{ "_id": "6a265f93794753ddbc3e5297", "Package": "idiogramFISH", "Title": "Shiny App. Idiograms with Marks and Karyotype Indices", "Version": "2.0.13.9000", "Date": "2024-06-06", "Authors@R": "c(person(\"Fernando\", \"Roa\", email = \"froao@unal.edu.co\", role = c(\"aut\", \"cre\") ), \nperson(given=\"Mariana PC Telles\", email = \"\", role = c(\"ctb\"))\n)", "Description": "Plot idiograms of karyotypes, plasmids, circular chr.\nhaving a set of data.frames for chromosome data and optionally\nmark data. Two styles of chromosomes can be used: without or\nwith visible chromatids. Supports micrometers, cM and Mb or any\nunit. Three styles of centromeres are available: triangle,\nrounded and inProtein; and six styles of marks are available:\nsquare (squareLeft), dots, cM (cMLeft), cenStyle, upArrow\n(downArrow), exProtein (inProtein); its legend (label) can be\ndrawn inline or to the right of karyotypes. Idiograms can also\nbe plotted in concentric circles. It is possible to calculate\nchromosome indices by Levan et al. (1964)\n, karyotype indices of\nWatanabe et al. (1999) and\nRomero-Zarco (1986) and classify\nchromosomes by morphology Guerra (1986) and Levan et al.\n(1964).", "License": "GPL (>= 2)", "Encoding": "UTF-8", "LazyData": "true", "VignetteBuilder": "rmdformats, knitr, kableExtra, rmarkdown, RCurl,\nrvcheck, badger, rentrez", "SystemRequirements": "pandoc (>= 3.2)", "URL": "https://ferroao.gitlab.io/manualidiogramfish/,\nhttps://ferroao.gitlab.io/idiogramfishhelppages", "BugReports": "https://gitlab.com/ferroao/idiogramFISH/-/issues", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.2.3", "Config/pak/sysreqs": "libicu-dev", "Repository": "https://fernandoroa.r-universe.dev", "Date/Publication": "2024-06-06 15:50:17 UTC", "RemoteUrl": "https://gitlab.com/ferroao/idiogramfish", "RemoteRef": "HEAD", "RemoteSha": "8f7ee88135dcfad5085ed79d292f98780c8a929d", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-07 07:13:26 UTC", "User": "root" }, "Author": "Fernando Roa [aut, cre],\nMariana PC Telles [ctb]", "Maintainer": "Fernando Roa ", "MD5sum": "c0758fab2b22148b222bb9e34b52ffc9", "_user": "fernandoroa", "_type": "src", "_file": "idiogramFISH_2.0.13.9000.tar.gz", "_fileid": "54451b77492ec5b7ddf8bd38bd1bc1eaa2eb8a468a00d5c8a55454f2edfb89c7", "_filesize": 16300210, "_sha256": "54451b77492ec5b7ddf8bd38bd1bc1eaa2eb8a468a00d5c8a55454f2edfb89c7", "_created": "2026-06-07T07:13:26.000Z", "_published": "2026-06-08T06:22:11.467Z", "_distro": "noble", "_jobs": [ { "job": 80033736540, "time": 192, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7461797673" }, { "job": 80033736722, "time": 225, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7461801493" }, { "job": 80033736205, "time": 124, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7472915589" }, { "job": 80033736569, "time": 136, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7461804166" }, { "job": 80033736063, "time": 272, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7461775531" }, { "job": 80033736641, "time": 153, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7461792805" }, { "job": 80033736653, "time": 153, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7461792776" }, { "job": 80033736790, "time": 154, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7461792871" }, { "job": 80033736916, "time": 144, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7461791734" } ], "_buildurl": "https://github.com/r-universe/fernandoroa/actions/runs/27085741311", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://gitlab.com/ferroao/idiogramfish", "_commit": { "id": "8f7ee88135dcfad5085ed79d292f98780c8a929d", "author": "Fernando Roa ", "committer": "Fernando