---
title: "idiogramFISH: Shiny App. Idiograms with Marks and Karyotype Indices"
author: "Fernando Roa"
date: "28 12 2021"
pkgdown:
  as_is: true
output:
  rmdformats::readthedown:
    highlight: tango
    includes:
      in_header: myheader.html
    toc_depth: 2
    number_sections: true
    pandoc_args: ["--lua-filter=refs/multiple-bibliographies.lua"]
    
bibliography_normal: [refs/normal_noabs.bib]
bibliography_software: [refs/software.bib]
bibliography_docs: [refs/docs.bib]
bibliography_shiny: [refs/shinyApp.bib]

csl: refs/clima5.csl
link-citations: yes
resource_files:
  - ../pkgdown/myheader.html
    
  - ../man/figures/readme.svg
  - ../man/figures/cranmanualbookdown.svg
  - ../man/figures/develmanualvignette.svg
  - ../man/figures/develmanualpkgdown.svg
  - ../man/figures/manual.svg
  - ../man/figures/cranversion.svg
  - ../man/figures/archive.svg
  - ../man/figures/pkgdownver.svg
  - ../man/figures/shiny.jpg
  - ../man/figures/colab2.jpg
  - ../man/figures/colab-badge.svg
  - ../man/figures/GitHub-Mark-120px-plus.png
  
  - ../man/figures/kofi1.svg
  
  - ../man/figures/gitbadge.svg
  - ../man/figures/doibadge.svg
  - ../man/figures/logo.png
  - ../man/figures/logo2.png
  - ../man/figures/realdownloads.svg
  - ../man/figures/NEWS.svg
  
  - ../man/figures/circular.png
  - ../man/figures/dfOfChrSize.svg

  - ../onlinefigures/ggplot.svg
  - ../onlinefigures/nostoc.jpg
  - ../onlinefigures/nostocSmall.jpg
  
  - firstplot2.png
  - secondplot2.png
  - thirdplot2.png
  - firstplot.png
  - secondplot.png
  - thirdplot.png
  - dfOfChrSize.svg
  - monoholoCS.png
  - climon.svg
  - dfOfChrSizeVector.png
  - bigdfChrSizeHolo.png
  - bigdfChrSizeHolo2.png
  - mydfChrSize2.png
  
  - refs/shinyApp.bib
  - refs/normal_noabs.bib
  - refs/software.bib
  - refs/docs.bib
  - refs/multiple-bibliographies.lua
  
  - js/jquery.min.js
  - js/clipboard.min.js
  - js/bootstrap.min.js
  - js/pkgdown2.js

  - css/mystyle.css

  - css/all.minMod.css
  - css/bootstrap.minO.css
  
  - css/fonts/fa-regular-400.svg
  - css/fonts/fa-regular-400.eot
  - css/fonts/fa-regular-400.ttf
  - css/fonts/fa-regular-400.woff
  - css/fonts/fa-regular-400.woff2
  
vignette: >
  %\VignetteIndexEntry{idiogramFISH vignette}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
  
