1. celda
  2. Commit ab01b66e07db1714ca55da43eb00754608912678
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Version bump and update docs for BioC 3.15

Joshua D. Campbell authored on 30/04/2022 20:00:25
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DESCRIPTION
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 Package: celda
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 Title: CEllular Latent Dirichlet Allocation
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-Version: 1.13.0
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+Version: 1.12.0
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 Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu",
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     role = c("aut", "cre")),
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     person("Shiyi", "Yang", email="syyang@bu.edu", role = c("aut")),
NEWS.md
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+# celda v1.12.0 (2022-04-30)
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+* Update to match Bioconductor 3.15 release version
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+
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+# celda v1.11.1 (2022-03-31)
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+* Fixes to reports
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+* Use smoothe splines for perplexity and RPC plots
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+
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 # celda v1.11.0 (2022-03-31)
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 * Improvments to decontX vignette
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 * Added ability to subsample to speed up perplexity calculations
docs/404.html
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       </button>
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       <span class="navbar-brand">
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         <a class="navbar-link" href="index.html">celda</a>
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-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.11.0</span>
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+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.12.0</span>
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       </span>
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     </div>
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docs/CONDUCT.html
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       </button>
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       <span class="navbar-brand">
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         <a class="navbar-link" href="index.html">celda</a>
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-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.11.0</span>
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+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.12.0</span>
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       </span>
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     </div>
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docs/LICENSE-text.html
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       </button>
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       <span class="navbar-brand">
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         <a class="navbar-link" href="index.html">celda</a>
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-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.11.0</span>
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+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.12.0</span>
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       </span>
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     </div>
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docs/articles/articles/celda_pbmc3k.html
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       </button>
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       <span class="navbar-brand">
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         <a class="navbar-link" href="../../index.html">celda</a>
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-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.11.0</span>
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+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.12.0</span>
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       </span>
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     </div>
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       <h1 data-toc-skip>Celda - Analysis of PBMC3K</h1>
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                         <h4 class="author">Joshua Campbell, Zhe Wang</h4>
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-            <h4 class="date">Compiled March 31, 2022</h4>
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+            <h4 class="date">Compiled April 30, 2022</h4>
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       <small class="dont-index">Source: <a href="https://github.com/campbio/celda/blob/master/vignettes/articles/celda_pbmc3k.Rmd"><code>vignettes/articles/celda_pbmc3k.Rmd</code></a></small>
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       <div class="hidden name"><code>celda_pbmc3k.Rmd</code></div>
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 <p><img src="celda_pbmc3k_files/figure-html/module_split_perplexity-1.png" width="700"></p>
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 <p>The perplexity alone often does not show a clear elbow or “leveling off”. However, the rate of perplexity change (RPC) can be more informative to determine when adding new modules does not add much additional information <a href="https://doi.org/10.1186/1471-2105-16-S13-S8" target="_blank">Zhao et al., 2015</a>). An RPC closer to zero indicates that the addition of new modules or cell clusters is not substantially decreasing the perplexity. The RPC of models can be visualized using function <code>plotRPC</code>:</p>
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 <div class="sourceCode" id="cb19"><pre class="downlit sourceCode r">
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-<code class="sourceCode R"><span class="fu"><a href="../../reference/plotRPC.html">plotRPC</a></span><span class="op">(</span><span class="va">moduleSplit</span>, altExpName <span class="op">=</span> <span class="va">altExpName</span>, sep <span class="op">=</span> <span class="fl">10</span>, n <span class="op">=</span> <span class="fl">30</span><span class="op">)</span></code></pre></div>
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+<code class="sourceCode R"><span class="fu"><a href="../../reference/plotRPC.html">plotRPC</a></span><span class="op">(</span><span class="va">moduleSplit</span>, altExpName <span class="op">=</span> <span class="va">altExpName</span><span class="op">)</span></code></pre></div>
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 <p><img src="celda_pbmc3k_files/figure-html/module_split_rpc-1.png" width="700"></p>
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 <p>In this case, we will choose an <code>L</code> of 80 as the RPC curve tends to level off at this point:</p>
