Draft core 2

README.md

@@ -0,0 +1,8 @@
+
+# BIO00088H-data
+
+<!-- badges: start -->
+<!-- badges: end -->
+
+The goal of BIO00088H-data is to ...
+

_site/omics/week-3/study_before_workshop.html

@@ -53,6 +53,8 @@
   <link href="../../site_libs/revealjs/plugin/quarto-line-highlight/line-highlight.css" rel="stylesheet">
   <link href="../../site_libs/revealjs/plugin/reveal-menu/menu.css" rel="stylesheet">
   <link href="../../site_libs/revealjs/plugin/reveal-menu/quarto-menu.css" rel="stylesheet">
+  <link href="../../site_libs/revealjs/plugin/reveal-chalkboard/font-awesome/css/all.css" rel="stylesheet">
+  <link href="../../site_libs/revealjs/plugin/reveal-chalkboard/style.css" rel="stylesheet">
   <link href="../../site_libs/revealjs/plugin/quarto-support/footer.css" rel="stylesheet">
   <style type="text/css">
 
@@ -355,7 +357,7 @@ <h1 class="title">Independent Study to prepare for workshop</h1>
 </div>
 </div>
 
-  <p class="date">13 September, 2023</p>
+  <p class="date">1 October, 2023</p>
 </section>
 <section id="omics-workshops" class="slide level2">
 <h2>Omics workshops</h2>
@@ -505,7 +507,7 @@ <h2>Deliverables</h2>
 </ol>
 
 <div class="footer footer-default">
-
+<p>🔗 <a href="https://3mmarand.github.io/BIO00088H-data/omics/week-3/overview.html">About Omics 1: Hello data!</a></p>
 </div>
 <div id="refs" class="references csl-bib-body hanging-indent" role="list">
 <div id="ref-nestorowa2016" class="csl-entry" role="listitem">
@@ -523,6 +525,7 @@ <h2>Deliverables</h2>
   <script src="../../site_libs/revealjs/plugin/pdf-export/pdfexport.js"></script>
   <script src="../../site_libs/revealjs/plugin/reveal-menu/menu.js"></script>
   <script src="../../site_libs/revealjs/plugin/reveal-menu/quarto-menu.js"></script>
+  <script src="../../site_libs/revealjs/plugin/reveal-chalkboard/plugin.js"></script>
   <script src="../../site_libs/revealjs/plugin/quarto-support/support.js"></script>
 
 
@@ -544,7 +547,8 @@ <h2>Deliverables</h2>
 'autoAnimateEasing': "ease",
 'autoAnimateDuration': 1,
 'autoAnimateUnmatched': true,
-'menu': {"side":"left","useTextContentForMissingTitles":true,"markers":false,"loadIcons":false,"custom":[{"title":"Tools","icon":"<i class=\"fas fa-gear\"></i>","content":"<ul class=\"slide-menu-items\">\n<li class=\"slide-tool-item active\" data-item=\"0\"><a href=\"#\" onclick=\"RevealMenuToolHandlers.fullscreen(event)\"><kbd>f</kbd> Fullscreen</a></li>\n<li class=\"slide-tool-item\" data-item=\"1\"><a href=\"#\" onclick=\"RevealMenuToolHandlers.speakerMode(event)\"><kbd>s</kbd> Speaker View</a></li>\n<li class=\"slide-tool-item\" data-item=\"2\"><a href=\"#\" onclick=\"RevealMenuToolHandlers.overview(event)\"><kbd>o</kbd> Slide Overview</a></li>\n<li class=\"slide-tool-item\" data-item=\"3\"><a href=\"#\" onclick=\"RevealMenuToolHandlers.togglePdfExport(event)\"><kbd>e</kbd> PDF Export Mode</a></li>\n<li class=\"slide-tool-item\" data-item=\"4\"><a href=\"#\" onclick=\"RevealMenuToolHandlers.keyboardHelp(event)\"><kbd>?</kbd> Keyboard Help</a></li>\n</ul>"}],"openButton":true},
+'menu': {"side":"left","useTextContentForMissingTitles":true,"markers":false,"loadIcons":false,"custom":[{"title":"Tools","icon":"<i class=\"fas fa-gear\"></i>","content":"<ul class=\"slide-menu-items\">\n<li class=\"slide-tool-item active\" data-item=\"0\"><a href=\"#\" onclick=\"RevealMenuToolHandlers.fullscreen(event)\"><kbd>f</kbd> Fullscreen</a></li>\n<li class=\"slide-tool-item\" data-item=\"1\"><a href=\"#\" onclick=\"RevealMenuToolHandlers.speakerMode(event)\"><kbd>s</kbd> Speaker View</a></li>\n<li class=\"slide-tool-item\" data-item=\"2\"><a href=\"#\" onclick=\"RevealMenuToolHandlers.overview(event)\"><kbd>o</kbd> Slide Overview</a></li>\n<li class=\"slide-tool-item\" data-item=\"3\"><a href=\"#\" onclick=\"RevealMenuToolHandlers.togglePdfExport(event)\"><kbd>e</kbd> PDF Export Mode</a></li>\n<li class=\"slide-tool-item\" data-item=\"4\"><a href=\"#\" onclick=\"RevealMenuToolHandlers.toggleChalkboard(event)\"><kbd>b</kbd> Toggle Chalkboard</a></li>\n<li class=\"slide-tool-item\" data-item=\"5\"><a href=\"#\" onclick=\"RevealMenuToolHandlers.toggleNotesCanvas(event)\"><kbd>c</kbd> Toggle Notes Canvas</a></li>\n<li class=\"slide-tool-item\" data-item=\"6\"><a href=\"#\" onclick=\"RevealMenuToolHandlers.downloadDrawings(event)\"><kbd>d</kbd> Download Drawings</a></li>\n<li class=\"slide-tool-item\" data-item=\"7\"><a href=\"#\" onclick=\"RevealMenuToolHandlers.keyboardHelp(event)\"><kbd>?</kbd> Keyboard Help</a></li>\n</ul>"}],"openButton":true},
+'chalkboard': {"buttons":true},
 'smaller': false,
 