---

<!-- centering rmdformats in mystyle2 -->

<!-- button show hide in mystyle3 -->

<!-- <link rel="stylesheet" href="css/mystyle3.css"> -->

```{css, echo=FALSE, eval=T}
body {
  counter-reset: counter-rchunks;
}

#header {
  padding-left: 3em;
}

#main {
  padding-left: 3em;
}

div.sourceCode {
  counter-increment: counter-rchunks;
  position: relative;
  overflow: visible;
}

div.sourceCode::before {
  content: 'Code [' counter(counter-rchunks) ']: ';
  display: inline;
  position: absolute;
  left: -5em;
  font-size: 0.7em;    
  color: rgb(48, 63, 159);
}
```

``` {r cssjs, results="asis", echo=FALSE, message=FALSE, eval=TRUE}
# <!-- pkgdown --> 
# <!-- jquery --><script src="js/jquery.min.js" crossorigin="anonymous"></script>

myfile<-"js/jquery.min.js"
if(file.exists(myfile)){
cat(paste0('<script src="',myfile,'" crossorigin="anonymous"></script> <!-- # -->'))
}
# <!-- clipboard.js --><script src="js/clipboard.min.js"  crossorigin="anonymous"></script>
myfile<-"js/clipboard.min.js"
if(file.exists(myfile)){
cat(paste0('<script src="',myfile,'" crossorigin="anonymous"></script>'))
}
myfile<-"js/hideOutput.js"
if(file.exists(myfile)){
cat(paste0('<script src="',myfile,'" crossorigin="anonymous"></script>'))
}
# <!-- Font Awesome icons --><link rel="stylesheet" href="css/all.minMod.css"  crossorigin="anonymous">
myfile<-"css/all.minMod.css"
if(file.exists(myfile)){
cat(paste0('<link rel="stylesheet" href="',myfile,'"  crossorigin="anonymous">'))
}
# <!-- Bootstrap --><link rel="stylesheet" href="css/bootstrap.minO.css" crossorigin="anonymous">
myfile<-"css/bootstrap.minO.css"
if(file.exists(myfile)){
cat(paste0('<link rel="stylesheet" href="',myfile,'"  crossorigin="anonymous">'))
}
# <!-- # <script src="js/bootstrap.min.js"  crossorigin="anonymous"></script> -->
myfile<-"js/bootstrap.min.js"
if(file.exists(myfile)){
cat(paste0('<script src="',myfile,'" crossorigin="anonymous"></script> <!-- # -->'))
}
myfile<-"js/pkgdown2.js"
if(file.exists(myfile)){
cat(paste0('<script src="',myfile,'"></script> <!-- # -->'))
}
```
<link rel="stylesheet" href="css/mystyle.css">
<link rel="stylesheet" href="css/mystyle2.css">
<link rel="stylesheet" href="css/mystyle3.css">


```{r setup, include=FALSE, eval=T}

#Create myheader.html

  line1<-'<script src="https://kit.fontawesome.com/af0a13599b.js" crossorigin="anonymous"></script>'
  line2<-'<link rel="shortcut icon" href="../man/figures/logo.png" />'
  file <- "myheader.html"

if(Sys.info()['sysname']=="Windows") {
  
  #check internet response
  res<-!as.logical(system(paste("ping", "www.google.com")) )
    if(res){
      write(line1,file=file)
      write(line2,file=file,append=TRUE)
    }
} else {
  write(line1,file=file)
  write(line2,file=file,append=TRUE)
}

require(idiogramFISH)

knitr::opts_chunk$set(eval = TRUE)

pasteLinks <- function(link){
cat(paste0("
</br>
Jupyter interactive version:
<br>
</br>
<table>
<tr>
<td>
[<img src='../man/figures/colab-badge.svg'>](https://colab.research.google.com/github/ferroao/IFjupyter/blob/main/"
,note
,"){target='_blank'}&emsp;
</td>
<td>
&emsp;&emsp;<img src='../man/figures/GitHub-Mark-120px-plus.png' height=25 width=25>&emsp;[Github](https://github.com/ferroao/IFjupyter/blob/main/"
,note
,"){target='_blank'}
</td>
<td>
&emsp;&emsp;[Raw](https://github.com/ferroao/IFjupyter/raw/main/"
,note
,"){target='_blank'}
</td>
</tr>
</table>
</br>
") )
}
```

``` {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])
# v<-tryCatch(suppressWarnings(rvcheck:::check_github_gitlab("ferroao/idiogramFISH", "gitlab")$latest_version), error=function(e) NA )
pkg<-"idiogramFISH"
link<-tryCatch(suppressWarnings(badger::badge_custom("Documentation", paste(pkg,v), "cornflowerblue") ), 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/manual.svg"
    writeLines(manual_cont, con = manual_contFile)
    manual_contFile <- normalizePath(manual_contFile)
    knitr::include_graphics(manual_contFile)
    # cat(paste0("&nbsp;![''](",knitr::include_graphics(manual_contFile),")" ) )
    }
  }
} # rcurl
```

