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McCarthy</em></h4> </div> <p><strong>Last updated:</strong> 2018-08-24</p> <strong>workflowr checks:</strong> <small>(Click a bullet for more information)</small> <ul> <li> <p><details> <summary> <strong style="color:blue;">✔</strong> <strong>R Markdown file:</strong> up-to-date </summary></p> <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> </details> </li> <li> <p><details> <summary> <strong style="color:blue;">✔</strong> <strong>Environment:</strong> empty </summary></p> <p>Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. 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Below is the status of the Git repository when the results were generated: <pre><code> Ignored files: Ignored: .DS_Store Ignored: .Rhistory Ignored: .Rproj.user/ Ignored: data/raw/ Ignored: src/.DS_Store Ignored: src/.ipynb_checkpoints/ Ignored: src/Rmd/.Rhistory Untracked files: Untracked: Snakefile_clonality Untracked: Snakefile_somatic_calling Untracked: code/analysis_for_garx.Rmd Untracked: code/yuanhua/ Untracked: data/canopy/ Untracked: data/cell_assignment/ Untracked: data/de_analysis_FTv62/ Untracked: data/donor_info_070818.txt Untracked: data/donor_info_core.csv Untracked: data/donor_neutrality.tsv Untracked: data/fdr10.annot.txt.gz Untracked: data/high-vs-low-exomes.v62.ft.alldonors-filt_lenient.all_filt_sites.vep_most_severe_csq.txt Untracked: data/high-vs-low-exomes.v62.ft.filt_lenient-alldonors.txt.gz Untracked: data/human_H_v5p2.rdata Untracked: data/human_c2_v5p2.rdata Untracked: data/human_c6_v5p2.rdata Untracked: data/neg-bin-rsquared-petr.csv Untracked: data/neutralitytestr-petr.tsv Untracked: data/sce_merged_donors_cardelino_donorid_all_qc_filt.rds Untracked: data/sce_merged_donors_cardelino_donorid_all_with_qc_labels.rds Untracked: data/sce_merged_donors_cardelino_donorid_unstim_qc_filt.rds Untracked: data/sces/ Untracked: data/simulations/ Untracked: data/variance_components/ Untracked: docs/figure/overview_lines.Rmd/ Untracked: figures/ Untracked: metadata/ Untracked: output/differential_expression/ Untracked: output/donor_specific/ Untracked: output/line_info.tsv Untracked: output/nvars_by_category_by_donor.tsv Untracked: output/nvars_by_category_by_line.tsv Untracked: output/variance_components/ Untracked: references/ </code></pre> 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. </details> </li> </ul> <details> <summary> <small><strong>Expand here to see past versions:</strong></small> </summary> <ul> <table style="border-collapse:separate; border-spacing:5px;"> <thead> <tr> <th style="text-align:left;"> File </th> <th style="text-align:left;"> Version </th> <th style="text-align:left;"> Author </th> <th style="text-align:left;"> Date </th> <th style="text-align:left;"> Message </th> </tr> </thead> <tbody> <tr> <td style="text-align:left;"> html </td> <td style="text-align:left;"> <a href="https://cdn.rawgit.com/davismcc/fibroblast-clonality/02a8343abed931029fae740e8e0877331bfae02b/docs/simulations.html" target="_blank">02a8343</a> </td> <td style="text-align:left;"> davismcc </td> <td style="text-align:left;"> 2018-08-24 </td> <td style="text-align:left;"> Build site. </td> </tr> <tr> <td style="text-align:left;"> Rmd </td> <td style="text-align:left;"> <a href="https://github.com/davismcc/fibroblast-clonality/blob/43f15d6d291c1d17bd298c810f97397e2d309a3c/analysis/simulations.Rmd" target="_blank">43f15d6</a> </td> <td style="text-align:left;"> davismcc </td> <td style="text-align:left;"> 2018-08-24 </td> <td style="text-align:left;"> Adding data pre-processing workflow and updating analyses. </td> </tr> <tr> <td style="text-align:left;"> html </td> <td style="text-align:left;"> <a href="https://cdn.rawgit.com/davismcc/fibroblast-clonality/43f15d6d291c1d17bd298c810f97397e2d309a3c/docs/simulations.html" target="_blank">43f15d6</a> </td> <td style="text-align:left;"> davismcc </td> <td style="text-align:left;"> 2018-08-24 </td> <td style="text-align:left;"> Adding data pre-processing workflow and updating analyses. </td> </tr> </tbody> </table> </ul> <p></details></p> <hr /> <div