Package: idiogramFISH 2.0.13.9000
idiogramFISH: Shiny App. Idiograms with Marks and Karyotype Indices
Plot idiograms of karyotypes, plasmids, circular chr. having a set of data.frames for chromosome data and optionally mark data. Two styles of chromosomes can be used: without or with visible chromatids. Supports micrometers, cM and Mb or any unit. Three styles of centromeres are available: triangle, rounded and inProtein; and six styles of marks are available: square (squareLeft), dots, cM (cMLeft), cenStyle, upArrow (downArrow), exProtein (inProtein); its legend (label) can be drawn inline or to the right of karyotypes. Idiograms can also be plotted in concentric circles. It is possible to calculate chromosome indices by Levan et al. (1964) <doi:10.1111/j.1601-5223.1964.tb01953.x>, karyotype indices of Watanabe et al. (1999) <doi:10.1007/PL00013869> and Romero-Zarco (1986) <doi:10.2307/1221906> and classify chromosomes by morphology Guerra (1986) and Levan et al. (1964).
Authors:
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idiogramFISH.pdf |idiogramFISH.html✨
idiogramFISH/json (API)
NEWS
| # Install 'idiogramFISH' in R: |
| install.packages('idiogramFISH', repos = c('https://fernandoroa.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://gitlab.com/ferroao/idiogramfish
- allChrSizeSample - Chr. basic data Monocen.
- allMarksSample - Mark Positional data - monocentrics
- bigdfChrSizeHolo - Chr. basic data Holo.
- bigdfMarkPosHolo - Mark Positional data - Holocen.
- bigdfMarkPosHolo2 - Mark Positional data - Holocen.
- bigdfOfChrSize - Chr. basic data Monocen.
- bigdfOfChrSize3Mb - Chr. basic data Holo.
- bigdfOfMarks - Mark Positional data - monocentrics
- bigdfOfMarks3Mb - Mark Positional data - Holocen.
- dfAlloParentMarks - Mark Positional data - monocentrics
- dfAlloParentMarksHolo - Mark Positional data - Holocen.
- dfChrSizeHolo - Chr. basic data Holo.
- dfMarkColor - Mark characteristics
- dfMarkColor5S25S - Mark characteristics
- dfMarkColorIn - Mark characteristics
- dfMarkPosHolo - Mark Positional data - Holocen.
- dfOfChrSize - Chr. basic data Monocen.
- dfOfMarks - Mark Positional data - monocentrics
- dfOfMarks2 - Mark Positional data - monocentrics
- humChr - Chr. basic data Monocen.
- humMarkColor - Mark characteristics
- humMarkPos - Mark Positional data - monocentrics
- mydfMaColor - Mark characteristics
- parentalAndHybChrSize - Chr. basic data Monocen.
- parentalAndHybHoloChrSize - Chr. basic data Holo.
- traspaMarks - Mark Positional data - monocentrics
- traspadf - Chr. basic data Monocen.
Last updated 9 months agofrom:8f7ee88135. Checks:1 OK, 7 NOTE. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Mar 03 2025 |
| R-4.5-win | NOTE | Mar 03 2025 |
| R-4.5-mac | NOTE | Mar 03 2025 |
| R-4.5-linux | NOTE | Mar 03 2025 |
| R-4.4-win | NOTE | Mar 03 2025 |
| R-4.4-mac | NOTE | Mar 03 2025 |
| R-4.3-win | NOTE | Mar 03 2025 |
| R-4.3-mac | NOTE | Mar 03 2025 |
Exports:armRatioCIasymmetryasymmetryA2citrusMarkPoscitrusSizefillMarkInfofillMarkInfo2genBankReadIFmake.uniqueIFmakedfMarkColorMycolorsmapGGChrmapGGChrMarkmarkOverCMAnamesToColumnsperMarkplotIdiogramsposCalcrobertrunBoardswapChrRegionDfSizeAndMarks
Dependencies:clicolorspacecpp11crayondplyrfansifarvergenericsgluelabelinglifecyclemagrittrmunsellpillarpkgconfigplyrpurrrR6RColorBrewerRcpprlangscalesstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| FUNCTIONS armRatioCI and swapChrRegionDfSizeAndMarks. | armRatioCI swapChrRegionDfSizeAndMarks |
| FUNCTIONS asymmetry and asymmetryA2. | asymmetry asymmetryA2 |
| Chr. basic data Holo. | bigdfChrSizeHolo bigdfOfChrSize3Mb chrbasicdataHolo dfChrSizeHolo parentalAndHybHoloChrSize |
| Chr. basic data Monocen. | allChrSizeSample bigdfOfChrSize chrbasicdatamono dfOfChrSize humChr parentalAndHybChrSize traspadf |
| FUNCTIONS: citrusSize, citrusMarkPos, markOverCMA | citrusMarkPos citrusSize markOverCMA |
| Mark characteristics | dfMarkColor dfMarkColor5S25S dfMarkColorIn dfMarkStyle humMarkColor mydfMaColor |
| FUNCTION genBankReadIF | genBankReadIF |
| FUNCTION make.uniqueIF | make.uniqueIF |
| FUNCTION to make a data.frame of Marks' characterisitcs | makedfMarkColorMycolors |
| FUNCTIONS mapGGChr and mapGGChrMark (for ggplot) | mapGGChr mapGGChrMark |
| Mark Positional data - Holocen. | bigdfMarkPosHolo bigdfMarkPosHolo2 bigdfOfMarks3Mb dfAlloParentMarksHolo dfMarkPosHolo markdataholo |
| Mark Positional data - monocentrics | allMarksSample bigdfOfMarks dfAlloParentMarks dfOfMarks dfOfMarks2 humMarkPos markposDFs traspaMarks |
| FUNCTION that modifies marks' names into columns | namesToColumns |
| FUNCTION perMark | perMark |
| Plot idiograms of karyotypes/genomes with and without centromere | plotIdiograms |
| FUNCTION posCalc and fillMarkInfo | fillMarkInfo fillMarkInfo2 posCalc |
| FUNCTION to produce a Robertsonian translocation | robert |
| FUNCTION runBoard | runBoard |
