knitr::opts_chunk$set( collapse = TRUE, comment = "#>", fig.path = "man/figures/README-", out.width = "70%" ) library(knitr)
img1_path <- "man/figures/logo.png" if(file.exists(img1_path)) { cat(paste0("<img src=",img1_path," align=\"right\" width=\"12%\" hspace=\"50\">") ) }
badge_devel_gitlab<-function(pkg, color){ v <- rvcheck:::check_github_gitlab(pkg, "gitlab")$latest_version url <- paste0("https://gitlab.com/", pkg) badger::badge_custom("devel version", v, color, url) }
``` {r, echo=F, message=FALSE, fig.show = "hold", fig.align = "default", results="asis"}
if (requireNamespace("RCurl", quietly = TRUE) ) { cranversion <- "https://www.r-pkg.org/badges/version/idiogramFISH" cranversion_cont <- tryCatch(suppressWarnings(RCurl::getURLContent(cranversion) ), error=function(e) NA )
crandownloads<-"https://cranlogs.r-pkg.org/badges/grand-total/idiogramFISH?color=orange" crandownloads_cont <- tryCatch(suppressWarnings(RCurl::getURLContent(crandownloads) ), error=function(e) NA )
newdownlink<-tryCatch(suppressWarnings(badger::badge_custom("CRAN", "downloads","green") ), error=function(e) NA ) if(!is.na(newdownlink)){ svgnewdownlink<-gsub("\[|\]|!|\(|\)","", newdownlink) realdo_cont <- tryCatch(suppressWarnings(RCurl::getURLContent(svgnewdownlink) ), error=function(e) NA ) }
doibadge <- "https://zenodo.org/badge/DOI/10.5281/zenodo.3579417.svg" doibadge_cont <- tryCatch(suppressWarnings(RCurl::getURLContent(doibadge) ), error=function(e) NA )
if (!is.na(cranversion_cont)) { cranversion_contFile <- "man/figures/cranversion.svg" writeLines(cranversion_cont, con = cranversion_contFile) cat(paste0(",")" ) ) }
# if (!is.na(crandownloads_cont)){ if (!is.na(realdo_cont)){ realdo_contFile <- "man/figures/realdownloads.svg" writeLines(realdo_cont, con = realdo_contFile) # message # link cat(paste0(" [![downloads](",knitr::include_graphics(realdo_contFile),")](https://ferroao.gitlab.io/idiogramfishhelppages/downloads.png)" ) ) } if (!is.na(doibadge_cont)){ cranCranddoi<-TRUE doibadge_contFile <- "man/figures/doibadge.svg" writeLines(doibadge_cont, con = doibadge_contFile) # doibadge_contFile <- normalizePath(doibadge_contFile) cat(paste0(" [![10.5281/zenodo.3579417](",knitr::include_graphics(doibadge_contFile),")](https://doi.org/10.5281/zenodo.3579417)" ) ) } # doi cont
} # rcurl
``` {r, echo=F, message=FALSE, fig.show = "hold", fig.align = "default", results="asis"} #`r badge_devel_gitlab("ferroao/idiogramFISH", color="green")` if (requireNamespace("RCurl", quietly = TRUE) ) { v<-sub("Version: ","",readLines("DESCRIPTION")[3]) link<-tryCatch(suppressWarnings(badger::badge_custom("devel version", v, "cornflowerblue","?logo=gitlab") ), error=function(e) NA ) if(!is.na(link)){ svglink<-gsub("\\[|\\]|!|\\(|\\)","", link) gitbadge_cont <- tryCatch(suppressWarnings(RCurl::getURLContent(svglink) ), error=function(e) NA ) if (!is.na(gitbadge_cont)){ gitbadge_contFile <- "man/figures/gitbadge.svg" writeLines(gitbadge_cont, con = gitbadge_contFile) cat(paste0(" ![gitlab.com/ferroao/idiogramFISH](",knitr::include_graphics(gitbadge_contFile)," )" ) ) } } } # rcurl
``` {r, echo=F, message=FALSE, fig.show = "hold", fig.align = "default", results="asis"}
cat("
")
cat("")
