To Do before BioC2023 workshop
jdrnevich opened this issue · 3 comments
jdrnevich commented
List of things still needing to be done:
- Put all required packages from each episode in learners/setup.md
- Add "Download handouts" see: carpentries-incubator/bioc-intro@a9a8490
- Remove beginning warnings from pages
- Check on callout box types - varnish package
- Check to see if SummarizedExperiment constructor checks genes/samples consistency
- New subsection in Lesson 3 about general data provenance and reproducibility
- Add discussion and/or coding challenge in lesson 3
- Add short discussion of design matrix in lesson 4 and link to lesson 8 for more info
- email attendees with set up instructions to be done BEFORE the workshop
- Run through entire workshop as learner with brand new R/RStudio
- Run through entire workshop as learner using BioC's Galaxy instance as backup: https://workshop.bioconductor.org/
- Why download_data.R run at the beginning of each episode? Add additional manipulations to it or have a second version for later episodes?
- Online note place?
- post-it notes and name tags
jokergoo commented
I have a solution for task 4: "Check on callout box types - varnish package"
Basically you add a small piece of Javascript code to the end of the Rmarkdown document. I also added the usage as comments in the following code:
<script>
$(function() {
// this part is for the "pre-defind callouts", including
// callout prereq
// callout challenge
// callout keypoints
// callout checklist
// callout testimonial
// callout discussion
var callout_class = "challenge"; // here pick one predefined callout class, e.g. "challenge"
var callout = $(".callout." + callout_class);
callout.css("border-color", "red"); // select a color, this is for the left border of the box
callout.find(".callout-square").css("background", "red"); // this is the background of the icon
// if it is a general "callout", we need to filter the callout title
// value for callout_title can be partial from the complete title
var callout_title = "reading"; // short for "further reading"
// then we select those callouts with the specified title
var callout = $(".callout").filter(function(index) {
var title = $(this).find(".callout-title").text();
return title.indexOf(callout_title) >= 0;
});
callout.css("border-color", "blue"); // select a color, this is for the left border of the box
callout.find(".callout-square").css("background", "blue"); // select a color, this is for the left border of the box
// if you want to replace the default icon, go to https://feathericons.com/, and get the source of the svg icon.
// here something is very important is you must add 'callout-icon' to the class of this svg
var svg = '<svg xmlns="http://www.w3.org/2000/svg" width="24" height="24" viewBox="0 0 24 24" fill="none" stroke="currentColor" stroke-width="2" stroke-linecap="round" stroke-linejoin="round" class="feather feather-award callout-icon"><circle cx="12" cy="8" r="7"></circle><polyline points="8.21 13.89 7 23 12 20 17 23 15.79 13.88"></polyline></svg>';
// then update it with the new icon
callout.find(".callout-square").html(svg);
});
</script>Validation: I changed the default icon to the "award" and the color from "deep green purple" to blue
Before:
After:
jokergoo commented
And for task 3, you can add a knitr global option in the beginning of the rmarkdown document:
```{r, echo = FALSE, message = FALSE}
library(knitr)
knitr::opts_chunk$set(
warning = FALSE
)
\```