlize package provides an implementation of circular layout generation in R as well as an enhancement of available software. Pi an experiment with circlize package. The documentation on circlize was extremely helpful to get me started! Below is the code I wrote for now, so I can remember what I have done in case I want to utilize circlize packages. an R/shiny application for creation of Circos plot interactively http://150. In circlize: Circular Visualization. July 2014; Categories. 0/ 2003-06-17 12:46 - 1. p_install("dlpyr") it will install the “deployer” package from CRAN. phylo function). The cell is the place that allow us to plot graph inside. We used circlize CRAN package to represent significant CNV (resulting from GAIA analysis) and recurrent mutations (selecting curated genetic variations retrieved from TCGA that are identified in at least two tumor samples) in LGG. Again create your own function, my_kable_styling() to standardize the resulting output of these libraries. This is especially relevant for genomic data. 1/ 2003-10-24 14:23 - 1. Provide the factor vector, and the numeric values to use for the X axis. This type of plot is also sometimes called fan tree plot (although the name fan-plot is also used for a different plot in time series analysis), radial tree plot, polar tree plot, circular tree plot, and probably other names as well. Cytoscape introduction! and communicate through R with RCy3 Package; Bonus. This is the repository for the Shiny application presented in "shinyCircos: an R/Shiny application for interactive creation of Circos plot" (Yu et al. One important advantage for the implementation in R is that R is an ideal environment which provides seamless connection between data analysis and data visualization. The flexibility of this package is based. R: A language and environment for statistical computing. Circlize comes with functions to render Circular layout which is an efficient way for the visualization of huge amounts of information. You can subdue the message using circos. Metformin is widely used in the treatment of type 2 diabetes (T2D), but its mechanism of action is poorly defined. If the R package GWASTools has not yet been installed on your computer, install the R package using the commands below. The XPI program was developed to quantify parallel reaction monitoring (PRM) data of stable isotope labeled peptides. The plot can be made using the circlize_dendrogram function (allowing for a much more refined control over the "fan" layout of the plot. 1/ 2002-10-15 15:06 - 1. 1BestCsharp blog 4,822,867 views. 8, License: MIT + file LICENSE Community examples. XINA imports these R packages: mclust, stringr, plyr, circlize, alluvial, ggplot2, RColorBrewer, graphics, gridExtra, igraph, STRINGdb, Biobase. This package aims to implement circular layout in R. You can use the powerful R programming language to create visuals in the Power BI service. 0), xtable, pbapply Suggests: randomForest, e1071 License: GPL (>= 2) Package: abbyyR Version: 0. 5281/zenodo. ComplexHeatmap is only available in the devel version of Bioconductor. arrow circos. Want to Create a Circular Heat Map. {"api_uri":"/api/packages/circlize","uri":"/packages/circlize","name":"circlize","created_at":"2016-06-06T11:13:08. Creating animated chord diagrams using circlize (chord diagrams), tweenr, magick (gifs) and tidyverse (data manipulations) Close. An R package to perform LPUE standardization and stock assessment of the English Channel cuttlefish stock using a two-stage biomass model cvAUC Cross-Validated Area Under the ROC Curve Confidence Intervals. bar, box, line, scatter, heat). 0/ 2002-04-28 08:31 - 1. By default, only ticks which are drawn from points within the plot region (up to a tolerance for rounding error) are plotted, but the ticks and their labels may well extend outside the plot region. After you run the PLINK association analysis, switch to R. Bioinformatics. If you have other chord diagram recommendations or requests, let me. 0 Depends: R (>= 2. The circos plots were generated using the R package circlize 115. As I did before, I used circlize package, which implements in R the features of Circos, a software to create stunning circular visualizations. 0 - Estimate Copy Number Aberrations (CNA) in Cancer Samples. In this case, you are responsible for configuring the R engine (i. Hadley Wickham创建的可视化包ggplot2可以流畅地进行优美的可视化，但是如果要通过ggplot2定制一套图形，尤其是适用于杂志期刊等出版物的图形，对于那些没有深入了解ggplot2的人来说就有点困难了，ggplot2的部分语法是很晦涩的。为此Alboukadel Kassambara创建了基于ggplot2的可视化包ggpubr用于绘制符合出版物. Skip to content. Software Packages in "buster", Subsection gnu-r elpa-ess (18. One important advantage for the implementation in R is that R is an ideal environment which provides seamless connection between data analysis and data visualization. chordDiagram function, R package circlize. warning=FALSE) The second problem is a result of a recent update to the circlize package. Contribute to jokergoo/circlize_book development by creating an account on GitHub. Bioinformatics. You need to change the. 0), xtable, pbapply Suggests: randomForest, e1071 License: GPL (>= 2) Package: abbyyR Version: 0. io/ circlize包circlize包在德国癌症中心的华人博士Zuguang Gu开发的，有兴趣的可以去看看他的Github主页（http…. Skip to content. After your selection, the left panel is updated with potential connection partners, ranked by the STRINGdatabase score in decreasing order. The interactive output provides flow value information when hovered over the line. Package: A3 Title: Accurate, Adaptable, and Accessible Error Metrics for Predictive Models Version: 1. In this video I talk about what is a Chord Diagram, how to interpret it and create using R. R package version 1. 