# Introduction {-}

<!-- <div style="width:150px;"> -->
<div style="float: right; width: 20%">
```{r, echo=F,  results="asis", eval=T}
img1_path <- "../man/figures/logo.png"
if(file.exists(img1_path)) {
cat(paste0("<img src=",img1_path,">") )
}
```
</div>

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].

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</div>

## Installation instructions {-}

``` {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 )

  if (!is.na(cranversion_cont)){
  cranversion_contFile <- "../man/figures/cranversion.svg"
  writeLines(cranversion_cont, con = cranversion_contFile)
  cranversion_contFile <- normalizePath(cranversion_contFile)
  # knitr::include_graphics(cranversion_contFile)
  # cat(paste0("![https://CRAN.R-project.org/package=idiogramFISH](",knitr::include_graphics(cranversion_contFile),")" ) )
  cat(paste0("[![CRAN repo](",knitr::include_graphics(cranversion_contFile),")](https://CRAN.R-project.org/package=idiogramFISH)" ) )
  } # cran version

# crandownloads<-"https://cranlogs.r-pkg.org/badges/grand-total/idiogramFISH?color=orange"
# crandownloads_cont <- tryCatch(suppressWarnings(RCurl::getURLContent(crandownloads) ), 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(doibadge_cont)){
  doibadge_contFile <- "../man/figures/doibadge.svg"
  writeLines(doibadge_cont, con = doibadge_contFile)
  doibadge_contFile <- normalizePath(doibadge_contFile)
  
  cat(paste0("&nbsp;[![10.5281/zenodo.3579417](",knitr::include_graphics(doibadge_contFile)         ,")](https://doi.org/10.5281/zenodo.3579417)" ) )
  } # doi

} # rcurl
```


You can install idiogramFISH from [CRAN](https://cran.r-project.org/package=idiogramFISH) with:

``` r
install.packages("idiogramFISH")
```

Windows users: To avoid installation of packages in OneDrive      

``` r
.libPaths("D:R/lib") # for example
.libPaths()          # set or read libraries
```

To do that permanently: Search (magnifier) "environment variables" and set R_LIBS_USER to 
`D:\R\lib` (example)

### Devel. version {-}

``` {r, echo=F, message=FALSE, warning=FALSE, include=TRUE, fig.show = "hold", fig.align = "default", results="asis"}
if (requireNamespace("RCurl", quietly = TRUE)  ) {
  # v<-tryCatch(suppressWarnings(rvcheck:::check_github_gitlab("ferroao/idiogramFISH", "gitlab")$latest_version), error=function(e) NA )
  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 <- tempfile(fileext = ".svg")
    gitbadge_contFile <- "../man/figures/gitbadge.svg"
    writeLines(gitbadge_cont, con = gitbadge_contFile)
    gitbadge_contFile <- normalizePath(gitbadge_contFile)
    cat(paste0("[![gitlab repo](",knitr::include_graphics(gitbadge_contFile),")](https://gitlab.com/ferroao/idiogramFISH){target='_blank'}") )
    }
  }
}
```

Install Gitlab dev. ver. with devtools [@R-devtools]:

Attention windows users, please install [Rtools](https://cran.r-project.org/bin/windows/Rtools/){target="_blank"} and [git](https://git-scm.com/download/win) (compilation tools).