         // Display controls in the bottom right corner
@@ -565,7 +569,7 @@ <h2>Deliverables</h2>
         progress: true,
 
         // Display the page number of the current slide
-        slideNumber: false,
+        slideNumber: 'c/t',
 
         // 'all', 'print', or 'speaker'
         showSlideNumber: 'all',
@@ -715,7 +719,7 @@ <h2>Deliverables</h2>
         },
 
         // reveal.js plugins
-        plugins: [QuartoLineHighlight, PdfExport, RevealMenu, QuartoSupport,
+        plugins: [QuartoLineHighlight, PdfExport, RevealMenu, RevealChalkboard, QuartoSupport,
 
           RevealMath,
           RevealNotes,

_site/search.json

@@ -431,6 +431,6 @@
     "href": "omics/week-3/study_before_workshop.html#deliverables",
     "title": "Independent Study to prepare for workshop",
     "section": "Deliverables",
-    "text": "Deliverables\n\nDescribe the data\n\nNumber of cells/samples/reps/treatments\nnumber of genes\ntype of expression values\nprior processing\nmissing values\noverview of expression\nclustering of genes/samples\n\nReport on differential expression between two groups\n\nnumber of DE at 1%, 5% and 10%.\ntable of expression, fold changes, signifcance at each sig.\nVolcano plot\n\nReport list of marker candidate gene IDs for a cell type of choice. Justify filters. Table with fold FC, p values, IDs, canonical gene names\nInterpret the biology by reporting on a few group of genes and the processes in which they are involved.\nReport on your chosen genes and explain why you think they are good candidates for follow up work\n\n\n\n\n\n\n\nNestorowa, Sonia, Fiona K. Hamey, Blanca Pijuan Sala, Evangelia Diamanti, Mairi Shepherd, Elisa Laurenti, Nicola K. Wilson, David G. Kent, and Berthold Göttgens. 2016. “A Single-Cell Resolution Map of Mouse Hematopoietic Stem and Progenitor Cell Differentiation.” Blood 128 (8): e20–31. https://doi.org/10.1182/blood-2016-05-716480."
+    "text": "Deliverables\n\nDescribe the data\n\nNumber of cells/samples/reps/treatments\nnumber of genes\ntype of expression values\nprior processing\nmissing values\noverview of expression\nclustering of genes/samples\n\nReport on differential expression between two groups\n\nnumber of DE at 1%, 5% and 10%.\ntable of expression, fold changes, signifcance at each sig.\nVolcano plot\n\nReport list of marker candidate gene IDs for a cell type of choice. Justify filters. Table with fold FC, p values, IDs, canonical gene names\nInterpret the biology by reporting on a few group of genes and the processes in which they are involved.\nReport on your chosen genes and explain why you think they are good candidates for follow up work\n\n\n\n🔗 About Omics 1: Hello data!\n\n\n\nNestorowa, Sonia, Fiona K. Hamey, Blanca Pijuan Sala, Evangelia Diamanti, Mairi Shepherd, Elisa Laurenti, Nicola K. Wilson, David G. Kent, and Berthold Göttgens. 2016. “A Single-Cell Resolution Map of Mouse Hematopoietic Stem and Progenitor Cell Differentiation.” Blood 128 (8): e20–31. https://doi.org/10.1182/blood-2016-05-716480."
   }
 ]

