Updated contents at 20230814-143302

2310-canvas/assets/footer-lab.Rmd

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+---
+title: " "
+---
+
+<footer class="footer">
+<div class="container footer-container">
+<div class="row">
+
+<div class="col-sm-8" style="text-align:left;vertical-align:middle;">
+<p class="small" style="color:#bdbdbd;">
+<b>2023</b> • [NBIS](https://nbis.se/) • [SciLifeLab](https://www.scilifelab.se/)
+</p>
+</div>
+
+<div class="col-sm-4" style="text-align:right;vertical-align:middle;">
+<p style="color:#bdbdbd;">
+<span>
+<span class="footericon" style="padding-right:4px; padding-left:4px">
+<a href="https://nbis.se/">`r fontawesome::fa("globe-americas",fill="#bdbdbd")`</a>
+</span>
+<span class="footericon" style="padding-right:4px; padding-left:4px">
+<a href="https://twitter.com/NBISwe">`r fontawesome::fa("twitter",fill="#bdbdbd")`</a>
+</span>
+<span class="footericon" style="padding-left:4px">
+<a href="https://www.linkedin.com/company/nbisweden/">`r fontawesome::fa("linkedin",fill="#bdbdbd")`</a>
+</span>
+</span>
+</p>
+</div>
+
+</div>
+</div>
+</footer>

2310-canvas/assets/footer-lab.html

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+
+<footer class="footer">
+<div class="container footer-container">
+<div class="row">
+
+<div class="footer-left col-sm-6">
+<p class="small">
+<b>2023</b> • <a href="https://nbis.se/">NBIS</a> • <a href="https://www.scilifelab.se/">SciLifeLab</a>
+</p>
+</div>
+
+<div class="footer-right col-sm-6">
+<p>
+<span>
+  <span class="footericon" style="padding-right:4px; padding-left:4px">
+    <a href="https://nbis.se/">
+      <svg style="height:0.8em;top:.04em;position:relative;fill:#bdbdbd;" viewBox="0 0 496 512"><path d="M248 8C111.03 8 0 119.03 0 256s111.03 248 248 248 248-111.03 248-248S384.97 8 248 8zm82.29 357.6c-3.9 3.88-7.99 7.95-11.31 11.28-2.99 3-5.1 6.7-6.17 10.71-1.51 5.66-2.73 11.38-4.77 16.87l-17.39 46.85c-13.76 3-28 4.69-42.65 4.69v-27.38c1.69-12.62-7.64-36.26-22.63-51.25-6-6-9.37-14.14-9.37-22.63v-32.01c0-11.64-6.27-22.34-16.46-27.97-14.37-7.95-34.81-19.06-48.81-26.11-11.48-5.78-22.1-13.14-31.65-21.75l-.8-.72a114.792 114.792 0 0 1-18.06-20.74c-9.38-13.77-24.66-36.42-34.59-51.14 20.47-45.5 57.36-82.04 103.2-101.89l24.01 12.01C203.48 89.74 216 82.01 216 70.11v-11.3c7.99-1.29 16.12-2.11 24.39-2.42l28.3 28.3c6.25 6.25 6.25 16.38 0 22.63L264 112l-10.34 10.34c-3.12 3.12-3.12 8.19 0 11.31l4.69 4.69c3.12 3.12 3.12 8.19 0 11.31l-8 8a8.008 8.008 0 0 1-5.66 