{"id":23340556,"url":"https://github.com/loukesio/ggvolc","last_synced_at":"2025-09-02T03:41:26.146Z","repository":{"id":187667897,"uuid":"677343283","full_name":"loukesio/ggvolc","owner":"loukesio","description":"𝐠𝐠𝐯𝐨𝐥𝐜 effortlessly translates differential expression datasets and RNAseq data into informative volcano plots. Highlight genes of interest with unprecedented ease. With just a single line of code, visualize complex datasets, gaining deeper insights and simplifying data representation","archived":false,"fork":false,"pushed_at":"2023-10-14T09:38:55.000Z","size":5794,"stargazers_count":64,"open_issues_count":1,"forks_count":4,"subscribers_count":4,"default_branch":"master","last_synced_at":"2025-04-10T00:14:20.597Z","etag":null,"topics":["bioinformatics","data-science","data-visualization","gro-seq","rna-seq"],"latest_commit_sha":null,"homepage":"","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/loukesio.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2023-08-11T10:34:11.000Z","updated_at":"2025-03-10T03:20:13.000Z","dependencies_parsed_at":null,"dependency_job_id":"3feab9dc-5b47-486f-9667-80c6b2581fe6","html_url":"https://github.com/loukesio/ggvolc","commit_stats":null,"previous_names":["loukesio/ggvolc"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/loukesio/ggvolc","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/loukesio%2Fggvolc","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/loukesio%2Fggvolc/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/loukesio%2Fggvolc/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/loukesio%2Fggvolc/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/loukesio","download_url":"https://codeload.github.com/loukesio/ggvolc/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/loukesio%2Fggvolc/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":273226944,"owners_count":25067634,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-09-02T02:00:09.530Z","response_time":77,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["bioinformatics","data-science","data-visualization","gro-seq","rna-seq"],"created_at":"2024-12-21T04:33:30.191Z","updated_at":"2025-09-02T03:41:26.092Z","avatar_url":"https://github.com/loukesio.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![lifecycle](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://www.tidyverse.org/lifecycle/#experimental)\n[![CRAN\\_Status\\_Badge](http://www.r-pkg.org/badges/version/icon)](https://cran.r-project.org/package=icons)\n[![License: MIT](https://img.shields.io/badge/License-MIT-green.svg)](https://opensource.org/licenses/MIT)\n\n## Install the `ggvolc` package\nInstall the package using the following commands  \u003cimg align=\"right\" src=\"logo/ggvolc_logo.png\" width=400\u003e\n\n```r\n# for now, you can install the developmental version of ltc\n# first you need to install the devtools package \n# in case you have not already installed\ninstall.packages(\"devtools\") \n# and load it\nlibrary(devtools)\n\n# then you can install the dev version of the ltc\ndevtools::install_github(\"loukesio/ggvolc\")\n# and load it\nlibrary(ggvolc)\n```\n\n\n\u003cbr\u003e\n\n\n### How do I start?\nLoad the library and explore the example datasets! \n\n```console\nlibrary(ggvolc)\n#\u003e Welcome to ggvolc version 0.1.0 !\n#\u003e \n#\u003e                                 888\n#\u003e                                 888\n#\u003e                                 888\n#\u003e  .d88b.   .d88b.  888  888  .d88b.  888  .d8888b\n#\u003e d88P\"88b d88P\"88b 888  888 d88\"\"88b 888 d88P\"\n#\u003e 888  888 888  888 Y88  88P 888  888 888 888\n#\u003e Y88b 888 Y88b 888  Y8bd8P  Y88..88P 888 Y88b.