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<pre><code>
Ignored files:
Ignored: .Rhistory
Ignored: .Rproj.user/
Ignored: .snakemake/
Ignored: NSForest/.Rhistory
Ignored: NSForest/NS-Forest_v3_Extended_Binary_Markers_Supplmental.csv
Ignored: NSForest/NS-Forest_v3_Full_Results.csv
Ignored: NSForest/NSForest3_medianValues.csv
Ignored: NSForest/NSForest_v3_Final_Result.csv
Ignored: NSForest/__pycache__/
Ignored: NSForest/data/
Ignored: RankCorr/picturedRocks/__pycache__/
Ignored: benchmarks/
Ignored: data/cellmarker/
Ignored: data/downloaded_data/
Ignored: data/expert_annotations/
Ignored: data/expert_mgs/
Ignored: data/special_real_data/
Ignored: figures/
Untracked files:
Untracked: analysis/de-pars-sims.Rmd
Untracked: analysis/implemetation-quality.Rmd
Untracked: analysis/inter-dataset-analysis.Rmd
Untracked: analysis/lawlor-expert-analysis.Rmd
Untracked: analysis/number-selected-analysis.Rmd
Untracked: analysis/ss3-pbmc-analysis.Rmd
Untracked: analysis/ss3-pbmc-expert-analysis.Rmd
Untracked: analysis/zeisel-expert-analysis.Rmd
Untracked: analysis/zhao-data.Rmd
Untracked: code/expert-annotation-utils.R
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</code></pre>
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Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.
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These are the previous versions of the repository in which changes were made to the R Markdown (<code>analysis/time.Rmd</code>) and HTML (<code>public/time.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>
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File
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Message
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Rmd
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<a href="https://gitlab.svi.edu.au/biocellgen-private/mage_2020_marker-gene-benchmarking/blob/50bca7c1f36680d5fcb00fbe642d0cf576795269/analysis/time.Rmd" target="_blank">50bca7c</a>
</td>
<td>
Jeffrey Pullin
</td>
<td>
2022-05-02
</td>
<td>
workflowr::wflow_publish(all = TRUE, republish = TRUE)
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html
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<a href="https://gitlab.svi.edu.au/biocellgen-private/mage_2020_marker-gene-benchmarking/blob/50bca7c1f36680d5fcb00fbe642d0cf576795269/public/time.html" target="_blank">50bca7c</a>
</td>
<td>
Jeffrey Pullin
</td>
<td>
2022-05-02
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<td>
workflowr::wflow_publish(all = TRUE, republish = TRUE)
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html
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<a href="https://gitlab.svi.edu.au/biocellgen-private/mage_2020_marker-gene-benchmarking/blob/5cc008f68e2dc2841fa7bbf645dd7e29515a3f0c/public/time.html" target="_blank">5cc008f</a>
</td>
<td>
Jeffrey Pullin
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<td>
2022-02-09
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<td>
Build site.
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<a href="https://gitlab.svi.edu.au/biocellgen-private/mage_2020_marker-gene-benchmarking/blob/d1aca16c0d03c5b27db12af526cfd75ea2609cea/analysis/time.Rmd" target="_blank">d1aca16</a>
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<td>
Jeffrey Pullin
</td>
<td>
2022-02-09
</td>
<td>
Refresh website
</td>
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html
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<a href="https://gitlab.svi.edu.au/biocellgen-private/mage_2020_marker-gene-benchmarking/blob/d1aca16c0d03c5b27db12af526cfd75ea2609cea/public/time.html" target="_blank">d1aca16</a>
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<td>
Jeffrey Pullin
</td>
<td>
2022-02-09
</td>
<td>
Refresh website
</td>
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<td>
Rmd
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<a href="https://gitlab.svi.edu.au/biocellgen-private/mage_2020_marker-gene-benchmarking/blob/aca9ad2b4da7f7f75ffea4eb425820c89f61a517/analysis/time.Rmd" target="_blank">aca9ad2</a>
</td>
<td>
Jeffrey Pullin
</td>
<td>
2021-11-29
</td>
<td>
Various changes made in the last days before thesis submission
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<td>
Rmd
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<td>
<a href="https://gitlab.svi.edu.au/biocellgen-private/mage_2020_marker-gene-benchmarking/blob/ddb1eeb5ce45c6c9c4aee5e862583e3f91c81949/analysis/time.Rmd" target="_blank">ddb1eeb</a>
</td>
<td>
Jeffrey Pullin
</td>
<td>
2021-09-28
</td>
<td>
Update time analyses
</td>
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<td>
Rmd
</td>
<td>
<a href="https://gitlab.svi.edu.au/biocellgen-private/mage_2020_marker-gene-benchmarking/blob/16c471e898b1c89051f7030e2ddb3e1108f2c2bc/analysis/time.Rmd" target="_blank">16c471e</a>
</td>
<td>
Jeffrey Pullin
</td>
<td>
2021-09-22
</td>
<td>
Polish time plots
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<td>
Rmd
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<a href="https://gitlab.svi.edu.au/biocellgen-private/mage_2020_marker-gene-benchmarking/blob/e552e955a1001568bf1d0d7ffb823c7c4d9112cf/analysis/time.Rmd" target="_blank">e552e95</a>
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<td>
Jeffrey Pullin
</td>
<td>
2021-09-21
</td>
<td>
Extend time analysis
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<td>
Rmd
</td>
<td>
<a href="https://gitlab.svi.edu.au/biocellgen-private/mage_2020_marker-gene-benchmarking/blob/17f2a0f49bf87afceb798596edd55242df1f108e/analysis/time.Rmd" target="_blank">17f2a0f</a>
</td>
<td>
Jeffrey Pullin
</td>
<td>
2021-08-07
</td>
<td>
Add new plots and analysis for lab meeting 5/8/2021
</td>
</tr>
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<td>
Rmd
</td>
<td>
<a href="https://gitlab.svi.edu.au/biocellgen-private/mage_2020_marker-gene-benchmarking/blob/ef9f1c7e5a6e1d2826077e93f1b9ed5196a5d58b/analysis/time.Rmd" target="_blank">ef9f1c7</a>
</td>
<td>
Jeffrey Pullin
</td>
<td>
2021-08-02
</td>
<td>
Add code to plot time of methods on real data
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<td>
Rmd
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<a href="https://gitlab.svi.edu.au/biocellgen-private/mage_2020_marker-gene-benchmarking/blob/864677c79aaabbd79d31f75a7a000e58866a4149/analysis/time.Rmd" target="_blank">864677c</a>
</td>
<td>
Jeffrey Pullin
</td>
<td>
2021-07-21
</td>
<td>
Add mini wilcoxon speed analysis
</td>
</tr>
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<td>
html
</td>
<td>
<a href="https://gitlab.svi.edu.au/biocellgen-private/mage_2020_marker-gene-benchmarking/blob/61ee24692959fb45e54f4a47e0251a58e3444251/public/time.html" target="_blank">61ee246</a>
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<td>
Jeffrey Pullin
</td>
<td>
2021-04-13
</td>
<td>
Build site.