_site/site_libs/revealjs/plugin/reveal-chalkboard/README.md

@@ -0,0 +1,160 @@
+# Chalkboard
+
+With this plugin you can add a chalkboard to reveal.js. The plugin provides two possibilities to include handwritten notes to your presentation:
+
+- you can make notes directly on the slides, e.g. to comment on certain aspects,
+- you can open a chalkboard or whiteboard on which you can make notes.
+
+The main use case in mind when implementing the plugin is classroom usage in which you may want to explain some course content and quickly need to make some notes.
+
+The plugin records all drawings made so that they can be play backed using the `autoSlide` feature or the `audio-slideshow` plugin.
+
+[Check out the live demo](https://rajgoel.github.io/reveal.js-demos/chalkboard-demo.html)
+
+The chalkboard effect is based on [Chalkboard](https://github.com/mmoustafa/Chalkboard) by Mohamed Moustafa.
+
+## Installation
+
+Copy the file `plugin.js` and the  `img` directory into the plugin folder of your reveal.js presentation, i.e. `plugin/chalkboard` and load the plugin as shown below.
+
+```html
+<script src="plugin/chalkboard/plugin.js"></script>
+<script src="plugin/customcontrols/plugin.js"></script>
+
+<script>
+    Reveal.initialize({
+        // ...
+        plugins: [ RevealChalkboard, RevealCustomControls ],
+        // ...
+    });
+</script>
+```
+
+The following stylesheet
+```html
+<link rel="stylesheet" href="plugin/chalkboard/style.css">
+<link rel="stylesheet" href="plugin/customcontrols/style.css">
+```
+has to be included to the `head` section of you HTML-file.
+
+
+In order to include buttons for opening and closing the notes canvas or the chalkboard you should make sure that `font-awesome` is available. The easiest way is to include
+```
+<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/font-awesome/4.5.0/css/font-awesome.min.css">
+```
+to the ```head``` section of you HTML-file.
+
+## Usage
+
+### Mouse or touch
+- Click on the pen symbols at the bottom left to toggle the notes canvas or chalkboard
+- Click on the color picker at the left to change the color (the color picker is only visible if the notes canvas or chalkboard is active)
+- Click on the up/down arrows on the left to the switch among multiple chalkboardd (the up/down arrows are only available for the chlakboard)
+- Click the left mouse button and drag to write on notes canvas or chalkboard
+- Click the right mouse button and drag to wipe away previous drawings
+- Touch and move to write on notes canvas or chalkboard
+- Touch and hold for half a second, then move to wipe away previous drawings
+
+### Keyboard
+- Press the 'BACKSPACE' key to delete all chalkboard drawings
+- Press the 'DEL' key to clear the notes canvas or chalkboard
+- Press the 'c' key to toggle the notes canvas
+- Press the 'b' key to toggle the chalkboard
+- Press the 'd' key to download drawings
+- Press the 'x' key to cycle colors forward
+- Press the 'y' key to cycle colors backward
+
+## Playback
+
+If the `autoSlide` feature is set or if the `audio-slideshow` plugin is used, pre-recorded chalkboard drawings can be played. The slideshow plays back the user interaction with the chalkboard in the same way as it was conducted when recording the data.
+
+## Multiplexing
+
+The plugin supports multiplexing via the [`multiplex` plugin](https://github.com/reveal/multiplex) or the [`seminar` plugin](https://github.com/rajgoel/reveal.js-plugins/tree/master/seminar).
+
+## PDF-Export
+
+If the slideshow is opened in [print mode](https://revealjs.com/pdf-export/), the chalkboard drawings in the session storage (see `storage` option - print version must be opened in the same tab or window as the original slideshow) or provided in a file (see `src` option) are included in the PDF-file. Each drawing on the chalkboard is added after the slide that was shown when opening the chalkboard. Drawings on the notes canvas are not included in the PDF-file.
+
+
+## Configuration
+
+The plugin has several configuration options:
+
+- ```boardmarkerWidth```: an integer, the drawing width of the boardmarker; larger values draw thicker lines.
+- ```chalkWidth```: an integer, the drawing width of the chalk; larger values draw thicker lines.
+- ```chalkEffect```: a float in the range ```[0.0, 1.0]```, the intesity of the chalk effect on the chalk board. Full effect (default) ```1.0```, no effect ```0.0```.
+- ```storage```: Optional variable name for session storage of drawings.