2.34h-8.99c-2.08 0-4.08.81-5.58 2.27l-9.92 9.65a8.008 8.008 0 0 0-1.58 9.31l15.59 31.19c2.66 5.32-1.21 11.58-7.15 11.58h-5.64c-1.93 0-3.79-.7-5.24-1.96l-9.28-8.06a16.017 16.017 0 0 0-15.55-3.1l-31.17 10.39a11.95 11.95 0 0 0-8.17 11.34c0 4.53 2.56 8.66 6.61 10.69l11.08 5.54c9.41 4.71 19.79 7.16 30.31 7.16s22.59 27.29 32 32h66.75c8.49 0 16.62 3.37 22.63 9.37l13.69 13.69a30.503 30.503 0 0 1 8.93 21.57 46.536 46.536 0 0 1-13.72 32.98zM417 274.25c-5.79-1.45-10.84-5-14.15-9.97l-17.98-26.97a23.97 23.97 0 0 1 0-26.62l19.59-29.38c2.32-3.47 5.5-6.29 9.24-8.15l12.98-6.49C440.2 193.59 448 223.87 448 256c0 8.67-.74 17.16-1.82 25.54L417 274.25z"></path>
+      </svg>
+    </a>
+    </span>
+    <span class="footericon" style="padding-right:4px; padding-left:4px">
+      <a href="https://twitter.com/NBISwe"><svg style="height:0.8em;top:.04em;position:relative;fill:#bdbdbd;" viewBox="0 0 512 512"><path d="M459.37 151.716c.325 4.548.325 9.097.325 13.645 0 138.72-105.583 298.558-298.558 298.558-59.452 0-114.68-17.219-161.137-47.106 8.447.974 16.568 1.299 25.34 1.299 49.055 0 94.213-16.568 130.274-44.832-46.132-.975-84.792-31.188-98.112-72.772 6.498.974 12.995 1.624 19.818 1.624 9.421 0 18.843-1.3 27.614-3.573-48.081-9.747-84.143-51.98-84.143-102.985v-1.299c13.969 7.797 30.214 12.67 47.431 13.319-28.264-18.843-46.781-51.005-46.781-87.391 0-19.492 5.197-37.36 14.294-52.954 51.655 63.675 129.3 105.258 216.365 109.807-1.624-7.797-2.599-15.918-2.599-24.04 0-57.828 46.782-104.934 104.934-104.934 30.213 0 57.502 12.67 76.67 33.137 23.715-4.548 46.456-13.32 66.599-25.34-7.798 24.366-24.366 44.833-46.132 57.827 21.117-2.273 41.584-8.122 60.426-16.243-14.292 20.791-32.161 39.308-52.628 54.253z"></path>
+    </svg>
+    </a>
+    </span>
+    <span class="footericon" style="padding-left:4px">
+      <a href="https://www.linkedin.com/company/nbisweden/">
+        <svg style="height:0.8em;top:.04em;position:relative;fill:#bdbdbd;" viewBox="0 0 448 512"><path d="M416 32H31.9C14.3 32 0 46.5 0 64.3v383.4C0 465.5 14.3 480 31.9 480H416c17.6 0 32-14.5 32-32.3V64.3c0-17.8-14.4-32.3-32-32.3zM135.4 416H69V202.2h66.5V416zm-33.2-243c-21.3 0-38.5-17.3-38.5-38.5S80.9 96 102.2 96c21.2 0 38.5 17.3 38.5 38.5 0 21.3-17.2 38.5-38.5 38.5zm282.1 243h-66.4V312c0-24.8-.5-56.7-34.5-56.7-34.6 0-39.9 27-39.9 54.9V416h-66.4V202.2h63.7v29.2h.9c8.9-16.8 30.6-34.5 62.9-34.5 67.2 0 79.7 44.3 79.7 101.9V416z"></path>
+        </svg>
+    </a>
+    </span>
+  </span>
+</p>
+</div>
+
+</div>
+</div>
+</footer>