id="load-libraries-and-simulation-results" class="section level2"> <h2>Load libraries and simulation results</h2> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">library</span>(ggpubr) <span class="kw">library</span>(tidyverse) <span class="kw">library</span>(cardelino) <span class="kw">library</span>(viridis) <span class="kw">library</span>(cowplot) lines <-<span class="st"> </span><span class="kw">c</span>(<span class="st">"euts"</span>, <span class="st">"fawm"</span>, <span class="st">"feec"</span>, <span class="st">"fikt"</span>, <span class="st">"garx"</span>, <span class="st">"gesg"</span>, <span class="st">"heja"</span>, <span class="st">"hipn"</span>, <span class="st">"ieki"</span>, <span class="st">"joxm"</span>, <span class="st">"kuco"</span>, <span class="st">"laey"</span>, <span class="st">"lexy"</span>, <span class="st">"naju"</span>, <span class="st">"nusw"</span>, <span class="st">"oaaz"</span>, <span class="st">"oilg"</span>, <span class="st">"pipw"</span>, <span class="st">"puie"</span>, <span class="st">"qayj"</span>, <span class="st">"qolg"</span>, <span class="st">"qonc"</span>, <span class="st">"rozh"</span>, <span class="st">"sehl"</span>, <span class="st">"ualf"</span>, <span class="st">"vass"</span>, <span class="st">"vuna"</span>, <span class="st">"wahn"</span>, <span class="st">"wetu"</span>, <span class="st">"xugn"</span>, <span class="st">"zoxy"</span>, <span class="st">"vils"</span>)</code></pre></div> <div id="load-simulation-results" class="section level3"> <h3>Load simulation results</h3> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">all_files <-<span class="st"> </span><span class="kw">paste0</span>(lines, <span class="st">".simulate.rds"</span>) assign_<span class="dv">0</span> <-<span class="st"> </span><span class="kw">matrix</span>(<span class="dv">0</span>, <span class="dt">nrow =</span> <span class="dv">500</span>, <span class="dt">ncol =</span> <span class="kw">length</span>(lines)) assign_<span class="dv">1</span> <-<span class="st"> </span><span class="kw">matrix</span>(<span class="dv">0</span>, <span class="dt">nrow =</span> <span class="dv">500</span>, <span class="dt">ncol =</span> <span class="kw">length</span>(lines)) prob_all <-<span class="st"> </span><span class="kw">matrix</span>(<span class="dv">0</span>, <span class="dt">nrow =</span> <span class="dv">500</span>, <span class="dt">ncol =</span> <span class="kw">length</span>(lines)) <span class="cf">for</span> (i <span class="cf">in</span> <span class="kw">seq_len</span>(<span class="kw">length</span>(all_files))) { afile <-<span class="st"> </span>all_files[i] sim_dat <-<span class="st"> </span><span class="kw">readRDS</span>(<span class="kw">file.path</span>(<span class="st">"data"</span>, <span class="st">"simulations"</span>, afile)) assign_<span class="dv">0</span>[, i] <-<span class="st"> </span><span class="kw">get_prob_label</span>(sim_dat<span class="op">$</span>I_sim) assign_<span class="dv">1</span>[, i] <-<span class="st"> </span><span class="kw">get_prob_label</span>(sim_dat<span class="op">$</span>prob_Gibbs) prob_all[, i] <-<span class="st"> </span><span class="kw">get_prob_value</span>(sim_dat<span class="op">$</span>prob_Gibbs, <span class="dt">mode =</span> <span class="st">"best"</span>) }</code></pre></div> </div> <div id="load-results-from-real-data" class="section level3"> <h3>Load results from real data</h3> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">all_files <-<span class="st"> </span><span class="kw">paste0</span>(<span class="st">"cardelino_results."