Vignettes (optional) use a lua filter, so you would need [pandoc](https://pandoc.org/installing.html){target="_blank"} ver. > 2. and `pandoc-citeproc` or `citeproc`. RStudio comes with pandoc. `rmarkdown::pandoc_version()` 

<div class="fold s">
``` {r, eval=FALSE}
# This installs package devtools, necessary for installing the dev version
install.packages("devtools")

url <- "https://gitlab.com/ferroao/idiogramFISH"

# Packages for vignettes: (optional)
list.of.packages <- c(
    "knitr",
    "kableExtra",
    "rmdformats",
    "rmarkdown",
    "RCurl",
    "rvcheck",
    "badger",
    "rentrez"
    )
new.packages <- list.of.packages[!(list.of.packages %in% installed.packages()[,"Package"])]
if(length(new.packages)) install.packages(new.packages)

# Linux with vignettes and Windows
devtools::install_git(url = url,build_vignettes = TRUE, force=TRUE)

# Mac with vignettes
devtools::install_git(url = url, build_opts=c("--no-resave-data","--no-manual") )
```
</div>

#### Installing in system terminal {-}

<div class="fold s">
``` {r, eval=FALSE}
# clone repository:
git clone "https://gitlab.com/ferroao/idiogramFISH"

R CMD build idiogramFISH
# install
R CMD INSTALL idiogramFISH_*.tar.gz
```
</div>

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</div>

## Releases {-}

``` {r, echo=F, message=FALSE, fig.show = "hold", fig.align = "default", results="asis"}
if (requireNamespace("RCurl", quietly = TRUE)  ) {
#cran version
v<-"NEWS"#tryCatch(suppressWarnings(rvcheck::check_cran("idiogramFISH")$latest_version), error=function(e) NA )

link<-tryCatch(suppressWarnings(badger::badge_custom("gitlab", paste(v), "orange","?logo=gitlab") ), error=function(e) NA )
  if(!is.na(link)){
  svglink<-gsub("\\[|\\]|!|\\(|\\)","", link)
  news_cont <- tryCatch(suppressWarnings(RCurl::getURLContent(svglink) ), error=function(e) NA )
    if (!is.na(news_cont)){
    news_cont_contFile <- "../man/figures/NEWS.svg"
    writeLines(news_cont, con = news_cont_contFile)
    cat(paste0("[![NEWS](",knitr::include_graphics(news_cont_contFile),")](https://gitlab.com/ferroao/idiogramFISH/blob/master/NEWS.md){target='_blank'}" ) )
    }
  }
} # rcurl
```

<!-- [CRAN archive](https://cran.r-project.org/src/contrib/Archive/idiogramFISH/) -->

``` {r, echo=F, message=FALSE, fig.show = "hold", fig.align = "default", results="asis"}
if (requireNamespace("RCurl", quietly = TRUE)  ) {
archivelink<-tryCatch(suppressWarnings(badger::badge_custom("CRAN",  "archive","gray") ), error=function(e) NA )
if(!is.na(archivelink)){
svgnewdownlink<-gsub("\\[|\\]|!|\\(|\\)","", archivelink)
archive_cont <- tryCatch(suppressWarnings(RCurl::getURLContent(svgnewdownlink) ), error=function(e) NA )
}
if (!is.na(archive_cont)){
      archive_contFile <- "../man/figures/archive.svg"
      writeLines(archive_cont, con = archive_contFile)
      cat(paste0("[![archive](",knitr::include_graphics(archive_contFile),")](https://cran.r-project.org/src/contrib/Archive/idiogramFISH/){target='_blank'}" ) )
}
} # rcurl
```

``` {r, echo=F, message=FALSE, fig.show = "hold", fig.align = "default", results="asis"}
if (requireNamespace("RCurl", quietly = TRUE)  ) {
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 )
}
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){target='_blank'}" ) )
}
} # rcurl
```

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</div>

## 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)){
    bookdown_contFile <- "../man/figures/cranmanualbookdown.svg"
    writeLines(manual_cont, con = bookdown_contFile)
#    manual_contFile <- normalizePath(manual_contFile)
    # knitr::include_graphics(manual_contFile)
    cat(paste0("[![https://ferroao.gitlab.io/manualidiogramfish](",knitr::include_graphics(bookdown_contFile),")](https://ferroao.gitlab.io/manualidiogramfish/)" ) )
    }
  }
} # rcurl
```

### Documentation in Pkgdown style {-}

