Commit ed221aff authored by Davis McCarthy's avatar Davis McCarthy
Browse files

Tweaks to workflowr pages

parent 8cdfd4d2
......@@ -14,9 +14,10 @@ knitr::opts_chunk$set(echo = TRUE)
In this workshop, we will introduce the data infrastructure for scRNA-seq analysis
in R and practice a workflow of scRNAseq analysis; from pre-processing, quality
control to dimensionality reduction aand clustering. We will then demonstrate the
control to dimensionality reduction and clustering. We will then demonstrate the
usage of marker genes for cell type annotation and an automatic approach for matching
query cells to a reference atlas with labels.
You can access everything at the [workshop website](https://biocellgen-public.svi.edu.au/SVI-SAHMRI_scRNA-seq-Workshop_2021-July/public/index.html).
1. [single-cell RNAseq analysis workflow for cell type identification](sahmri_analysis-workflow.html)
---
title: "BIOS_analysis-workflow"
title: "SVI-SAHMRI scRNA-seq analysis workshop"
author: "Ruqian Lyu, Christina Azodi, Jeffrey Pullin, Davis J McCarthy"
date: "2021-07-08"
output: html_document
......@@ -7,7 +7,7 @@ output: html_document
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE,dpi=100)
knitr::opts_chunk$set(echo = TRUE, dpi = 100, warnings = FALSE)
```
## Introduction
......
......@@ -501,7 +501,7 @@ div.tocify {
<p>
<button type="button" class="btn btn-default btn-workflowr btn-workflowr-report" data-toggle="collapse" data-target="#workflowr-report">
<span class="glyphicon glyphicon-list" aria-hidden="true"></span> workflowr <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span>
<span class="glyphicon glyphicon-list" aria-hidden="true"></span> workflowr <span class="glyphicon glyphicon-exclamation-sign text-danger" aria-hidden="true"></span>
</button>
</p>
<div id="workflowr-report" class="collapse">
......@@ -510,7 +510,7 @@ div.tocify {
<a data-toggle="tab" href="#summary">Summary</a>
</li>
<li>
<a data-toggle="tab" href="#checks"> Checks <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> </a>
<a data-toggle="tab" href="#checks"> Checks <span class="glyphicon glyphicon-exclamation-sign text-danger" aria-hidden="true"></span> </a>
</li>
<li>
<a data-toggle="tab" href="#versions">Past versions</a>
......@@ -522,7 +522,7 @@ div.tocify {
<strong>Last updated:</strong> 2021-06-29
</p>
<p>
<strong>Checks:</strong> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> 7 <span class="glyphicon glyphicon-exclamation-sign text-danger" aria-hidden="true"></span> 0
<strong>Checks:</strong> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> 6 <span class="glyphicon glyphicon-exclamation-sign text-danger" aria-hidden="true"></span> 1
</p>
<p>
<strong>Knit directory:</strong> <code>svi-sahmri_scrna-seq-workshop_2021-july/</code> <span class="glyphicon glyphicon-question-sign" aria-hidden="true" title="This is the local directory in which the code in this file was executed."> </span>
......@@ -538,12 +538,12 @@ This reproducible <a href="http://rmarkdown.rstudio.com">R Markdown</a> analysis
<div class="panel panel-default">
<div class="panel-heading">
<p class="panel-title">
<a data-toggle="collapse" data-parent="#workflowr-checks" href="#strongRMarkdownfilestronguptodate"> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> <strong>R Markdown file:</strong> up-to-date </a>
<a data-toggle="collapse" data-parent="#workflowr-checks" href="#strongRMarkdownfilestronguncommittedchanges"> <span class="glyphicon glyphicon-exclamation-sign text-danger" aria-hidden="true"></span> <strong>R Markdown file:</strong> uncommitted changes </a>
</p>
</div>
<div id="strongRMarkdownfilestronguptodate" class="panel-collapse collapse">
