install section link + smaller branch fig

97-git.Rmd

@@ -252,7 +252,7 @@ traditional command line.
 This section of the course is based on the *Happy Git and GitHub for
 the useR* [tutorial](https://happygitwithr.com/) by Jennifer Bryan.
 
-### Install Git
+### Install Git {#sec-install-git}
 
 Git needs to be install first on your computer for RStudio to use
 it. Installation is different depending on the operating system of
@@ -524,7 +524,7 @@ default (main) branch below, and a *work* branch. Once the work in the
 *work* branch is completed, its changes can be merged back into the
 *main* branch.
 
-```{r branch, fig.cap="Git branches.", echo=FALSE, purl=FALSE, out.width='100%', fig.align='center'}
+```{r branch, fig.cap="Git branches.", echo=FALSE, purl=FALSE, out.width='60%'}
 knitr::include_graphics("figs/branch.png")
 ```
 

docs/reference-keys.txt

@@ -155,7 +155,7 @@ automated-version-control
 introduction-to-git-and-github
 getting-started
 git-and-rstudio
-install-git
+sec-install-git
 connect-rstudio-to-your-github-repo
 git-and-command-line
 handling-conflicts

docs/sec-git.html

@@ -488,9 +488,9 @@ <h2>
 traditional command line.</p>
 <p>This section of the course is based on the <em>Happy Git and GitHub for
 the useR</em> <a href="https://happygitwithr.com/">tutorial</a> by Jennifer Bryan.</p>
-<div id="install-git" class="section level3" number="11.5.1">
+<div id="sec-install-git" class="section level3" number="11.5.1">
 <h3>
-<span class="header-section-number">11.5.1</span> Install Git<div class="tooltip"><button class="internal-link-btn" onclick="copy_link('install-git')" onmouseout="reset_tooltip('install-git-tooltip')"><span class="tooltiptext" id="install-git-tooltip">Copy link</span><i class="fa fa-link"></i></button></div>
+<span class="header-section-number">11.5.1</span> Install Git<div class="tooltip"><button class="internal-link-btn" onclick="copy_link('sec-install-git')" onmouseout="reset_tooltip('sec-install-git-tooltip')"><span class="tooltiptext" id="sec-install-git-tooltip">Copy link</span><i class="fa fa-link"></i></button></div>
 </h3>
 <p>Git needs to be install first on your computer for RStudio to use
 it. Installation is different depending on the operating system of
@@ -744,12 +744,12 @@ <h3>Branches<div class="tooltip"><button class="internal-link-btn" onclick="copy
 default (main) branch below, and a <em>work</em> branch. Once the work in the
 <em>work</em> branch is completed, its changes can be merged back into the
 <em>main</em> branch.</p>
-<div class="figure" style="text-align: center">
+<div class="figure">
 <span style="display:block;" id="fig:branch"></span>
 <p class="caption marginnote shownote">
 Figure 11.5: Git branches.
 </p>
-<img src="figs/branch.png" alt="Git branches." width="100%">
+<img src="figs/branch.png" alt="Git branches." width="60%">
 </div>
 <p>At this point, if the same lines where modified in the <em>main</em> and
 <em>work</em> branches, conflicts would need to be addressed, as seen above.</p>

docs/sec-hts.html

@@ -706,8 +706,8 @@ <h2>
 the raw counts of each gene in that sample.</p>
 <div class="sourceCode" id="cb92"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb92-1"><a href="sec-hts.html#cb92-1" tabindex="-1"></a>counts_result <span class="ot">&lt;-</span> <span class="fu">read_tsv</span>(<span class="at">file =</span> <span class="st">"wsbim2122_data/count_data/sample1_counts.tsv.gz"</span>)</span>
 <span id="cb92-2"><a href="sec-hts.html#cb92-2" tabindex="-1"></a><span class="fu">datatable</span>(<span class="fu">head</span>(counts_result))</span></code></pre></div>
-<div class="datatables html-widget html-fill-item" id="htmlwidget-9de02a3ebad8d64efe56" style="width:100%;height:auto;"></div>
-<script type="application/json" data-for="htmlwidget-9de02a3ebad8d64efe56">{"x":{"filter":"none","vertical":false,"data":[["1","2","3","4","5","6"],["ENSG00000223972","ENSG00000227232","ENSG00000278267","ENSG00000243485","ENSG00000284332","ENSG00000237613"],["1;1;1;1;1;1;1;1;1","1;1;1;1;1;1;1;1;1;1;1","1","1;1;1;1;1","1","1;1;1;1;1"],["11869;12010;12179;12613;12613;12975;13221;13221;13453","14404;15005;15796;16607;16858;17233;17606;17915;18268;24738;29534","17369","29554;30267;30564;30976;30976","30366","34554;35245;35277;35721;35721"],["12227;12057;12227;12721;12697;13052;13374;14409;13670","14501;15038;15947;16765;17055;17368;17742;18061;18366;24891;29570","17436","30039;30667;30667;31109;31097","30503","35174;35481;35481;36073;36081"],["+;+;+;+;+;+;+;+;+","-;-;-;-;-;-;-;-;-;-;-","-","+;+;+;+;+","+","-;-;-;-;-"],[1735,1351,68,1021,138,1219],[0,14,8,0,0,0]],"container":"<table class=\"display\">\n  <thead>\n    <tr>\n      <th> <\/th>\n      <th>Geneid<\/th>\n      <th>Chr<\/th>\n      <th>Start<\/th>\n      <th>End<\/th>\n      <th>Strand<\/th>\n      <th>Length<\/th>\n      <th>../processed_data/bam/sample1.bam<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"columnDefs":[{"className":"dt-right","targets":[6,7]},{"orderable":false,"targets":0},{"name":" ","targets":0},{"name":"Geneid","targets":1},{"name":"Chr","targets":2},{"name":"Start","targets":3},{"name":"End","targets":4},{"name":"Strand","targets":5},{"name":"Length","targets":6},{"name":"../processed_data/bam/sample1.bam","targets":7}],"order":[],"autoWidth":false,"orderClasses":false}},"evals":[],"jsHooks":[]}</script><div class="question">