``` {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])
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"
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("[![https://ferroao.gitlab.io/idiogramFISH](",knitr::include_graphics(pkgdownmanual_contFile)," )](https://ferroao.gitlab.io/idiogramFISH)" ) )
    }
  }
} # rcurl
```


### 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])
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("vignettes", paste(pkg,v), "cornflowerblue") ), error=function(e) NA )
  if(!is.na(link)){
  vignettelink<-gsub("\\[|\\]|!|\\(|\\)","", link)
  vignettemanual_cont <- tryCatch(suppressWarnings(RCurl::getURLContent(vignettelink) ), error=function(e) NA )
    if (!is.na(vignettemanual_cont)){
    vignettemanual_contFile <- "../man/figures/develmanualvignette.svg"
    writeLines(vignettemanual_cont, con = vignettemanual_contFile)
#    manual_contFile <- normalizePath(manual_contFile)
    # knitr::include_graphics(manual_contFile)
    cat(paste0("[![https://ferroao.gitlab.io/idiogramfishhelppages](",knitr::include_graphics(vignettemanual_contFile),")](https://ferroao.gitlab.io/idiogramfishhelppages)" ) )
    }
  }
} # rcurl
```

Launch vignettes from R for the installed version:
``` r
library(idiogramFISH)
packageVersion("idiogramFISH")
browseVignettes("idiogramFISH")
```
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</div>

## Citation {-}

```{r citation, echo=FALSE, comment=NA,results='asis'} 
print(citation("idiogramFISH"),bibtex=FALSE )
```

To write citation to file:
```{r, echo=TRUE, results=FALSE, eval=FALSE}
sink("idiogramFISH.bib")
toBibtex(citation("idiogramFISH"))
sink()
```
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</div>

## Authors {-}

```{r, echo=F,  results="asis", eval=T}
img1_path <- "../man/figures/kofi1.png"
img1_path <- normalizePath(img1_path)

if(file.exists(img1_path)) {
  cat(paste0("[Fernando Roa](https://ferroao.gitlab.io/curriculumpu/){target='_blank'}&nbsp;&nbsp;<a href='https://ko-fi.com/X7X71PZZG' target='_blank'><img src=",img1_path," width=\"10%\">") )
} else {
  cat(paste0("[Fernando Roa](https://ferroao.gitlab.io/curriculumpu/){target='_blank'}"))  
}
```

``` {r, echo=F, message=FALSE, fig.show = "hold", fig.align = "default", results="asis", eval=FALSE}
cat("<a href='https://ko-fi.com/X7X71PZZG' target='_blank'><img height='12' style='border:0px;height:12px;' src='../man/figures/kofi1.png' border='0' alt='Buy Me a Coffee at ko-fi.com' /></a>")
```

