{"id":22313920,"url":"https://github.com/ctb/2020-stacked-dot-plots","last_synced_at":"2026-03-19T22:23:37.442Z","repository":{"id":56097643,"uuid":"315069227","full_name":"ctb/2020-stacked-dot-plots","owner":"ctb","description":null,"archived":false,"fork":false,"pushed_at":"2020-12-01T14:39:47.000Z","size":8929,"stargazers_count":2,"open_issues_count":1,"forks_count":1,"subscribers_count":3,"default_branch":"latest","last_synced_at":"2025-01-30T23:47:56.844Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"HTML","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-3-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/ctb.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}},"created_at":"2020-11-22T15:29:09.000Z","updated_at":"2023-05-25T15:27:40.000Z","dependencies_parsed_at":"2022-08-15T13:10:20.105Z","dependency_job_id":null,"html_url":"https://github.com/ctb/2020-stacked-dot-plots","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ctb%2F2020-stacked-dot-plots","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ctb%2F2020-stacked-dot-plots/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ctb%2F2020-stacked-dot-plots/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ctb%2F2020-stacked-dot-plots/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ctb","download_url":"https://codeload.github.com/ctb/2020-stacked-dot-plots/tar.gz/refs/heads/latest","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":245579416,"owners_count":20638675,"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":"2024-12-03T22:08:31.870Z","updated_at":"2026-01-06T01:45:44.641Z","avatar_url":"https://github.com/ctb.png","language":"HTML","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Stacked dot plots\n\n[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/ctb/2020-stacked-dot-plots/latest?filepath=examples.ipynb)\n\n## an exploratory repository\n\nRun [mashmap](https://github.com/marbl/MashMap) or\n[nucmer](https://github.com/mummer4/mummer) to find alignments between\na query genome and one or more target genomes; plot in a few different\nways.\n\nSee [the source in `alignplot.py`](./alignplot.py) and\n[the `examples` notebook](./examples.ipynb) for more info.\n\nThe first two examples below are of \"non-stacked\" dotplots, as in,\nthey are just pairwise dotplots.\n\nThe third example below \"stacks\" the dotplots on the x axis, so that you can\nsee two dotplots against the same query genome in the query genome\ncoordinates, but with the target genomes split out.\n\nThe fourth and fifth examples below are in a \"sloped alignment\"\nreporting format that I used extensively in\n[a 2005 paper](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-6-70), and resurrected here in matplotlib-land.\n\n## installation and running\n\nFor now, if you want to try this out for yourself --\n\n* you'll need python3 installed\n* you'll need mummer4 and/or mashmap installed, along with matplotlib and numpy.\n* you'll need to put genomes somewhere (e.g. the `genomes/` directory)\n* you can add names or replace names in info.csv\n* see [the source in `alignplot.py`](./alignplot.py) and\n[the `examples` notebook](./examples.ipynb) for more info on actually running.\n\n(More work to be done here -- will binderize eventually :)\n\n## examples\n\n### A gallery\n\nPlease see\n[the rendered examples](https://ctb.github.io/2020-stacked-dot-plots/examples.html)\nfor a gallery of comparisons along with some basic code. Some example figures\nare below.\n\n### Shared sequences (contamination?) between two Genbank genomes.\n\nHere, the Rokubacterium (red, x axis) is probably contaminated by sequences\nfrom the Acidobacterium (y axis coordinates).\n\n![](images/example1.png)\n\n### Shared sequences between a TARA MAG and a Genbank genome.\n\nThe TARA binned genome/MAG is on the y axis, the Genbank genome is on x in\nred.\n\n![](images/example2.png)\n\n### Shared sequences between a TARA MAG and two Genbank genomes.\n\nThe TARA binned genome/MAG is on the y axis, the first Genbank genome\nis on x in red, the second is on x in blue.\n\n![](images/example3.png)\n\n### A small set of shared sequences between two genbank genomes\n\nComparing `GCF_001683825.1`, a Flavobacterium, with `GCF_000181835.1`,\na strain of *Bacillus anthracis*.\n\n![](images/example4.png)\n\n![](images/example5.png)\n\n## contact\n\nTitus Brown, titus@idyll.org\n\nAll code here is Copyright: 2020, The Regents of the University of\nCalifornia. It is freely available for use and reuse under the BSD\n3-Clause license; please see the `LICENSE` file for more info.\n\nCTB Nov 2020\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fctb%2F2020-stacked-dot-plots","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fctb%2F2020-stacked-dot-plots","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fctb%2F2020-stacked-dot-plots/lists"}