<!-- badges: end --> The left side menu of the shiny app consists of three pages with several tabs: * Examples (presets) + Load example + Upload presets * Nucleotides + Search * data.frame (input) + Chr. data data.frame + Mark Pos. data d.f. + Marks' Style + Notes * Parameters & Plot + Parameters (plot and download preset) + Log + code (download data.frames and code) * stats (output) + Indices + Marks * About The goal of idiogramFISH functions or shiny-app is to plot karyotypes, plasmids and circular chr. having a set of data.frames for chromosome data and optionally marks' data [@Roa2021]. Karyotypes can also be plotted in concentric circles.<br> <br>It is possible to calculate also chromosome and karyotype indexes [@Watanabe1999;@Zarco1986new] and classify chromosome morphology in the categories of Levan [-@Levan1964], and [Guerra](https://ferroao.gitlab.io/guerra1986/Guerra1986.pdf) [-@Guerra1986d].<br> <br>Six styles of marks are available: square (squareLeft), dots, cM (cMLeft), cenStyle, upArrow (downArrow), exProtein (inProtein) (column `style` in `dfMarkColor` data.frame); its legend (label) (parameter `legend`) can be drawn inline or to the right of karyotypes. Three styles of centromere are available: rounded, triangle and inProtein (`cenFormat` parameter). Chromosome regions (column `chrRegion` in `dfMarkPos` data.frame) for monocentrics are `p`, `q`, `cen`, `pcen`, `qcen`. The last three cannot accommodate most mark styles, but can be colored. The region `w` can be used both in monocentrics and holocentrics. IdiogramFISH was written in R [@R-base] and also uses crayon [@R-crayon], tidyr [@R-tidyr], plyr [@plyr2011] and dplyr packages [@R-dplyr]. Documentation was written with R-packages roxygen2 [@R-roxygen2], usethis [@R-usethis], bookdown [@bookdown2016], knitr [@Xie2015], pkgdown [@R-pkgdown], Rmarkdown [@rmarkdown2018], rvcheck [@R-rvcheck], badger [@R-badger], kableExtra [@R-kableExtra], rmdformats [@R-rmdformats] and RCurl [@R-RCurl]. For some vignette figures, packages rentrez [@rentrez2017], phytools [@phytools2012], ggtree [@ggtree2018], ggplot2 [@ggplot22016] and ggpubr [@R-ggpubr] were used. In addition, the shiny app `runBoard()` uses shiny [@R-shiny], shinydashboard [@R-shinydashboard], rhandsontable [@R-rhandsontable], gtools [@R-gtools] and rclipboard [@R-rclipboard]. <!-- badger --> ## Releases [News](https://gitlab.com/ferroao/idiogramFISH/blob/master/NEWS.md) [CRAN archive](https://cran.r-project.org/src/contrib/Archive/idiogramFISH/) [Download history](https://ferroao.gitlab.io/idiogramfishhelppages/downloads.png) ## Need help? #### Manual in Bookdown style ``` {r, echo=F, message=FALSE, fig.show = "hold", fig.align = "default", results="asis"} if (requireNamespace("RCurl", quietly = TRUE) ) { # version of manual # v <- tryCatch(suppressWarnings(rvcheck:::check_github_gitlab("ferroao/idiogramFISH", "gitlab")$latest_version), error=function(e) NA ) #cran version v<-tryCatch(suppressWarnings(rvcheck::check_cran("idiogramFISH")$latest_version), error=function(e) NA ) pkg<-"idiogramFISH" link<-tryCatch(suppressWarnings(badger::badge_custom("bookdown", paste(pkg,v), "orange") ), error=function(e) NA ) if(!is.na(link)){ svglink<-gsub("\\[|\\]|!