[Mariana PC Telles](http://lattes.cnpq.br/4648436798023532)  

```{r include=FALSE,eval=FALSE}
# automatically create a bib database for R packages, this is currently not used by vignette refs/packages2.bib
knitr::write_bib(c(
  .packages(), 'bookdown', 'knitr', 'rmarkdown',"devtools","pkgdown","crayon","ggtree","ggplot2","ggpubr","phytools","plyr","dplyr","tidyr","rentrez"
), 'refs/packages2.bib')
```
<div class="goright95">
<a href="#header">top <i class="fa fa-caret-square-o-up" aria-hidden="true"></i></a>
</div>

```{r, echo=F}
chapterFile_jupyter<- "../parts/01-jupyter.Rmd"
if(file.exists(chapterFile_jupyter)){
  childExists_jupyter<-TRUE
  child_docs_jupyter <- chapterFile_jupyter
} else {
  childExists_jupyter<-FALSE
  child_docs_jupyter <- ""
}
```

```{r, child = child_docs_jupyter, eval=childExists_jupyter}
```


```{r, echo=F}
chapterFile_first<- "../parts/02-first.Rmd"
if(file.exists(chapterFile_first)){
  childExists_first<-TRUE
  child_docs_first <- chapterFile_first
} else {
  childExists_first<-FALSE
  child_docs_first <- ""
}
```

```{r, child = child_docs_first, eval=childExists_first}
```

```{r, echo=F}
chapterFile_minimal<- "../chaptersBLOCK/03-minimal.Rmd"
if(file.exists(chapterFile_minimal)){
  childExists_minimal<-TRUE
  child_docs_minimal <- chapterFile_minimal
} else {
  childExists_minimal<-FALSE
  child_docs_minimal <- ""
}
```

```{r, child = child_docs_minimal, eval=childExists_minimal}
```

```{r, results="asis", eval=!childExists_minimal, echo=FALSE}
cat("# Minimal Examples")
```

```{r, results="asis", eval=!childExists_minimal, echo=FALSE}
cat("[https://ferroao.gitlab.io/idiogramfishhelppages](https://ferroao.gitlab.io/idiogramfishhelppages/#minimal-examples)")
```

```{r , echo=FALSE, results="asis", message=FALSE, eval=!childExists_minimal, comment=NA}
note<-"03-minimal.ipynb"
pasteLinks(note)
``` 

```{r, echo=F}
chapterFile_plotting<- "../chaptersBLOCK/04-plotting.Rmd"
if(file.exists(chapterFile_plotting)){
  childExists_plotting<-TRUE
  child_docs_plotting <- chapterFile_plotting
} else {
  childExists_plotting<-FALSE
  child_docs_plotting <- ""
}
```

```{r, child = child_docs_plotting, eval=childExists_plotting}
```


```{r, results="asis", eval=!childExists_plotting, echo=FALSE}
cat("# Plotting chromosomes")
```

```{r, results="asis", eval=!childExists_plotting, echo=FALSE}
cat("[https://ferroao.gitlab.io/idiogramfishhelppages](https://ferroao.gitlab.io/idiogramfishhelppages/#plotting-chromosomes)")
```

```{r , echo=FALSE, results="asis", message=FALSE, eval=!childExists_plotting, comment=NA}
note<-"04-plotting.ipynb"
pasteLinks(note)
``` 

```{r, echo=F}
chapterFile_multiple<- "../chaptersBLOCK/05-multiple.Rmd"
if(file.exists(chapterFile_multiple)){
  childExists_multiple<-TRUE
  child_docs_multiple <- chapterFile_multiple
} else {
  childExists_multiple<-FALSE
  child_docs_multiple <- ""
}
```

```{r, child = child_docs_multiple, eval=childExists_multiple}
```

```{r, results="asis", eval=!childExists_multiple, echo=FALSE}
cat("# Several OTUs")
```
```{r, results="asis", eval=!childExists_multiple, echo=FALSE}
cat("[https://ferroao.gitlab.io/idiogramfishhelppages](https://ferroao.gitlab.io/idiogramfishhelppages/#multiple-otus)")
```