Roa ", "message": "Merge branch 'docs.update.06_2024' into 'master'\n\nDocs.update.06 2024\n\nSee merge request ferroao/idiogramFISH!10", "time": 1717689017 }, "_maintainer": { "name": "Fernando Roa", "email": "froao@unal.edu.co", "login": "fernandoroa", "description": "Shiny developer", "uuid": 98838147 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5", "role": "Depends" }, { "package": "rlang", "role": "Imports" }, { "package": "crayon", "role": "Imports" }, { "package": "plyr", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "scales", "role": "Imports" }, { "package": "rentrez", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "ggpubr", "role": "Suggests" }, { "package": "ggtree", "role": "Suggests" }, { "package": "phytools", "role": "Suggests" }, { "package": "treeio", "role": "Suggests" }, { "package": "rmdformats", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "kableExtra", "role": "Suggests" }, { "package": "rvcheck", "role": "Suggests" }, { "package": "badger", "role": 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{ "version": "1.16.6", "date": "2020-09-17" }, { "version": "1.16.7", "date": "2020-10-15" }, { "version": "1.16.8", "date": "2020-12-01" }, { "version": "2.0.0", "date": "2021-02-06" }, { "version": "2.0.2", "date": "2021-03-04" }, { "version": "2.0.3", "date": "2021-04-13" }, { "version": "2.0.4", "date": "2021-04-25" }, { "version": "2.0.5", "date": "2021-05-21" }, { "version": "2.0.6", "date": "2021-09-30" }, { "version": "2.0.8", "date": "2022-01-11" }, { "version": "2.0.9", "date": "2022-09-16" }, { "version": "2.0.10", "date": "2023-04-05" }, { "version": "2.0.11", "date": "2023-04-11" }, { "version": "2.0.12", "date": "2023-06-08" }, { "version": "2.0.13", "date": "2023-08-24" } ], "_exports": [ "armRatioCI", "asymmetry", "asymmetryA2", "citrusMarkPos", "citrusSize", "fillMarkInfo", "fillMarkInfo2", "genBankReadIF", "make.uniqueIF", "makedfMarkColorMycolors", "mapGGChr", "mapGGChrMark", "markOverCMA", "namesToColumns", "perMark", "plotIdiograms", "posCalc", "robert", "runBoard", "swapChrRegionDfSizeAndMarks" ], "_datasets": [ { "name": "allChrSizeSample", "title": "Chr. basic data Monocen.", "object": "allChrSizeSample", "class": [ "data.frame" ], "fields": [ "chrName", "shortArmSize", "longArmSize", "OTU" ], "rows": 75, "table": true, "tojson": true }, { "name": "allMarksSample", "title": "Mark Positional data - monocentrics", "object": "allMarksSample", "class": [ "data.frame" ], "fields": [ "chrName", "markName", "OTU", "chrRegion", "markSize", "markDistCen" ], "rows": 43, "table": true, "tojson": true }, { "name": "bigdfChrSizeHolo", "title": "Chr. basic data Holo.", "object": "bigdfChrSizeHolo", "class": [ "data.frame" ], "fields": [ "OTU", "chrName", "chrSize" ], "rows": 12, "table": true, "tojson": true }, { "name": "bigdfMarkPosHolo", "title": "Mark Positional data - Holocen.", "object": "bigdfMarkPosHolo", "class": [ "data.frame" ], "fields": [ "OTU", "chrName", "markName", "markPos", "markSize" ], "rows": 6, "table": true, "tojson": true }, { "name": "bigdfMarkPosHolo2", "title": "Mark Positional data - Holocen.", "object": "bigdfMarkPosHolo2", "class": [ "data.frame" ], "fields": [ "OTU", "chrName", "markName", "markPos", "markSize", "chrRegion" ], "rows": 18, "table": true, "tojson": true }, { "name": "bigdfOfChrSize", "title": "Chr. basic data Monocen.", "object": "bigdfOfChrSize", "class": [ "data.frame" ], "fields": [ "OTU", "chrName", "shortArmSize", "longArmSize" ], "rows": 50, "table": true, "tojson": true }, { "name": "bigdfOfChrSize3Mb", "title": "Chr. basic data Holo.", "object": "bigdfOfChrSize3Mb", "class": [ "data.frame" ], "fields": [ "OTU", "chrName", "chrSize" ], "rows": 14, "table": true, "tojson": true }, { "name": "bigdfOfMarks", "title": "Mark Positional data - monocentrics", "object": "bigdfOfMarks", "class": [ "data.frame" ], "fields": [ "OTU", "chrName", "markName", "chrRegion", "markDistCen", "markSize" ], "rows": 12, "table": true, "tojson": true }, { "name": "bigdfOfMarks3Mb", "title": "Mark Positional data - Holocen.", "object": "bigdfOfMarks3Mb", "class": [ "data.frame" ], "fields": [ "OTU", "chrName", "markName", "markPos", "markSize" ], "rows": 12, "table": true, "tojson": true }, { "name": "dfAlloParentMarks", "title": "Mark Positional data - monocentrics", "object": "dfAlloParentMarks", "class": [ "data.frame" ], "fields": [ "OTU", "chrName", "markName", "chrRegion" ], "rows": 16, "table": true, "tojson": true }, { "name": "dfAlloParentMarksHolo", "title": "Mark Positional data - Holocen.", "object": "dfAlloParentMarksHolo", "class": [ "data.frame" ], "fields": [ "OTU", "chrName", "markName", "chrRegion" ], "rows": 13, "table": true, "tojson": true }, { "name": "dfChrSizeHolo", "title": "Chr. basic data Holo.", "object": "dfChrSizeHolo", "class": [ "data.frame" ], "fields": [ "chrName", "chrSize" ], "rows": 4, "table": true, "tojson": true }, { "name": "dfMarkColor", "title": "Mark characteristics", "object": "dfMarkColor", "class": [ "data.frame" ], "fields": [ "markName", "markColor", "style" ], "rows": 4, "table": true, "tojson": true }, { "name": "dfMarkColor5S25S", "title": "Mark characteristics", "object": "dfMarkColor5S25S", "class": [ "data.frame" ], "fields": [ "markName", "markColor", "style" ], "rows": 2, "table": true, "tojson": true }, { "name": "dfMarkColorIn", "title": "Mark characteristics", "object": "dfMarkColorIn", "class": [ "data.frame" ], "fields": [ "markName", "markColor", "style" ], "rows": 5, "table": true, "tojson": true }, { "name": "dfMarkPosHolo", "title": "Mark Positional data - Holocen.", "object": "dfMarkPosHolo", "class": [ "data.frame" ], "fields": [ "chrName", "markName", "markPos", "markSize" ], "rows": 6, "table": true, "tojson": true }, { "name": "dfOfChrSize", "title": "Chr. basic data Monocen.", "object": "dfOfChrSize", "class": [ "data.frame" ], "fields": [ "chrName", "shortArmSize", "longArmSize" ], "rows": 4, "table": true, "tojson": true }, { "name": "dfOfMarks", "title": "Mark Positional data - monocentrics", "object": "dfOfMarks", "class": [ "data.frame" ], "fields": [ "chrName", "markName", "chrRegion", "markSize", "markDistCen" ], "rows": 4, "table": true, "tojson": true }, { "name": "dfOfMarks2", "title": "Mark Positional data - monocentrics", "object": "dfOfMarks2", "class": [ "data.frame" ], "fields": [ "chrName", "markName", "chrRegion", "markSize", "markDistCen" ], "rows": 6, "table": true, "tojson": true }, { "name": "humChr", "title": "Chr. basic data Monocen.", "object": "humChr", "class": [ "data.frame" ], "fields": [ "chrName", "group", "shortArmSize", "longArmSize" ], "rows": 24, "table": true, "tojson": true }, { "name": "humMarkColor", "title": "Mark characteristics", "object": "humMarkColor", "class": [ "data.frame" ], "fields": [ "markName", "markColor", "style" ], "rows": 395, "table": true, "tojson": true }, { "name": "humMarkPos", "title": "Mark Positional data - monocentrics", "object": "humMarkPos", "class": [ "data.frame" ], "fields": [ "chrName", "markName", "chrRegion", "markDistCen", "markSize" ], "rows": 395, "table": true, "tojson": true }, { "name": "mydfMaColor", "title": "Mark characteristics", "object": "mydfMaColor", "class": [ "data.frame" ], "fields": [ "markName", "markColor", "style" ], "rows": 6, "table": true, "tojson": true }, { "name": "parentalAndHybChrSize", "title": "Chr. basic