<div id="strongRMarkdownfilestronguncommittedchanges" class="panel-collapse collapse">
<div class="panel-body">
<p>Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.</p>
<p>The R Markdown file has unstaged changes. To know which version of the R Markdown file created these results, you’ll want to first commit it to the Git repo. If you’re still working on the analysis, you can ignore this warning. When you’re finished, you can run <code>wflow_publish</code> to commit the R Markdown file and build the HTML.</p>
</div>
</div>
</div>
......@@ -610,16 +610,16 @@ This reproducible <a href="http://rmarkdown.rstudio.com">R Markdown</a> analysis
<div class="panel panel-default">
<div class="panel-heading">
<p class="panel-title">
<a data-toggle="collapse" data-parent="#workflowr-checks" href="#strongRepositoryversionstrongahrefhttpsgitlabsvieduaubiocellgenpublicsvisahmriscrnaseqworkshop2021julytreee12dd3814dba0bc23ad5152774540d663a2364ectargetblanke12dd38a"> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> <strong>Repository version:</strong> <a href="https://gitlab.svi.edu.au/biocellgen-public/svi-sahmri_scrna-seq-workshop_2021-july/tree/e12dd3814dba0bc23ad5152774540d663a2364ec" target="_blank">e12dd38</a> </a>
<a data-toggle="collapse" data-parent="#workflowr-checks" href="#strongRepositoryversionstrongahrefhttpsgitlabsvieduaubiocellgenpublicsvisahmriscrnaseqworkshop2021julytree8cdfd4d2208ce4b2f974bbffa1cc13fed04dcd8ctargetblank8cdfd4da"> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> <strong>Repository version:</strong> <a href="https://gitlab.svi.edu.au/biocellgen-public/svi-sahmri_scrna-seq-workshop_2021-july/tree/8cdfd4d2208ce4b2f974bbffa1cc13fed04dcd8c" target="_blank">8cdfd4d</a> </a>
</p>
</div>
<div id="strongRepositoryversionstrongahrefhttpsgitlabsvieduaubiocellgenpublicsvisahmriscrnaseqworkshop2021julytreee12dd3814dba0bc23ad5152774540d663a2364ectargetblanke12dd38a" class="panel-collapse collapse">
<div id="strongRepositoryversionstrongahrefhttpsgitlabsvieduaubiocellgenpublicsvisahmriscrnaseqworkshop2021julytree8cdfd4d2208ce4b2f974bbffa1cc13fed04dcd8ctargetblank8cdfd4da" class="panel-collapse collapse">
<div class="panel-body">
<p>
Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.
</p>
<p>
The results in this page were generated with repository version <a href="https://gitlab.svi.edu.au/biocellgen-public/svi-sahmri_scrna-seq-workshop_2021-july/tree/e12dd3814dba0bc23ad5152774540d663a2364ec" target="_blank">e12dd38</a>. See the <em>Past versions</em> tab to see a history of the changes made to the R Markdown and HTML files.
The results in this page were generated with repository version <a href="https://gitlab.svi.edu.au/biocellgen-public/svi-sahmri_scrna-seq-workshop_2021-july/tree/8cdfd4d2208ce4b2f974bbffa1cc13fed04dcd8c" target="_blank">8cdfd4d</a>. See the <em>Past versions</em> tab to see a history of the changes made to the R Markdown and HTML files.
</p>
<p>
Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use <code>wflow_publish</code> or <code>wflow_git_commit</code>). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:
......@@ -629,15 +629,12 @@ Ignored files:
Ignored: .Rproj.user/
Untracked files:
Untracked: .gitignore
Untracked: _workflowr.yml
Untracked: analysis/
Untracked: raw_data/
Untracked: svi-sahmri_scrna-seq-workshop_2021-july.Rproj
Untracked: untar_path/
Unstaged changes:
Modified: README.md
Modified: analysis/index.Rmd
</code></pre>
<p>
......@@ -650,16 +647,77 @@ Note that any generated files, e.g. HTML, png, CSS, etc., are not included in t
<hr>
</div>
<div id="versions" class="tab-pane fade">
<p>
There are no past versions. Publish this analysis with <code>wflow_publish()</code> to start tracking its development.