```{r , echo=FALSE, results="asis", message=FALSE, eval=!childExists_multiple, comment=NA}
note<-"05-multiple.ipynb"
pasteLinks(note)
``` 

```{r, echo=F}
chapterFile_units<- "../chaptersBLOCK/06-units.Rmd"
if(file.exists(chapterFile_units)){
  childExists_units<-TRUE
  child_docs_units <- chapterFile_units
} else {
  childExists_units<-FALSE
  child_docs_units <- ""
}
```

```{r, child = child_docs_units, eval=childExists_units}
```

```{r, results="asis", eval=!childExists_units, echo=FALSE}
cat("# Changing Units")
```
```{r, results="asis", eval=!childExists_units, echo=FALSE}
cat("[https://ferroao.gitlab.io/idiogramfishhelppages](https://ferroao.gitlab.io/idiogramfishhelppages/#changing-units)")
```

```{r , echo=FALSE, results="asis", message=FALSE, eval=!childExists_units, comment=NA}
note<-"06-units.ipynb"
pasteLinks(note)
``` 

```{r, echo=F}
chapterFile0<- "../chaptersBLOCK/07-gish.Rmd"
if(file.exists(chapterFile0)){
  childExists0<-TRUE
  child_docs0 <- chapterFile0
} else {
  childExists0<-FALSE
  child_docs0 <- ""
}
```

```{r, child = child_docs0, eval=childExists0}
```

```{r, results="asis", eval=!childExists0, echo=FALSE}
cat("# GISH")
```
```{r, results="asis", eval=!childExists0, echo=FALSE}
cat("[https://ferroao.gitlab.io/idiogramfishhelppages](https://ferroao.gitlab.io/idiogramfishhelppages/#gish)")
```

```{r , echo=FALSE, results="asis", message=FALSE, eval=!childExists0, comment=NA}
note<-"07-gish.ipynb"
pasteLinks(note)
``` 

```{r, echo=F}
chapterFile1<- "../chaptersBLOCK/08-groups.Rmd"
if(file.exists(chapterFile1)){
  childExists1<-TRUE
  child_docs1 <- chapterFile1
} else {
  childExists1<-FALSE
  child_docs1 <- ""
}
```

```{r, child = child_docs1, eval=childExists1}
```

```{r, results="asis", eval=!childExists1, echo=FALSE}
cat("# Using groups")
```
```{r, results="asis", eval=!childExists1, echo=FALSE}
cat("[https://ferroao.gitlab.io/idiogramfishhelppages](https://ferroao.gitlab.io/idiogramfishhelppages/#groups)")
```

```{r , echo=FALSE, results="asis", message=FALSE, eval=!childExists1, comment=NA}
note<-"08-groups.ipynb"
pasteLinks(note)
``` 

```{r, echo=F}
chapterFile2<- "../chaptersBLOCK/09-circular.Rmd"
if(file.exists(chapterFile2)){
  childExists2<-TRUE
  child_docs2 <- chapterFile2
} else {
  childExists2<-FALSE
  child_docs2<-""
}
```

```{r, child = child_docs2, eval = childExists2}
```

```{r, results="asis", eval=!childExists2, echo=FALSE}
cat("# Circular plots")
```

```{r, results="asis", eval=!childExists2, echo=FALSE}
cat("[https://ferroao.gitlab.io/idiogramfishhelppages](https://ferroao.gitlab.io/idiogramfishhelppages/#circular-plots)")
```

```{r , echo=FALSE, results="asis", message=FALSE, eval=!childExists2, comment=NA}
note<-"09-circular.ipynb"
pasteLinks(note)
``` 

```{r, echo=F}
chapterFile3<- "../chaptersBLOCK/10-phylogeny.Rmd"
if(file.exists(chapterFile3)){
  childExists3<-TRUE
  child_docs3 <- chapterFile3
} else {
  childExists3<-FALSE
  child_docs3<-""
}
```

```{r, child = child_docs3, eval=childExists3}
```

```{r, results="asis", eval=!childExists3, echo=FALSE}
cat("# Plotting alongside phylogeny")
```
```{r, results="asis", eval=!childExists3, echo=FALSE}
cat("[https://ferroao.gitlab.io/idiogramfishhelppages](https://ferroao.gitlab.io/idiogramfishhelppages/#plotting-alongside-phylogeny)")