</span>, lines, <span class="st">".filt_lenient.cell_coverage_sites.rds"</span>) n_sites <-<span class="st"> </span><span class="kw">rep</span>(<span class="dv">0</span>, <span class="kw">length</span>(lines)) n_clone <-<span class="st"> </span><span class="kw">rep</span>(<span class="dv">0</span>, <span class="kw">length</span>(lines)) recall_all <-<span class="st"> </span><span class="kw">rep</span>(<span class="dv">0</span>, <span class="kw">length</span>(lines)) <span class="cf">for</span> (i <span class="cf">in</span> <span class="kw">seq_len</span>(<span class="kw">length</span>(all_files))) { afile <-<span class="st"> </span>all_files[i] carde_dat <-<span class="st"> </span><span class="kw">readRDS</span>(<span class="kw">file.path</span>(<span class="st">"data"</span>, <span class="st">"cell_assignment"</span>, afile)) n_sites[i] <-<span class="st"> </span><span class="kw">nrow</span>(carde_dat<span class="op">$</span>D) n_clone[i] <-<span class="st"> </span><span class="kw">ncol</span>(carde_dat<span class="op">$</span>prob_mat) recall_all[i] <-<span class="st"> </span><span class="kw">mean</span>(<span class="kw">get_prob_value</span>(carde_dat<span class="op">$</span>prob_mat, <span class="dt">mode =</span> <span class="st">"best"</span>) <span class="op">></span><span class="st"> </span><span class="fl">0.5</span>) }</code></pre></div> <p>Overall correlation in assignment rates (recall) from simulated and observed data is 0.959.</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">precision_simu <-<span class="st"> </span><span class="kw">rep</span>(<span class="dv">0</span>, <span class="kw">length</span>(lines)) <span class="cf">for</span> (i <span class="cf">in</span> <span class="kw">seq_len</span>(<span class="kw">length</span>(lines))) { idx <-<span class="st"> </span>prob_all[, i] <span class="op">></span><span class="st"> </span><span class="fl">0.5</span> precision_simu[i] <-<span class="st"> </span><span class="kw">mean</span>(assign_<span class="dv">0</span>[idx, i] <span class="op">==</span><span class="st"> </span>assign_<span class="dv">1</span>[idx, i]) } df <-<span class="st"> </span><span class="kw">data.frame</span>(<span class="dt">line =</span> lines, <span class="dt">n_sites =</span> n_sites, <span class="dt">n_clone =</span> n_clone, <span class="dt">recall_real =</span> recall_all, <span class="dt">recall_simu =</span> <span class="kw">colMeans</span>(prob_all <span class="op">></span><span class="st"> </span><span class="fl">0.5</span>), <span class="dt">precision_simu =</span> precision_simu)</code></pre></div> </div> </div> <div id="plot-observed-vs-simulated-assignment-rates-recall" class="section level2"> <h2>Plot observed vs simulated assignment rates (recall)</h2> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">df <span class="op">%>%</span> <span class="st"> </span>dplyr<span class="op">::</span><span class="kw">mutate</span>(<span class="dt">sites_per_clone =</span> <span class="kw">cut</span>(n_sites <span class="op">/</span><span class="st"> </span><span class="kw">pmax</span>(n_clone <span class="op">-</span><span class="st"> </span><span class="dv">1</span>, <span class="dv">1</span>), <span class="dt">breaks =</span> <span class="kw">c</span>(<span class="dv">0</span>, <span class="dv">3</span>, <span class="dv">8</span>, <span class="dv">15</span>, <span class="dv">25</span>, <span class="dv">60</span>))) <span class="op">%>%</span> <span class="st"> </span><span class="kw">ggplot</span>( <span class="kw">aes</span>(<span class="dt">x =</span> recall_simu, <span class="dt">y =</span> recall_real, <span class="dt">fill =</span> sites_per_clone)) <span class="op">+</span> <span class="st"> </span><span class="kw">geom_abline</span>(<span class="dt">slope =</span> <span class="dv">1</span>, <span class="dt">intercept =</span> <span class="dv">0</span>, <span class="dt">colour =</span> <span class="st">"gray40"</span>, <span class="dt">linetype =</span> <span class="dv">2</span>) <span class="op">+</span> <span class="st"> </span><span class="kw">geom_smooth</span>(<span class="kw">aes</span>(<span class="dt">group =</span> <span class="dv">1</span>), <span class="dt">method =</span> <span class="st">"lm"</span>, <span class="dt">colour =</span> <span class="st">"firebrick"</span>) <span class="op">+</span> <span class="st"> </span><span class="kw">geom_point</span>(<span class="dt">size =</span> <span class="dv">3</span>, <span class="dt">shape =</span> <span class="dv">21</span>) <span class="op">+</span> <span class="st"> </span><span class="kw">xlim</span>(<span class="dv">0</span>, <span class="dv">1</span>) <span class="op">+</span><span