These are the previous versions of the repository in which changes were made to the R Markdown (<code>analysis/index.Rmd</code>) and HTML (<code>public/index.html</code>) files. If you’ve configured a remote Git repository (see <code>?wflow_git_remote</code>), click on the hyperlinks in the table below to view the files as they were in that past version.
</p>
<div class="table-responsive">
<table class="table table-condensed table-hover">
<thead>
<tr>
<th>
File
</th>
<th>
Version
</th>
<th>
Author
</th>
<th>
Date
</th>
<th>
Message
</th>
</tr>
</thead>
<tbody>
<tr>
<td>
Rmd
</td>
<td>
<a href="https://gitlab.svi.edu.au/biocellgen-public/svi-sahmri_scrna-seq-workshop_2021-july/blob/8cdfd4d2208ce4b2f974bbffa1cc13fed04dcd8c/analysis/index.Rmd" target="_blank">8cdfd4d</a>
</td>
<td>
Davis McCarthy
</td>
<td>
2021-06-29
</td>
<td>
Updating materials for workshop in July 2021
</td>
</tr>
<tr>
<td>
html
</td>
<td>
<a href="https://gitlab.svi.edu.au/biocellgen-public/svi-sahmri_scrna-seq-workshop_2021-july/blob/8cdfd4d2208ce4b2f974bbffa1cc13fed04dcd8c/public/index.html" target="_blank">8cdfd4d</a>
</td>
<td>
Davis McCarthy
</td>
<td>
2021-06-29
</td>
<td>
Updating materials for workshop in July 2021
</td>
</tr>
</tbody>
</table>
</div>
<hr>
</div>
</div>
</div>
<div id="introduction" class="section level2">
<h2>Introduction</h2>
<p>In this workshop, we will introduce the data infrastructure for scRNA-seq analysis in R and practice a workflow of scRNAseq analysis; from pre-processing, quality control to dimensionality reduction aand clustering. We will then demonstrate the usage of marker genes for cell type annotation and an automatic approach for matching query cells to a reference atlas with labels.</p>
<p>In this workshop, we will introduce the data infrastructure for scRNA-seq analysis in R and practice a workflow of scRNAseq analysis; from pre-processing, quality control to dimensionality reduction and clustering. We will then demonstrate the usage of marker genes for cell type annotation and an automatic approach for matching query cells to a reference atlas with labels.</p>
<p>Workshop website: [<a href="https://biocellgen-public.svi.edu.au/SVI-SAHMRI_scRNA-seq-Workshop_2021-July/public/index.html" class="uri">https://biocellgen-public.svi.edu.au/SVI-SAHMRI_scRNA-seq-Workshop_2021-July/public/index.html</a>]</p>
<ol style="list-style-type: decimal">
<li><a href="sahmri_analysis-workflow.html">single-cell RNAseq analysis workflow for cell type identification</a></li>
</ol>
......@@ -727,6 +785,7 @@ There are no past versions. Publish this analysis with <code>wflow_publish()</co
usethis 1.6.3 2020-09-17 [1] CRAN (R 4.0.2)
utf8 1.2.1 2021-03-12 [1] CRAN (R 4.0.2)
vctrs 0.3.7 2021-03-29 [1] CRAN (R 4.0.2)
whisker 0.4 2019-08-28 [1] CRAN (R 4.0.2)
withr 2.4.2 2021-04-18 [1] CRAN (R 4.0.2)
workflowr 1.6.2 2020-04-30 [1] CRAN (R 4.0.2)
xfun 0.19 2020-10-30 [1] CRAN (R 4.0.2)
......
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