```

```{r , echo=FALSE, results="asis", message=FALSE, eval=!childExists3, comment=NA}
note<-"10-phylogeny.ipynb"
pasteLinks(note)
``` 

```{r, echo=F}
chapterFile<- "../chaptersBLOCK/11-citrushelp.Rmd"
if(file.exists(chapterFile)){
  childExists<-TRUE
  child_docs <- chapterFile
} else {
  childExists<-FALSE
  child_docs<-""
}
```

```{r, child = child_docs, eval=childExists}
```

```{r, results="asis", eval=!childExists, echo=FALSE}
cat("# *Citrus*")
```
```{r, results="asis", eval=!childExists, echo=FALSE}
cat("[https://ferroao.gitlab.io/idiogramfishhelppages](https://ferroao.gitlab.io/idiogramfishhelppages/#citrus)")
```

```{r , echo=FALSE, results="asis", message=FALSE, eval=!childExists, comment=NA}
note<-"11-citrushelp.ipynb"
pasteLinks(note)
``` 

```{r, echo=F}
chapterFile4<- "../chaptersBLOCK/12-human.Rmd"
if(file.exists(chapterFile4)){
  childExists4<-TRUE
  child_docs4 <- chapterFile4
} else {
  childExists4<-FALSE
  child_docs4<-""
}
```

```{r, child = child_docs4, eval=childExists4}
```

```{r, results="asis", eval=!childExists4, echo=FALSE}
cat("# Human karyotype")
```
```{r, results="asis", eval=!childExists4, echo=FALSE}
cat("[https://ferroao.gitlab.io/idiogramfishhelppages](https://ferroao.gitlab.io/idiogramfishhelppages/#human-karyotype)")
```

```{r , echo=FALSE, results="asis", message=FALSE, eval=!childExists4, comment=NA}
note<-"12-human.ipynb"
pasteLinks(note)
``` 

```{r, echo=F}
chapterFile_param<- "../chaptersBLOCK/13-functions.Rmd"
if(file.exists(chapterFile_param)){
  childExists_param<-TRUE
  child_docs_param <- chapterFile_param
} else {
  childExists_param<-FALSE
  child_docs_param<-""
}
```

```{r, child = child_docs_param, eval=childExists_param}
```

```{r, results="asis", eval=!childExists_param, echo=FALSE}
cat("# Functions")
```
```{r, results="asis", eval=!childExists_param, echo=FALSE}
cat("[https://ferroao.gitlab.io/idiogramfishhelppages](https://ferroao.gitlab.io/idiogramfishhelppages/#functions)")
```


```{r, echo=F}
chapterFile_data<- "../chaptersBLOCK/14-datasets.Rmd"
if(file.exists(chapterFile_data)){
  childExists_data<-TRUE
  child_docs_data <- chapterFile_data
} else {
  childExists_data<-FALSE
  child_docs_data<-""
}
```

```{r, child = child_docs_data, eval=childExists_data}
```

```{r, results="asis", eval=!childExists_data, echo=FALSE}
cat("# Datasets")
```
```{r, results="asis", eval=!childExists_data, echo=FALSE}
cat("[https://ferroao.gitlab.io/idiogramfishhelppages](https://ferroao.gitlab.io/idiogramfishhelppages/#datasets)")
```

```{r, echo=F}
chapterFile_news<- "../chaptersBLOCK/15-news.Rmd"
if(file.exists(chapterFile_news)){
  childExists_news<-TRUE
  child_docs_news <- chapterFile_news
} else {
  childExists_news<-FALSE
  child_docs_news<-""
}
```

```{r, child = child_docs_news, eval=childExists_news}
```

```{r, results="asis", eval=!childExists_news, echo=FALSE}
cat("# News {-}")
```
```{r, results="asis", eval=!childExists_news, echo=FALSE}
cat("[https://ferroao.gitlab.io/idiogramfishhelppages](https://ferroao.gitlab.io/idiogramfishhelppages/#news)")
```

# References {-}

::: {#refs_normal}
:::

## R-packages {-}

::: {#refs_software}
:::

## Shiny App {-}

::: {#refs_shiny}
:::

## Documentation {-}

::: {#refs_docs}
:::