13 comments. 0/ 2003-06-17 12:46 - 1. TidyTuesday is a weekly podcast and community activity brought to you by the R4DS Online Learning Community. Here this package provides an implementation of circular layout generation in R as well as an enhancement of available software. Maybe start with reading through t. CRUK Summer School 2017 - Day 4 (SV bedpe format) into R. > suppressPackageStartupMessages(library(ComplexHeatmap)) > suppressPackageStartupMessages(library(circlize)) ## Create row. CRAN links CRAN homepage CRAN repository policy Submit a package. chromosomes). Gu, Thank you very much for the answer. The author has done an amazing job at explaining the package [5]. The final plot represents the first 2. Alternatively, use the “Packages”" tab in the bottom-right corner of the RStudio interface. Cultural Importance Indices: A Comparative Analysis Based on the Useful Wild Plants of Southern Cantabria (Northern Spain) 1. packages("circlize"). There are two packages that purport to do it, circlize and plotrix. XPI (The extracted PRM peak intensity) Description. Sander and Abel used them effectively in their representation of global migration flows which was published in the Science Magazine. A fundamental package for reproducible data analysis is rmarkdown, which lets you integrate R code and outputs into notebooks and dynamically-generated reports. It will even allow multiple arrows between two nodes. ===== # Create the data frame as above. Here this package provides an implementation of circular layout generation in R as well as an enhancement of available software. One important advantage for the implementation in R is that R is an ideal environment which provides seamless connection between data analysis and data visualization. 0 (8/19/2016). Use cutting-edge techniques with R, NLP and Machine Learning to model topics in text and build your own music recommendation system! This is part Two-B of a three-part tutorial series in which you will continue to use R to perform a variety of analytic tasks on a case study of musical lyrics by the legendary artist Prince, as well as other artists and authors. You start with a grid of images like this (Keith Haring's doodle). In this tutorial, we show what plots flavors may help in champions performances comparison, timeline visualization, player-to-player and player-to-tournament relationships. DataCamp created an infographic comparing SAS, R and SPSS. Such a CUDF document can then be passed to aspcud along with an optimization criteria to obtain a solution to the given package problem. The flexibility of this package is based on the usage of low-level graphics functions such that self-defined high-level graphics can be easily implemented by users for specific purposes. There are other reasons why a circular layout is advantageous, not the least being the fact that it is attractive. R provides package to handle big data (ff), allow parallelism, plot graphs (ggplot2), analyze data through different algorithm available (ABCp2 etc etc. Posts about migest written by Guy Abel. Episode 1: Nuclear Explosions August 27th, 2019 | 5 mins 52 secs. Here the circlize package provides an implementation of circular layout generation in R as well as an enhancement of available software. However, it would be a good challenge if we can replicate this visual in R using the Circlize Package. A Sankey Diagram is a visualisation technique that allows to display flows. In this case, you are responsible for configuring the R engine (i. R package. The adjacency matrix displays all origins in rows, and all destinations in columns. To use highlight. rm (list = ls ()) #очистить workspace. Genome level Trellis graph visualizes genomic data conditioned by genomic categories (e. circlize: Circular Visualization. In each chapter, we load the necessary packages with the library() or require() function when we use the. July 2014; Categories. 16; 벤다이어 그램 그리기 2017. 000 digits of Phi: You can hear an advancement of their new album here , which is called “Phi”. The plot is built using circlize R package. This is a short demonstration of visualizing events by time-of-day using ggplot2 and circular packages. There are so many amazing #rstats packages packages published these days. The XPI program was developed to quantify parallel reaction monitoring (PRM) data of stable isotope labeled peptides. clear circos. The 2 first columns contains information on car band and model owned and the next two columns to the brand and model the respondent migrated to. There are two packages that purport to do it, circlize and plotrix. 1 Installation and loading. Thumbs up for Circlize,. font` in `circos. However, later I discovered another site where you can download. Here the circlize package provides an implementation of circular layout generation in R as well as an enhancement of available software. After an adjacency matrix is created (you may download the example data to practice), and the “circlize” package is installed in R, follow the steps to generate a basic chord diagram:. March 28, 2014. RCircos package provides a simple and flexible way to make Circos 2D track plots with R and could be easily integrated into other R data processing and graphic manipulation pipelines for presenting large-scale multi-sample genomic research data. The 2 first columns contains information on car band and model owned and the next two columns to the brand and model the respondent migrated to. In efforts to develop more efficient software programs for generating circular plots, researchers have looked to the R package, a common environment for statistical computing and graphic visualization of large genomic data sets. 16; 벤다이어 그램 그리기 2017. Gu, Thank you very much for the answer. The circlize package from Zuguang Gu is fantastic for drawing chord plots, amongst other things. R Package Installation from Remote Repositories, Including 'GitHub' 2020-02-15 : RGoogleFit: R Interface to Google Fit API : 2020-02-15 : RWsearch: Lazy Search in R Packages, Task Views, CRAN, the Web. taoyan：R语言中文社区专栏作者，伪码农，R语言爱好者，爱开源。 