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:Fernando Roa [aut, cre], Mariana PC Telles [ctb]

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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'))

Peer review:

Bug tracker:https://gitlab.com/ferroao/idiogramfish

Datasets:

On CRAN:

4.00 score 5 scripts 962 downloads 20 exports 31 dependencies

Last updated 5 months agofrom:8f7ee88135. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 03 2024
R-4.5-winNOTENov 03 2024
R-4.5-linuxNOTENov 03 2024
R-4.4-winNOTENov 03 2024
R-4.4-macNOTENov 03 2024
R-4.3-winNOTENov 03 2024
R-4.3-macNOTENov 03 2024

Exports:armRatioCIasymmetryasymmetryA2citrusMarkPoscitrusSizefillMarkInfofillMarkInfo2genBankReadIFmake.uniqueIFmakedfMarkColorMycolorsmapGGChrmapGGChrMarkmarkOverCMAnamesToColumnsperMarkplotIdiogramsposCalcrobertrunBoardswapChrRegionDfSizeAndMarks

Dependencies:clicolorspacecpp11crayondplyrfansifarvergenericsgluelabelinglifecyclemagrittrmunsellpillarpkgconfigplyrpurrrR6RColorBrewerRcpprlangscalesstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr

idiogramFISH

Rendered fromAVignette.Rmdusingknitr::rmarkdownon Nov 03 2024.

Last update: 2024-06-06
Started: 2020-09-17

idiogramFISH: Shiny App. Idiograms with Marks and Karyotype Indices

Rendered fromindex.Rmdusingknitr::rmarkdownon Nov 03 2024.

Last update: 2024-06-06
Started: 2019-09-02

Readme and manuals

Help Manual

Help pageTopics
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, markOverCMAcitrusMarkPos citrusSize markOverCMA
Mark characteristicsdfMarkColor dfMarkColor5S25S dfMarkColorIn dfMarkStyle humMarkColor mydfMaColor
FUNCTION genBankReadIFgenBankReadIF
FUNCTION make.uniqueIFmake.uniqueIF
FUNCTION to make a data.frame of Marks' characterisitcsmakedfMarkColorMycolors
FUNCTIONS mapGGChr and mapGGChrMark (for ggplot)mapGGChr mapGGChrMark
Mark Positional data - Holocen.bigdfMarkPosHolo bigdfMarkPosHolo2 bigdfOfMarks3Mb dfAlloParentMarksHolo dfMarkPosHolo markdataholo
Mark Positional data - monocentricsallMarksSample bigdfOfMarks dfAlloParentMarks dfOfMarks dfOfMarks2 humMarkPos markposDFs traspaMarks
FUNCTION that modifies marks' names into columnsnamesToColumns
FUNCTION perMarkperMark
Plot idiograms of karyotypes/genomes with and without centromereplotIdiograms
FUNCTION posCalc and fillMarkInfofillMarkInfo fillMarkInfo2 posCalc
FUNCTION to produce a Robertsonian translocationrobert
FUNCTION runBoardrunBoard