class="st"> </span><span class="kw">ylim</span>(<span class="dv">0</span>, <span class="dv">1</span>) <span class="op">+</span> <span class="st"> </span><span class="kw">scale_fill_manual</span>(<span class="dt">name =</span> <span class="st">"mean</span><span class="ch">\n</span><span class="st"># variants</span><span class="ch">\n</span><span class="st">per clonal</span><span class="ch">\n</span><span class="st">branch"</span>, <span class="dt">values =</span> <span class="kw">magma</span>(<span class="dv">6</span>)[<span class="op">-</span><span class="dv">1</span>]) <span class="op">+</span> <span class="st"> </span><span class="kw">guides</span>(<span class="dt">colour =</span> <span class="ot">FALSE</span>, <span class="dt">group =</span> <span class="ot">FALSE</span>) <span class="op">+</span> <span class="st"> </span><span class="kw">xlab</span>(<span class="st">"Assignment rate: simulated"</span>) <span class="op">+</span> <span class="st"> </span><span class="kw">ylab</span>(<span class="st">"Assignment rate: observed"</span>)</code></pre></div> <p><img src="figure/simulations.Rmd/unnamed-chunk-4-1.png" width="672" style="display: block; margin: auto;" /></p> <details> <summary><em>Expand here to see past versions of unnamed-chunk-4-1.png:</em></summary> <table style="border-collapse:separate; border-spacing:5px;"> <thead> <tr> <th style="text-align:left;"> Version </th> <th style="text-align:left;"> Author </th> <th style="text-align:left;"> Date </th> </tr> </thead> <tbody> <tr> <td style="text-align:left;"> <a href="https://github.com/davismcc/fibroblast-clonality/blob/02a8343abed931029fae740e8e0877331bfae02b/docs/figure/simulations.Rmd/unnamed-chunk-4-1.png" target="_blank">02a8343</a> </td> <td style="text-align:left;"> davismcc </td> <td style="text-align:left;"> 2018-08-24 </td> </tr> </tbody> </table> <p></details></p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">ggsave</span>(<span class="st">"figures/simulations/assign_rate_obs_v_sim.png"</span>, <span class="dt">height =</span> <span class="fl">4.5</span>, <span class="dt">width =</span> <span class="dv">5</span>) <span class="kw">ggsave</span>(<span class="st">"figures/simulations/assign_rate_obs_v_sim.pdf"</span>, <span class="dt">height =</span> <span class="fl">4.5</span>, <span class="dt">width =</span> <span class="dv">5</span>)</code></pre></div> </div> <div id="plot-simulation-precision-recall-curve" class="section level2"> <h2>Plot simulation precision-recall curve</h2> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">df <span class="op">%>%</span> <span class="st"> </span>dplyr<span class="op">::</span><span class="kw">mutate</span>(<span class="dt">sites_per_clone =</span> <span class="kw">cut</span>(n_sites <span class="op">/</span><span class="st"> </span>n_clone, <span class="dt">breaks =</span> <span class="kw">c</span>(<span class="dv">0</span>, <span class="dv">5</span>, <span class="dv">10</span>, <span class="dv">20</span>, <span class="dv">40</span>))) <span class="op">%>%</span> <span class="st"> </span><span class="kw">ggplot</span>( <span class="kw">aes</span>(<span class="dt">x =</span> recall_simu, <span class="dt">y =</span> precision_simu, <span class="dt">fill =</span> sites_per_clone)) <span class="op">+</span> <span class="st"> </span><span class="kw">geom_hline</span>(<span class="dt">yintercept =</span> <span class="fl">0.85</span>, <span class="dt">colour =</span> <span class="st">"gray40"</span>, <span class="dt">linetype =</span> <span class="dv">2</span>) <span class="op">+</span> <span class="st"> </span><span class="kw">geom_smooth</span>(<span class="kw">aes</span>(<span class="dt">group =</span> <span class="dv">1</span>), <span class="dt">method =</span> <span class="st">"lm"</span>, <span class="dt">colour =</span> <span class="st">"firebrick"</span>) <span class="op">+</span> <span class="st"> </span><span class="kw">geom_point</span>(<span class="dt">size =</span> <span class="dv">3</span>, <span class="dt">shape =</span> <span class="dv">21</span>) <span class="op">+</span> <span class="st"> </span><span class="kw">xlim</span>(<span