+- ```src```: Optional filename for pre-recorded drawings.
+- ```readOnly```: Configuation option allowing to prevent changes to existing drawings. If set to ```true``` no changes can be made, if set to false ```false``` changes can be made, if unset or set to ```undefined``` no changes to the drawings can be made after returning to a slide or fragment for which drawings had been recorded before. In any case the recorded drawings for a slide or fragment can be cleared by pressing the 'DEL' key (i.e. by using the ```RevealChalkboard.clear()``` function).
+- ```transition```: Gives the duration (in milliseconds) of the transition for a slide change, so that the notes canvas is drawn after the transition is completed.
+- ```theme```: Can be set to either ```"chalkboard"``` or ```"whiteboard"```.
+
+The following configuration options allow to change the appearance of the notes canvas and the chalkboard. All of these options require two values, the first gives the value for the notes canvas, the second for the chalkboard.
+
+- ```background```: The first value expects a (semi-)transparent color which is used to provide visual feedback that the notes canvas is enabled, the second value expects a filename to a background image for the chalkboard.
+- ```grid```: By default whiteboard and chalkboard themes include a grid pattern on the background. This pattern can be modified by setting the color, the distance between lines, and the line width, e.g. ```{ color: 'rgb(127,127,255,0.1)', distance: 40, width: 2}```. Alternatively, the grid can be removed by setting the value to ```false```.
+- ```eraser```: An image path and radius for the eraser.
+- ```boardmarkers```: A list of boardmarkers with given color and cursor.
+- ```chalks```: A list of chalks with given color and cursor.
+- ```rememberColor```: Whether to remember the last selected color for the slide canvas or the board.
+
+All of the configurations are optional and the default values shown below are used if the options are not provided.
+
+```javascript
+Reveal.initialize({
+	// ...
+    chalkboard: {
+        boardmarkerWidth: 3,
+        chalkWidth: 7,
+        chalkEffect: 1.0,
+        storage: null,
+        src: null,
+        readOnly: undefined,
+        transition: 800,
+        theme: "chalkboard",
+        background: [ 'rgba(127,127,127,.1)' , path + 'img/blackboard.png' ],
+        grid: { color: 'rgb(50,50,10,0.5)', distance: 80, width: 2},
+        eraser: { src: path + 'img/sponge.png', radius: 20},
+        boardmarkers : [
+                { color: 'rgba(100,100,100,1)', cursor: 'url(' + path + 'img/boardmarker-black.png), auto'},
+                { color: 'rgba(30,144,255, 1)', cursor: 'url(' + path + 'img/boardmarker-blue.png), auto'},
+                { color: 'rgba(220,20,60,1)', cursor: 'url(' + path + 'img/boardmarker-red.png), auto'},
+                { color: 'rgba(50,205,50,1)', cursor: 'url(' + path + 'img/boardmarker-green.png), auto'},
+                { color: 'rgba(255,140,0,1)', cursor: 'url(' + path + 'img/boardmarker-orange.png), auto'},
+                { color: 'rgba(150,0,20150,1)', cursor: 'url(' + path + 'img/boardmarker-purple.png), auto'},
+                { color: 'rgba(255,220,0,1)', cursor: 'url(' + path + 'img/boardmarker-yellow.png), auto'}
+        ],
+        chalks: [
+                { color: 'rgba(255,255,255,0.5)', cursor: 'url(' + path + 'img/chalk-white.png), auto'},
+                { color: 'rgba(96, 154, 244, 0.5)', cursor: 'url(' + path + 'img/chalk-blue.png), auto'},
+                { color: 'rgba(237, 20, 28, 0.5)', cursor: 'url(' + path + 'img/chalk-red.png), auto'},
+                { color: 'rgba(20, 237, 28, 0.5)', cursor: 'url(' + path + 'img/chalk-green.png), auto'},
+                { color: 'rgba(220, 133, 41, 0.5)', cursor: 'url(' + path + 'img/chalk-orange.png), auto'},
+                { color: 'rgba(220,0,220,0.5)', cursor: 'url(' + path + 'img/chalk-purple.png), auto'},
+                { color: 'rgba(255,220,0,0.5)', cursor: 'url(' + path + 'img/chalk-yellow.png), auto'}
+        ]
+    },
+    customcontrols: {
+  		controls: [
+  			{ icon: '<i class="fa fa-pen-square"></i>',
+  			  title: 'Toggle chalkboard (B)',
+  			  action: 'RevealChalkboard.toggleChalkboard();'
+  			},
+  			{ icon: '<i class="fa fa-pen"></i>',
+  			  title: 'Toggle notes canvas (C)',
+  			  action: 'RevealChalkboard.toggleNotesCanvas();'
+  			}
+  		]
+    },
+    // ...
+
+});
+```
+
+
+## License
+
+MIT licensed
+
+Copyright (C) 2021 Asvin Goel