个人博客: https://ytlogos. The data contains around 3 million rows of values corresponding to the chromosomal locations. # Since most of the figures are composed of points, lines and polygons, # we just need to implement low-level functions for drawing points, lines and polygons. 0/ 2003-10. Data was visualized using R packages ggplot2, Mapdeck, Circlize and ChordDiag - the latter two being multidisciplinary R packages originally used in the visualization of genetic data. This post explores creating Circos-style genomic data plots in R using R package circlize. axis circos. 2() [gplots R package]: Draws an enhanced heatmap compared to the R base function. The author has done an amazing job at explaining the package [5]. Plot a circlized dendrograms using the circlize package (must be installed for the function to work). , differential expression analysis, identifying. 2/ 2002-12-19 15:36 - 1. As a single data source is limited in its point of view, this provides more insight and the opportunity to investigate how the variables are interconnected. 10) Mass cytometry (CyTOF) uses heavy metal isotopes rather than fluorescent tags as reporters to label antibodies, thereby substantially decreasing spectral overlap and allowing for examination of over 50 parameters at the single cell level. Additional information about FFTs, and the FFTrees package can be found at Phillips, Neth, Woike & Gaissmaier, 2017. For processing in the OpenLand package, the original multi-year shape file was transformed into rasters and then saved as a 5-layer RasterStack (SaoLourencoBasin), available from a public repository (10. GNU R package providing routines for the logspline density estimation r-cran-loo (2. This can be time-consuming, though, and needed to change. GGobi is an open source visualization program for exploring high-dimensional data. 10) » science » paraview. Package: A3 Version: 1. Circular Migration Flow Plots in R. Please anyone help me in writing the code and making the plot. Fast LD computation from a VCF file using vcftools, bcftools and tomahawk. The R circlize package allows us to draw a chord diagram without much scripting in R. The R and Python graph galleries are 2 websites providing hundreds of chart example, always providing the reproducible code. Here we will perform alignment as if we do not have any labels (case 3), but we will use the labels after alignment to check its accuracy. The function is added to circlize very recently, you may update circlize to the newest version. Question: Circlize package ? 0. io Find an R package R language docs Run R in your browser R Notebooks. 0/ 2003-10. Three steps are required to build a circular plot:. To use highlight. axis circos. Mapdeck is an R package that allows the visualization of flow data on an interactive map, utilising the Mapbox GL and Deck. u/rharrington31. In addition, neither of them support plotmath expressions in text. Here's snippets of code I've used to create above. The power of the package is based on the implementation of basic low-level graphics functions (e. 6 days ago. This book is primarily about using R packages to analyze genomics data, therefore if you want to reproduce the analysis in this book you need to install the relevant packages in each chapter using install. # # Current there are following low-level graphic. 10) » science » paraview. Therefore, it is flexible to customize new types of graphics without difficulty. The list is subjective and intended only as a starting point. Here this package provides an implementation of circular layout generation in R as well as an enhancement of available software. After that, we can use the packages on R Console. Prizes on offer for the best R graphic mapping the locations of R user groups. For the estimates of flows by regions, users can hopefully replicate the plots (so long as the circlize and plyr packages are installed… hit enter a couple of times. drawing points and lines). You can (1) Adjust a tree's graphical parameters - the color, size, type, etc of its branches, nodes and labels. Pairwise correlations between clusters were visualized as chord diagrams in R using the circlize package (Gu et al. Fast LD computation from VCF files using Tomahawk. As a single data source is limited in its point of view, this provides more insight and the opportunity to investigate how the variables are interconnected. UpSetR: an R package for the visualization of intersecting sets and their properties Jake R Conway Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA. I have a table consisting of different rows with repeated names and different columns. 上一篇: c – 我的shared_ptr声明中的错误是什么？ 下一篇: Android,日历,将RRULE添加到事件永远不会有效. ggdend function. In R, circular plots are made using the circlize package. Carries out mapping between assorted color spaces including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar CIELAB. Here I will demonstrate. This post follows the previous introduction to the circlize package. If you use the simple. Pathway enrichment and visualization 21,114 were conducted using the R package ReactomePA 79.