class="dv">0</span>, <span class="dv">1</span>) <span class="op">+</span><span class="st"> </span><span class="kw">ylim</span>(<span class="dv">0</span>, <span class="dv">1</span>) <span class="op">+</span> <span class="st"> </span><span class="kw">scale_fill_manual</span>(<span class="dt">name =</span> <span class="st">"mean</span><span class="ch">\n</span><span class="st"># variants</span><span class="ch">\n</span><span class="st">per clone"</span>, <span class="dt">values =</span> <span class="kw">magma</span>(<span class="dv">5</span>)[<span class="op">-</span><span class="dv">1</span>]) <span class="op">+</span> <span class="st"> </span><span class="kw">guides</span>(<span class="dt">colour =</span> <span class="ot">FALSE</span>, <span class="dt">group =</span> <span class="ot">FALSE</span>) <span class="op">+</span> <span class="st"> </span><span class="kw">xlab</span>(<span class="st">"Assignment rate (recall)"</span>) <span class="op">+</span> <span class="st"> </span><span class="kw">ylab</span>(<span class="st">"Precision"</span>)</code></pre></div> <p><img src="figure/simulations.Rmd/unnamed-chunk-5-1.png" width="672" style="display: block; margin: auto;" /></p> <details> <summary><em>Expand here to see past versions of unnamed-chunk-5-1.png:</em></summary> <table style="border-collapse:separate; border-spacing:5px;"> <thead> <tr> <th style="text-align:left;"> Version </th> <th style="text-align:left;"> Author </th> <th style="text-align:left;"> Date </th> </tr> </thead> <tbody> <tr> <td style="text-align:left;"> <a href="https://github.com/davismcc/fibroblast-clonality/blob/02a8343abed931029fae740e8e0877331bfae02b/docs/figure/simulations.Rmd/unnamed-chunk-5-1.png" target="_blank">02a8343</a> </td> <td style="text-align:left;"> davismcc </td> <td style="text-align:left;"> 2018-08-24 </td> </tr> </tbody> </table> <p></details></p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">ggsave</span>(<span class="st">"figures/simulations/sim_precision_v_recall.png"</span>, <span class="dt">height =</span> <span class="fl">4.5</span>, <span class="dt">width =</span> <span class="fl">5.5</span>) <span class="kw">ggsave</span>(<span class="st">"figures/simulations/sim_precision_v_recall.pdf"</span>, <span class="dt">height =</span> <span class="fl">4.5</span>, <span class="dt">width =</span> <span class="fl">5.5</span>)</code></pre></div> </div> <div id="clone-statistics" class="section level2"> <h2>Clone statistics</h2> <p>Table showing the number of lines with 2, 3 and 4 clones.</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">table</span>(df<span class="op">$</span>n_clone)</code></pre></div> <pre><code> 2 3 4 4 24 4 </code></pre> <p>Summary of the average number of mutations per clonal branch across lines.</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(df<span class="op">$</span>n_sites <span class="op">/</span><span class="st"> </span>(df<span class="op">$</span>n_clone <span class="op">-</span><span class="st"> </span><span class="dv">1</span>))</code></pre></div> <pre><code> Min. 1st Qu. Median Mean 3rd Qu. Max. 3.00 8.50 11.50 18.69 25.00 57.50 </code></pre> </div> <div id="session-information" class="section level2"> <h2>Session information</h2> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">devtools<span class="op">::</span><span class="kw">session_info</span>()</code></pre></div> <pre><code>Session info -------------------------------------------------------------</code></pre> <pre><code> setting value version R version 3.5.1 (2018-07-02) system x86_64, darwin15.6.0 ui X11 language (EN) collate en_GB.UTF-8 tz Europe/London date 2018-08-24 </code></pre> <pre><code>Packages -----------------------------------------------------------------</code></pre> <pre><code> package * version date source AnnotationDbi 1.42.1 2018-05-08 Bioconductor ape 5.1 2018-04-04 CRAN (R 3.5.0) assertthat 0.2.0 2017-04-11 CRAN (R 3.5.0) backports 1.1.2 2017-12-13 CRAN (R 3.5.0) base * 3.5.1 2018-07-05 local bindr 0.1.1 2018-03-13 CRAN (R 3.5.0) bindrcpp * 0.2.2 2018-03-29 CRAN (R 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