core/core.qmd

@@ -11,24 +11,18 @@ Good organisation is important because you will want to be able to set work asid
 
 ## Week 1 Core 1 Organising reproducible data analyses
 
-This week you will revise some essential concepts for scientific computing: file system organisation, file types, working directories and paths. The workshop will cover a rationale for working reproducibly, project oriented workflow, naming things and documenting your work. We will also examine some file types and the concept of tidy data.
+This week you will revise some essential concepts for scientific computing: file system organisation, file types, working directories and paths. The workshop will cover a rationale for working reproducibly, project oriented workflow, naming things and documenting your work.
 
 
-## Week 2 Core 2 Workflow tips
+## Week 2 Core 2 File types, workflow tips and other tools
 
 <!-- Before  -->
 <!-- Apply to GitHub Global Campus as a student -->
 
-<!-- -   Reference managers: Zotero -->
-<!-- -   github copilot -->
-<!-- -   chat gtp -->
-<!-- -   Data management -->
-<!--     -   google drive: https://www.york.ac.uk/it-services/services/drive/#tab-6 -->
 
 
-<!-- Workshop -->
 
-<!-- Code formatting and style, 😎 Cool code Tips, Code 'algorithmically.', Writing functions (R and python??) (BIO00058M-Data-science-2020/slides/03_repro_and_intro_to_rmarkdown) -->
+
 
 
 <!-- After -->

core/week-1/styles.css

@@ -0,0 +1,16 @@
+/* css styles */
+
+
+@import url('https://fonts.googleapis.com/css2?family=Open+Sans&family=Source+Code+Pro&display=swap');
+
+
+// fonts
+
+$font-family-monospace: "Source Code Pro";
+
+/*-- scss:rules --*/
+
+code.sourceCode {
+  font-size: 1.3em;
+}
+

core/week-2/overview.qmd

@@ -1,33 +1,42 @@
 ---
 title: "Overview"
-subtitle: "Core 2:  Workflow tips"
+subtitle: "Core 2: File types, workflow tips and other tools"
 ---
 
-xxxxx
+This week
 
 ### Learning objectives
 
--   dd
--   dd.
--   dd
--   d
+The successful student will be able to:
+
+-   explain why RStudio are useful/essential and be able to use the **`usethis`** package 
+-   write cool 😎 code not 😩 ugly code
+-   explain the value of code which expresses the structure of the problem/solution.
+-   describe some common file types for biological data
+-   use some useful shortcuts to help write cool 😎 code
+-   know what the command line is and how to use it for simple tasks
+-   use Google colab to run code
+-   recognise some of the differences between R and Python
 
 ### Instructions
 
-1.  [Prepare](study_before_workshop.qmd)
+1.  [Prepare](study_before_workshop.qmd) 20 mins reading on RStudio Projects revisited, formatting code and coding algorithmically
 
-    i.  📖 Read 
 
 2.  [Workshop](workshop.qmd)
 
-    i.  💻 dd.
+    i.  💬 Types of biological data files
 
-    ii. 💻 ddd
+    ii. 🪄 Workflow tips and shortcuts
 
-    iii. 💻 ddd
+    iii. 💻 The command line
+
+    iv.  💻 Google colab
+
+    v.  💻 Python
 
 3.  [Consolidate](study_after_workshop.qmd)
 
-    i.  💻 dd
+    i.  💻 not sure yet :)
+
 
-    ii. 💻 dd

core/week-2/study_after_workshop.qmd

@@ -7,19 +7,4 @@ format:
     code-summary: "Answer - don't look until you have tried!"
 ---
 
-# Set up
-
-If you have just opened RStudio you will want to load the packages and import the data.
-
-```{r}
-#| code-fold: false
-library(tidyverse)
-library(readxl)
-```
-
-1.  💻 xx.
-
-```{r}
-
-
-```
+# bbbb