data Monocen.", "object": "parentalAndHybChrSize", "class": [ "data.frame" ], "fields": [ "OTU", "chrName", "shortArmSize", "longArmSize" ], "rows": 13, "table": true, "tojson": true }, { "name": "parentalAndHybHoloChrSize", "title": "Chr. basic data Holo.", "object": "parentalAndHybHoloChrSize", "class": [ "data.frame" ], "fields": [ "OTU", "chrName", "chrSize" ], "rows": 13, "table": true, "tojson": true }, { "name": "traspadf", "title": "Chr. basic data Monocen.", "object": "traspadf", "class": [ "data.frame" ], "fields": [ "chrName", "shortArmSize", "longArmSize", "OTU" ], "rows": 12, "table": true, "tojson": true }, { "name": "traspaMarks", "title": "Mark Positional data - monocentrics", "object": "traspaMarks", "class": [ "data.frame" ], "fields": [ "chrName", "chrRegion", "distcen", "markName", "markDistCen", "markSize", "OTU" ], "rows": 18, "table": true, "tojson": true } ], "_help": [ { "page": "armRatioCI", "title": "FUNCTIONS armRatioCI and swapChrRegionDfSizeAndMarks.", "topics": [ "armRatioCI", "swapChrRegionDfSizeAndMarks" ] }, { "page": "asymmetry", "title": "FUNCTIONS asymmetry and asymmetryA2.", "topics": [ "asymmetry", "asymmetryA2" ] }, { "page": "chrbasicdataHolo", "title": "Chr. basic data Holo.", "topics": [ "bigdfChrSizeHolo", "bigdfOfChrSize3Mb", "chrbasicdataHolo", "dfChrSizeHolo", "parentalAndHybHoloChrSize" ] }, { "page": "chrbasicdatamono", "title": "Chr. basic data Monocen.", "topics": [ "allChrSizeSample", "bigdfOfChrSize", "chrbasicdatamono", "dfOfChrSize", "humChr", "parentalAndHybChrSize", "traspadf" ] }, { "page": "citrusSize", "title": "FUNCTIONS: citrusSize, citrusMarkPos, markOverCMA", "topics": [ "citrusMarkPos", "citrusSize", "markOverCMA" ] }, { "page": "dfMarkStyle", "title": "Mark characteristics", "topics": [ "dfMarkColor", "dfMarkColor5S25S", "dfMarkColorIn", "dfMarkStyle", "humMarkColor", "mydfMaColor" ] }, { "page": "genBankReadIF", "title": "FUNCTION genBankReadIF", "topics": [ "genBankReadIF" ] }, { "page": "make.uniqueIF", "title": "FUNCTION make.uniqueIF", "topics": [ "make.uniqueIF" ] }, { "page": "makedfMarkColorMycolors", "title": "FUNCTION to make a data.frame of Marks' characterisitcs", "topics": [ "makedfMarkColorMycolors" ] }, { "page": "mapGGChr", "title": "FUNCTIONS mapGGChr and mapGGChrMark (for ggplot)", "topics": [ "mapGGChr", "mapGGChrMark" ] }, { "page": "markdataholo", "title": "Mark Positional data - Holocen.", "topics": [ "bigdfMarkPosHolo", "bigdfMarkPosHolo2", "bigdfOfMarks3Mb", "dfAlloParentMarksHolo", "dfMarkPosHolo", "markdataholo" ] }, { "page": "markposDFs", "title": "Mark Positional data - monocentrics", "topics": [ "allMarksSample", "bigdfOfMarks", "dfAlloParentMarks", "dfOfMarks", "dfOfMarks2", "humMarkPos", "markposDFs", "traspaMarks" ] }, { "page": "namesToColumns", "title": "FUNCTION that modifies marks' names into columns", "topics": [ "namesToColumns" ] }, { "page": "perMark", "title": "FUNCTION perMark", "topics": [ "perMark" ] }, { "page": "plotIdiograms", "title": "Plot idiograms of karyotypes/genomes with and without centromere", "topics": [ "plotIdiograms" ] }, { "page": "posCalc", "title": "FUNCTION posCalc and fillMarkInfo", "topics": [ "fillMarkInfo", "fillMarkInfo2", "posCalc" ] }, { "page": "robert", "title": "FUNCTION to produce a Robertsonian translocation", "topics": [ "robert" ] }, { "page": "runBoard", "title": "FUNCTION runBoard", "topics": [ "runBoard" ] } ], "_pkglogo": "https://gitlab.com/ferroao/idiogramfish/raw/HEAD/man/figures/logo.png", "_readme": "https://gitlab.com/ferroao/idiogramfish/raw/HEAD/README.md", "_rundeps": [ "cli", "cpp11", "crayon", "dplyr", "farver", 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