idiogramFISH: Shiny App. Idiograms with Marks and Karyotype Indices

In idiogramFISH: Shiny App. Idiograms with Marks and Karyotype Indices

```{css, echo=FALSE, eval=T} body { counter-reset: counter-rchunks; } :root { --pale-blue: #5A7B9C; --strong-blue: #003366; --blue: #303F9F; --light-blue: #a6b5c6; --light-gray: #f6f6f6; }

content {

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: var(--blue); }

postamble {

background:var(--pale-blue); border-top:solid 10px var(--pale-blue); }

postamble .date {

color: white; } .title { text-align: center; color: var(--strong-blue); } .subtitle { color: var(--strong-blue); } h1, h2, h3, h4, h5, h6, legend { color: var(--pale-blue); }

main :not(.leaflet-control) > a {

color: var(--pale-blue); background-image: linear-gradient(180deg,var(--pale-blue),var(--pale-blue)); }

sidebar h2 {

background-color: var(--pale-blue); }

main .nav-pills > li.active > a,

main .nav-pills > li.active > a:hover,

main .nav-pills > li.active > a:focus {

background-color: var(--pale-blue); }

sidebar #toc, #sidebar {

background-color: var(--light-gray) !important; }

sidebar #toc ul li a:hover {

background-color: var(--light-blue); color: white; }

toc ul.nav li.active ul li.active a {

background-color: var(--light-blue); } code { color: var(--strong-blue); }

``` {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> <!-- # -->'))
}

# 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/fernandoroa/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/fernandoroa/IFjupyter/blob/main/",
    note,
    "){target='_blank'}
</td>
<td>
&emsp;&emsp;[Raw](https://github.com/fernandoroa/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(" ,")" ) ) } } } # rcurl

# Introduction {-}

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