2310-canvas/assets/footer-slide.Rmd

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+.end-text[
+<p class="smaller">
+<span class="small" style="line-height: 1.2;">Graphics from </span><img src="./assets/freepik.jpg" style="max-height:20px; vertical-align:middle;"><br>
+`r paste0("Created: ",format(Sys.time(),format='%d-%b-%Y'))` • Roy Francis • <a href="https://www.scilifelab.se/">SciLifeLab</a> • <a href="https://nbis.se/">NBIS</a>
+</p>
+]

2310-canvas/assets/header-lab.Rmd

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+<!-- rmd lab header -->
+
+```{r,include=FALSE,cache=FALSE}
+# load libraries
+library(knitr) # runs pandoc
+library(bookdown) # for markdown
+library(captioner) # for table and figure captions
+library(fontawesome) # icons
+
+# fontawesome dependency
+fa <- rmarkdown::html_dependency_font_awesome()
+fa$attachment <- "fonts/fontawesome-webfont.ttf"
+htmltools::tagList(fa)
+
+# prepare captions
+tc <- captioner::captioner(prefix="<b>Tab. </b>")
+fc <- captioner::captioner(prefix="<b>Fig. </b>")
+
+# turn off terminal colors
+options(crayon.enabled = FALSE)
+
+# knitr options
+knitr::opts_knit$set(progress=TRUE,verbose=TRUE)
+knitr::opts_chunk$set(dev="png",fig.retina=2,results="hold",fig.show="hold",fig.align="left",
+                      echo=TRUE,warning=FALSE,message=FALSE,accordion=NULL,
+                      chunk.title=NULL)
+color_primary <- "#95b540"
+color_text <- "#424949"
+```
+
+```{r,include=FALSE,cache=FALSE}
+# custom hooks
+## collapsible panel
+knitr::knit_hooks$set(accordion=function(before,options,envir) {
+  if(before) {
+    id <- paste0("acc",format(Sys.time(),"%Y%m%d%H%S"),sample(c(0:9),1),sample(c(0:9),1),sample(c(0:9),1),sample(c(0:9),1))
+    if(is.null(options$btn.type)) {btn.type <- "normal"}else{btn.type <- options$btn.type}
+    paste0('<p>',
+          '<button class="btn btn-sm btn-primary btn-collapse btn-collapse-',btn.type,' collapsed" type="button" data-toggle="collapse" data-target="#',id,'" aria-expanded="false" aria-controls="',id,'">',
+          '</button>',
+          '</p>',
+          '<div class="collapse" id="',id,'">',
+          '<div class="card card-body">')
+  }else{
+    paste0("</div>","</div>")
+  }
+})
+
+## blur panel
+knitr::knit_hooks$set(blur=function(before,options,envir) {
+  if(before) {
+    if(is.null(options$blur.title)) {blur.title <- ""}else{blur.title <- options$blur.title}
+    paste0('<div class="blur-outer">',
+           '<div class="blur-title">',blur.title,'</div>',
+           '<div class="blur-content">')
+  }else{
+    paste0("</div>","</div>")
+  }
+})
+
+## chunk.title for code
+knitr::knit_hooks$set(chunk.title=function(before,options,envir) {
+
+out_class <- NULL
+if(is.null(options$class.output)) {
+if(options$echo) out_class <- options$engine
+if((!options$echo) & (options$results != "hide")) out_class <- "Output"
+}else{
+  out_class <- options$class.output
+}
+
+  if(before) {
+    paste0('<div class="chunk-title-parent"><div class="chunk-title small">',out_class,'</div>')
+  }else{
+    paste0('</div>')
+  }
+})
+
+# knit engine output
+
+eng_output <- function(options) {
+  out <- ''
+  engine_output(options, options$code, out)
+}
+
+knitr::knit_engines$set(output=eng_output)
+
+# custom fontawesome fa function
+fa1 <- function (name=NULL,style="height:0.8em;top:0.04em;position:relative;fill:#424949;",extra_style=NULL)
+{
+    full_name <- NULL
+    if (name %in% fontawesome:::fa_tbl$full_name) {
+        svg <- fontawesome:::fa_tbl[which(fontawesome:::fa_tbl$full_name == name), ][1, 4]
+    }
+    else if (name %in% fontawesome:::fa_tbl$name) {
+        svg <- fontawesome:::fa_tbl[which(fontawesome:::fa_tbl$name == name), ][1, 4]
+    }
+    else {
+        return("")
+    }
+
+    if(!is.null(extra_style)) style <- paste0(style,extra_style)
+    style <- paste0("style=\"", style, "\"")
+
+    if (!grepl(style, pattern = "style=\"\"")) {
+        svg <- gsub(pattern = "^<svg", replacement = paste0("<svg ",
+            style), x = svg)
+    }
+    svg <- htmltools::HTML(svg)
+    class(svg) <- c("fontawesome", class(svg))
+    return(paste0("<span>",svg,"</span>"))
+}
+
+fa2 <- function(name=NULL,style="height:0.8em;top:0.04em;position:relative;fill:white;margin-left:0.45em;margin-bottom: 0.1em;") {
+  return(fa1(name,style))
+}
+```
+
+<br>

2310-canvas/assets/header-slide.Rmd

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+<link href="https://fonts.googleapis.com/css?family=Roboto|Source+Sans+Pro:300,400,600|Ubuntu+Mono&amp;subset=latin-ext" rel="stylesheet">
+<link rel="stylesheet" href="https://use.fontawesome.com/releases/v5.3.1/css/all.css" integrity="sha384-mzrmE5qonljUremFsqc01SB46JvROS7bZs3IO2EmfFsd15uHvIt+Y8vEf7N7fWAU" crossorigin="anonymous">
+
+```{r,include=FALSE,eval=knitr::opts_knit$get("rmarkdown.pandoc.to")=="html"}
+# Enables Font Awesome in HTML based bookdown outputs.
+fa <- rmarkdown::html_dependency_font_awesome()
+fa$attachment <- "fonts/fontawesome-webfont.ttf"
+htmltools::tagList(fa)
+```
+
+```{r,echo=FALSE,message=FALSE,warning=FALSE,results='hide'}
+# run setup code
+
+# load libraries
+library(knitr) # runs pandoc
+library(bookdown) # for markdown
+
+color_primary <- "#95b540"
+color_text <- "#424949"
+
+# turn off terminal colors
+options(crayon.enabled = FALSE)
+
+# knitr options
+knitr::opts_knit$set(progress=TRUE,verbose=TRUE)
+knitr::opts_chunk$set(dev="png",fig.retina=2,results="hold",fig.show="hold",fig.align="left",echo=TRUE,warning=FALSE,message=FALSE)
+```