|\\(|\\)","", link) manual_cont <- tryCatch(suppressWarnings(RCurl::getURLContent(svglink) ), error=function(e) NA ) if (!is.na(manual_cont)){ manual_contFile <- "man/figures/cranmanualbookdown.svg" writeLines(manual_cont, con = manual_contFile) cat(paste0(" [![https://ferroao.gitlab.io/manualidiogramfish](",knitr::include_graphics(manual_contFile),")](https://ferroao.gitlab.io/manualidiogramfish/)" ) ) } else { cat(paste0(" [https://ferroao.gitlab.io/manualidiogramfish](https://ferroao.gitlab.io/manualidiogramfish/){target='_blank'}" ) ) } } } else { cat(paste0(" [https://ferroao.gitlab.io/manualidiogramfish](https://ferroao.gitlab.io/manualidiogramfish/){target='_blank'}" ) ) }
``` {r, echo=F, message=FALSE, fig.show = "hold", fig.align = "default", results="asis"} if (requireNamespace("RCurl", quietly = TRUE) ) {
v<-sub("Version: ","",readLines("DESCRIPTION")[3])
pkg<-"idiogramFISH" pkglink<-tryCatch(suppressWarnings(badger::badge_custom("pkgdown", paste(pkg,v), "cornflowerblue") ), error=function(e) NA ) if(!is.na(pkglink)){ pkgsvglink<-gsub("\[|\]|!|\(|\)","", pkglink) develpkgmanual_cont <- tryCatch(suppressWarnings(RCurl::getURLContent(pkgsvglink) ), error=function(e) NA ) if (!is.na(develpkgmanual_cont)){ pkgdownmanual_contFile <- "man/figures/pkgdownver.svg" writeLines(develpkgmanual_cont, con = pkgdownmanual_contFile) cat(paste0(" ," )" ) ) } else { cat(paste0(" https://ferroao.gitlab.io/idiogramFISH{target='_blank'}" ) ) } } } else { cat(paste0(" https://ferroao.gitlab.io/idiogramFISH{target='_blank'}" ) ) }
#### Vignettes: {-} Online: ``` {r, echo=F, message=FALSE, fig.show = "hold", fig.align = "default", results="asis"} if (requireNamespace("RCurl", quietly = TRUE) ) { # version of manual v<-sub("Version: ","",readLines("DESCRIPTION")[3]) pkg<-"idiogramFISH" link<-tryCatch(suppressWarnings(badger::badge_custom("vignettes", paste(pkg,v), "cornflowerblue") ), error=function(e) NA ) if(!is.na(link)){ svglink<-gsub("\\[|\\]|!|\\(|\\)","", link) develmanual_cont <- tryCatch(suppressWarnings(RCurl::getURLContent(svglink) ), error=function(e) NA ) if (!is.na(develmanual_cont)){ vignettemanual_contFile <- "man/figures/develmanualvignette.svg" writeLines(develmanual_cont, con = vignettemanual_contFile) cat(paste0(" [![https://ferroao.gitlab.io/idiogramfishhelppages](",knitr::include_graphics(vignettemanual_contFile),")](https://ferroao.gitlab.io/idiogramfishhelppages)" ) ) } else { cat(paste0(" [https://ferroao.gitlab.io/idiogramfishhelppages](https://ferroao.gitlab.io/idiogramfishhelppages){target='_blank'} " ) ) } } } else { cat(paste0(" [https://ferroao.gitlab.io/idiogramfishhelppages](https://ferroao.gitlab.io/idiogramfishhelppages){target='_blank'} " ) ) }
Launch vignettes from R for the installed version:
library(idiogramFISH) packageVersion("idiogramFISH") browseVignettes("idiogramFISH")
print(citation("idiogramFISH"),bibtex=FALSE)
To write citation to file:
sink("idiogramFISH.bib") toBibtex(citation("idiogramFISH")) sink()
Fernando Roa
Mariana PC Telles
::: {#refs_normal} :::
::: {#refs_software} :::
::: {#refs_shiny} :::
::: {#refs_docs} :::
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