+<div class="datatables html-widget html-fill-item" id="htmlwidget-6398bd89bb30a8a0b584" style="width:100%;height:auto;"></div>
+<script type="application/json" data-for="htmlwidget-6398bd89bb30a8a0b584">{"x":{"filter":"none","vertical":false,"data":[["1","2","3","4","5","6"],["ENSG00000223972","ENSG00000227232","ENSG00000278267","ENSG00000243485","ENSG00000284332","ENSG00000237613"],["1;1;1;1;1;1;1;1;1","1;1;1;1;1;1;1;1;1;1;1","1","1;1;1;1;1","1","1;1;1;1;1"],["11869;12010;12179;12613;12613;12975;13221;13221;13453","14404;15005;15796;16607;16858;17233;17606;17915;18268;24738;29534","17369","29554;30267;30564;30976;30976","30366","34554;35245;35277;35721;35721"],["12227;12057;12227;12721;12697;13052;13374;14409;13670","14501;15038;15947;16765;17055;17368;17742;18061;18366;24891;29570","17436","30039;30667;30667;31109;31097","30503","35174;35481;35481;36073;36081"],["+;+;+;+;+;+;+;+;+","-;-;-;-;-;-;-;-;-;-;-","-","+;+;+;+;+","+","-;-;-;-;-"],[1735,1351,68,1021,138,1219],[0,14,8,0,0,0]],"container":"<table class=\"display\">\n  <thead>\n    <tr>\n      <th> <\/th>\n      <th>Geneid<\/th>\n      <th>Chr<\/th>\n      <th>Start<\/th>\n      <th>End<\/th>\n      <th>Strand<\/th>\n      <th>Length<\/th>\n      <th>../processed_data/bam/sample1.bam<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"columnDefs":[{"className":"dt-right","targets":[6,7]},{"orderable":false,"targets":0},{"name":" ","targets":0},{"name":"Geneid","targets":1},{"name":"Chr","targets":2},{"name":"Start","targets":3},{"name":"End","targets":4},{"name":"Strand","targets":5},{"name":"Length","targets":6},{"name":"../processed_data/bam/sample1.bam","targets":7}],"order":[],"autoWidth":false,"orderClasses":false}},"evals":[],"jsHooks":[]}</script><div class="question">
 <p class="question-begin">
 ► Question
 </p>

docs/sec-linmod.html

@@ -618,8 +618,8 @@ <h2>
 some genes will increase in the mutant under dry conditions while they
 will decrease (or change to a lesser extend at least) under humid
 conditions.</p>
-<div class="datatables html-widget html-fill-item" id="htmlwidget-154d62cc3ae1980012a6" style="width:100%;height:auto;"></div>
-<script type="application/json" data-for="htmlwidget-154d62cc3ae1980012a6">{"x":{"filter":"none","vertical":false,"data":[[1,2,3,4,5,6,7,8,9,10,11,12],["WT","WT","WT","WT","WT","WT","MT","MT","MT","MT","MT","MT"],["normal","dry","humid","normal","dry","humid","normal","dry","humid","normal","dry","humid"]],"container":"<table class=\"cell-border stripe\">\n  <thead>\n    <tr>\n      <th>sample<\/th>\n      <th>genotype<\/th>\n      <th>condition<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"pageLength":12,"autoWidth":true,"columnDefs":[{"className":"dt-right","targets":0},{"name":"sample","targets":0},{"name":"genotype","targets":1},{"name":"condition","targets":2}],"order":[],"orderClasses":false,"lengthMenu":[10,12,25,50,100]}},"evals":[],"jsHooks":[]}</script><p>Such situation require a new model formula syntax</p>
+<div class="datatables html-widget html-fill-item" id="htmlwidget-ca6c51c775fe0061b0b3" style="width:100%;height:auto;"></div>
+<script type="application/json" data-for="htmlwidget-ca6c51c775fe0061b0b3">{"x":{"filter":"none","vertical":false,"data":[[1,2,3,4,5,6,7,8,9,10,11,12],["WT","WT","WT","WT","WT","WT","MT","MT","MT","MT","MT","MT"],["normal","dry","humid","normal","dry","humid","normal","dry","humid","normal","dry","humid"]],"container":"<table class=\"cell-border stripe\">\n  <thead>\n    <tr>\n      <th>sample<\/th>\n      <th>genotype<\/th>\n      <th>condition<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"pageLength":12,"autoWidth":true,"columnDefs":[{"className":"dt-right","targets":0},{"name":"sample","targets":0},{"name":"genotype","targets":1},{"name":"condition","targets":2}],"order":[],"orderClasses":false,"lengthMenu":[10,12,25,50,100]}},"evals":[],"jsHooks":[]}</script><p>Such situation require a new model formula syntax</p>
 <div class="sourceCode" id="cb36"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb36-1"><a href="sec-linmod.html#cb36-1" tabindex="-1"></a><span class="sc">~</span> genotype <span class="sc">*</span> condition</span></code></pre></div>
 <p>which is equivalent to</p>
 <div class="sourceCode" id="cb37"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb37-1"><a href="sec-linmod.html#cb37-1" tabindex="-1"></a><span class="sc">~</span> genotype <span class="sc">+</span> condition <span class="sc">+</span> genotype <span class="sc">*</span> condition</span></code></pre></div>