{"id":23191923,"url":"https://github.com/moold/paf2dotplot","last_synced_at":"2025-06-17T20:41:33.593Z","repository":{"id":103035771,"uuid":"422520969","full_name":"moold/paf2dotplot","owner":"moold","description":"Draw a dot plot from a paf alignment","archived":false,"fork":false,"pushed_at":"2024-12-20T07:07:24.000Z","size":712,"stargazers_count":26,"open_issues_count":0,"forks_count":4,"subscribers_count":3,"default_branch":"main","last_synced_at":"2025-04-06T10:42:51.792Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/moold.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}},"created_at":"2021-10-29T09:44:12.000Z","updated_at":"2025-03-05T11:40:44.000Z","dependencies_parsed_at":"2023-03-13T15:09:42.112Z","dependency_job_id":null,"html_url":"https://github.com/moold/paf2dotplot","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/moold/paf2dotplot","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/moold%2Fpaf2dotplot","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/moold%2Fpaf2dotplot/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/moold%2Fpaf2dotplot/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/moold%2Fpaf2dotplot/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/moold","download_url":"https://codeload.github.com/moold/paf2dotplot/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/moold%2Fpaf2dotplot/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":260439068,"owners_count":23009269,"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","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":[],"created_at":"2024-12-18T12:19:26.329Z","updated_at":"2025-06-17T20:41:28.572Z","avatar_url":"https://github.com/moold.png","language":"R","funding_links":[],"categories":["Comparative"],"sub_categories":[],"readme":"# Paf2dotplot\nDraw a dot plot from a paf alignment (usually generated by [minimap2](https://github.com/lh3/minimap2)). Paf2dotplot is adapted from [dotPlotly](https://github.com/tpoorten/dotPlotly/), but it has some extra features and parameters, for details, just have a try!\n\n## Dependencies  \nThe script requires two R packages: `optparse`, `ggplot2`\n\n## Installation  \n```sh\n# download\ngit clone https://github.com/moold/paf2dotplot.git\n# install R packages\nR --slave -e 'install.packages(c(\"optparse\", \"ggplot2\"))'\n```\n\n## Usage\n```sh\n# do asm-to-ref mapping\nminimap2 -cx asm10 asm1.fa asm2.fa \u003e aln.paf\n# draw\n./paf2dotplot.r -f -b aln.paf\n```\nThis will generate a result file `aln.paf.pdf` in the current directory. You can use [ImageMagick](https://github.com/ImageMagick/ImageMagick) command to do some format conversion or modification.\nHere are two example images generated by Paf2dotplot:  \n![1-to-many](./example/test1.paf.png) ![many-to-many](./example/test2.paf.png)\n\n## Parameters\nUse `./paf2dotplot.r -h` to see options.\n\n\n\n\n\n\t","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmoold%2Fpaf2dotplot","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmoold%2Fpaf2dotplot","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmoold%2Fpaf2dotplot/lists"}