\n#\u003e  \"Y88888  \"Y88888   Y88P    \"Y88P\"  888  \"Y8888P\n#\u003e      888      888\n#\u003e Y8b d88P Y8b d88P\n#\u003e  \"Y88P\"   \"Y88P\"\n#\u003e\n```\n```\ndata(all_genes)     # data.frame that contains the output of differentially expressed genes\nhead(all_genes,5)   # have a look at the first 5 rows \n\n#\u003e       genes   baseMean log2FoldChange     lfcSE       stat       pvalue\n#\u003e 1      GCR1  7201.5782       2.244064 0.2004959  11.192564 4.434241e-29\n#\u003e 2     OPI10  1009.4171      -2.257454 0.2096469 -10.767889 4.880607e-27\n#\u003e 3      AGA2   249.1173       3.829474 0.3623263  10.569132 4.143136e-26\n#\u003e 4 FIM1_1376  5237.5035       2.550409 0.2560379   9.961059 2.256459e-23\n#\u003e 5      HMG1 10838.1037       2.214300 0.2229065   9.933763 2.968371e-23\n#\u003e           padj\n#\u003e 1 2.153711e-25\n#\u003e 2 1.185255e-23\n#\u003e 3 6.707736e-23\n#\u003e 4 2.739905e-20\n#\u003e 5 2.883475e-20\n\n\ndata(attention_genes)     # here is a data.frame with genes that I want to mention to the volcano plot\nhead(attention_genes,5)   # have a look at the first five rows \n#\u003e     genes   baseMean log2FoldChange     lfcSE      stat       pvalue\n#\u003e 1   THI13   480.5194       1.585811 0.5219706  3.038122 2.380572e-03\n#\u003e 2    FBP1 22710.8428      -2.366733 0.3533032 -6.698871 2.100354e-11\n#\u003e 3    TRA1  4491.1343      -1.410696 0.4384316 -3.217595 1.292700e-03\n#\u003e 4 YDR222W   591.2289      -4.045918 0.9133881 -4.429572 9.442026e-06\n#\u003e 5    BRL1  4434.7712       2.375919 0.5037264  4.716686 2.397176e-06\n#\u003e           padj\n#\u003e 1 1.371582e-02\n#\u003e 2 3.290780e-09\n#\u003e 3 8.565681e-03\n#\u003e 4 1.819838e-04\n#\u003e 5 5.850796e-05\n```\n\u003csup\u003eCreated on 2023-08-11 with [reprex v2.0.2](https://reprex.tidyverse.org)\u003c/sup\u003e\n\n\n### 1. Plot a simple volcano plot! \n\nInstall the package using the following commands \n\n```\nggvolc(all_genes)\n```\n\u003cimg align=\"center\" src=\"logo/plot1_basic.png\" width=750\u003e\n\n### 2. Add the genes of attention.\n\n```\nggvolc(all_genes, attention_genes)\n```\n\u003cimg align=\"center\" src=\"logo/plot2_AttentionGenes.png\" width=750\u003e\n\n### 3. Add segments to indicate areas of significance.\n\n```\nggvolc(all_genes, attention_genes, add_seg = TRUE) +\n  labs(title=\"Add segments of significance\")\n```\n\u003cimg align=\"center\" src=\"logo/plot3_Segments.png\" width=750\u003e\n\n### 4. Indicate the size of point based on the log2FoldChange column.\n\n```\nggvolc(all_genes, attention_genes, size_var = \"log2FoldChange\", add_seg = TRUE)\n```\n\u003cimg align=\"center\" src=\"logo/plot4_scale_Log2foldChange.png\" width=750\u003e\n\n###  5. Indicate the size of the point based on the pvalue.\n\n```\nggvolc(all_genes, attention_genes, size_var = \"pvalue\", add_seg = TRUE)\n```\n\u003cimg align=\"center\" src=\"logo/plot5_scalePvalue.png\" width=750\u003e\n\n###  6. Add a table with the genes of interest.\n\n```\nplot \u003c- ggvolc(all_genes, attention_genes, add_seg = TRUE) +\n  labs(title=\"Add a table with the genes of interest\")\n\nplot %\u003e%\n  genes_table(attention_genes)\n```\n\n\u003cimg align=\"center\" src=\"logo/plot6_adding_table.png\" width=750\u003e\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Floukesio%2Fggvolc","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Floukesio%2Fggvolc","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Floukesio%2Fggvolc/lists"}