</td>
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<tr>
<td>
Rmd
</td>
<td>
<a href="https://gitlab.svi.edu.au/biocellgen-private/mage_2020_marker-gene-benchmarking/blob/b5b2a8869f5c93012958ab071b80ac0259313124/analysis/time.Rmd" target="_blank">b5b2a88</a>
</td>
<td>
Jeffrey Pullin
</td>
<td>
2021-04-13
</td>
<td>
Add new results
</td>
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<tr>
<td>
Rmd
</td>
<td>
<a href="https://gitlab.svi.edu.au/biocellgen-private/mage_2020_marker-gene-benchmarking/blob/3a4cb2e5d193865dbac065509e628faf618d1161/analysis/time.Rmd" target="_blank">3a4cb2e</a>
</td>
<td>
Jeffrey Pullin
</td>
<td>
</td>
<td>
Update 16/3/2021
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html
</td>
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<a href="https://gitlab.svi.edu.au/biocellgen-private/mage_2020_marker-gene-benchmarking/blob/ca82ce0376f0d272dfbf5135342387dfeb6cd8d9/public/time.html" target="_blank">ca82ce0</a>
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<td>
Jeffrey Pullin
</td>
<td>
2021-02-16
</td>
<td>
Build site.
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html
</td>
<td>
<a href="https://gitlab.svi.edu.au/biocellgen-private/mage_2020_marker-gene-benchmarking/blob/2863555c1b0ccc7c310f34dc03f5a1b37670b576/public/time.html" target="_blank">2863555</a>
</td>
<td>
Jeffrey Pullin
</td>
<td>
2021-02-10
</td>
<td>
Build site.
</td>
</tr>
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<td>
Rmd
</td>
<td>
<a href="https://gitlab.svi.edu.au/biocellgen-private/mage_2020_marker-gene-benchmarking/blob/ffe660ce607d30e8f2848f52bbb8de1ad7099c2e/analysis/time.Rmd" target="_blank">ffe660c</a>
</td>
<td>
Jeffrey Pullin
</td>
<td>
2021-02-09
</td>
<td>
Update 9/2/2021
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<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(tibble)</span>
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(dplyr)</span>
<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(ggplot2)</span>
<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(tidyr)</span>
<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(purrr)</span>
<span id="cb1-6"><a href="#cb1-6" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(forcats)</span>
<span id="cb1-7"><a href="#cb1-7" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(patchwork)</span>
<span id="cb1-8"><a href="#cb1-8" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(stringr)</span>
<span id="cb1-9"><a href="#cb1-9" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(ggrepel)</span>
<span id="cb1-10"><a href="#cb1-10" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-11"><a href="#cb1-11" aria-hidden="true" tabindex="-1"></a><span class="fu">source</span>(here<span class="sc">::</span><span class="fu">here</span>(<span class="st">"code"</span>, <span class="st">"analysis-utils.R"</span>))</span>
<span id="cb1-12"><a href="#cb1-12" aria-hidden="true" tabindex="-1"></a><span class="fu">source</span>(here<span class="sc">::</span><span class="fu">here</span>(<span class="st">"code"</span>, <span class="st">"plot-utils.R"</span>))</span></code></pre></div>
<div id="aim" class="section level1">
<h1>Aim</h1>
<p>Measure the time different methods take to run.</p>
</div>
<div id="simulated-data" class="section level1">
<h1>Simulated data</h1>
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a>sim_pars <span class="ot"><-</span> <span class="fu">retrive_simulation_parameters</span>()</span>
<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a>num_cells_time_data <span class="ot"><-</span> sim_pars <span class="sc">%>%</span> </span>
<span id="cb2-4"><a href="#cb2-4" aria-hidden="true" tabindex="-1"></a> <span class="fu">filter</span>(sim_label <span class="sc">==</span> <span class="st">"num_cells"</span>) <span class="sc">%>%</span> </span>
<span id="cb2-5"><a href="#cb2-5" aria-hidden="true" tabindex="-1"></a> <span class="fu">rowwise</span>() <span class="sc">%>%</span> </span>