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 <div class="sourceCode" id="cb47"><pre class="downlit sourceCode r">
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 <code class="sourceCode R"><span class="co"># Plot differentially expressed genes that pass additional thresholds 'minClustExprPerc' and 'maxCtrlExprPerc'</span>
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 <span class="fu"><a href="https://rdrr.io/pkg/singleCellTK/man/plotMarkerDiffExp.html">plotMarkerDiffExp</a></span><span class="op">(</span><span class="va">sce</span>, topN <span class="op">=</span> <span class="fl">5</span>, log2fcThreshold <span class="op">=</span> <span class="fl">0</span>, rowLabel <span class="op">=</span> <span class="cn">TRUE</span>, fdrThreshold <span class="op">=</span> <span class="fl">0.05</span>, minClustExprPerc <span class="op">=</span> <span class="fl">0.6</span>, maxCtrlExprPerc <span class="op">=</span> <span class="fl">0.4</span>, minMeanExpr <span class="op">=</span> <span class="fl">0</span><span class="op">)</span></code></pre></div>
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 <p>Other parameters such as <code>minClustExprPerc</code> (the minimum number of cells expressing the marker gene in the cluster) and <code>maxCtrlExprPerc</code> (the maximum number of cells expression the marker gene in other clusters) can be used to control how specific each marker gene is to each cell populations. Similarly, adding a log2 fold-change cutoff (e.g. 1) can select for markers that are more strongly up-regulated in a cell population.</p>
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 </div>
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 <div id="violin-plots-for-marker-genes" class="section level2">
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 ## other attached packages:
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 ##  [1] scater_1.18.6               kableExtra_1.3.4
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 ##  [3] knitr_1.31                  ggplot2_3.3.5
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-##  [5] celda_1.11.0                singleCellTK_2.4.1
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 ##  [7] TENxPBMCData_1.8.0          HDF5Array_1.18.1
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 ##  [9] rhdf5_2.34.0                DelayedArray_0.16.2
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 ## [11] Matrix_1.3-2                SingleCellExperiment_1.12.0
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-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.11.0</span>
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       Boston University School of Medicine<br><a class="author_email" href="mailto:#"></a><a href="mailto:camp@bu.edu" class="email">camp@bu.edu</a>
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       </address>
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       <small class="dont-index">Source: <a href="https://github.com/campbio/celda/blob/master/vignettes/articles/decontX_pbmc4k.Rmd"><code>vignettes/articles/decontX_pbmc4k.Rmd</code></a></small>
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 <a href="#load-pbmc4k-data-from-10x" class="anchor"></a>Load PBMC4k data from 10X</h1>
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 <p>We will utilize the 10X PBMC 4K dataset as an example in this vignette. This data can be easily retrieved from the package <a href="http://bioconductor.org/packages/release/data/experiment/html/TENxPBMCData.html">TENxPBMCData</a>. Make sure the the column names are set before running decontX.</p>
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-<code class="sourceCode R"><span class="co"># Install TENxPBMCData if is it not already</span>
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-<span class="kw">if</span> <span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/ns-load.html">requireNamespace</a></span><span class="op">(</span><span class="st">"TENxPBMCData"</span>, quietly <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span>
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-<span class="co"># Load PBMC data</span>
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 <span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va">TENxPBMCData</span><span class="op">)</span>
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 <span class="fu"><a href="https://rdrr.io/r/base/colnames.html">colnames</a></span><span class="op">(</span><span class="va">sce</span><span class="op">)</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html">paste</a></span><span class="op">(</span><span class="va">sce</span><span class="op">$</span><span class="va">Sample</span>, <span class="va">sce</span><span class="op">$</span><span class="va">Barcode</span>, sep <span class="op">=</span> <span class="st">"_"</span><span class="op">)</span>
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+<span class="fu"><a href="https://rdrr.io/pkg/SingleCellExperiment/man/assays.html">counts</a></span><span class="op">(</span><span class="va">sce</span><span class="op">)</span> <span class="op">&lt;-</span> <span class="fu">as</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/pkg/SingleCellExperiment/man/assays.html">counts</a></span><span class="op">(</span><span class="va">sce</span><span class="op">)</span>, <span class="st">"dgCMatrix"</span><span class="op">)</span></code></pre></div>
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 </div>
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 ##  [1] scater_1.18.6               ggplot2_3.3.5
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 ##  [3] TENxPBMCData_1.8.0          HDF5Array_1.18.1
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 ##  [5] rhdf5_2.34.0                DelayedArray_0.16.2
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 ##  [9] SingleCellExperiment_1.12.0 SummarizedExperiment_1.20.0
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 ## [11] Biobase_2.50.0              GenomicRanges_1.42.0
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 ## [13] GenomeInfoDb_1.26.4         IRanges_2.24.1
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             <address class="author_afil">
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       Boston University School of Medicine<br><h4 class="author">Yusuke Koga</h4>
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             <address class="author_afil">
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       <small class="dont-index">Source: <a href="https://github.com/campbio/celda/blob/master/vignettes/celda.Rmd"><code>vignettes/celda.Rmd</code></a></small>
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 ## [8] methods   base
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 ##
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 ## other attached packages:
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-##  [1] celda_1.11.0                Matrix_1.3-2
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 ##  [3] SingleCellExperiment_1.12.0 SummarizedExperiment_1.20.0
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 ##  [5] Biobase_2.50.0              GenomicRanges_1.42.0
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 ##  [7] GenomeInfoDb_1.26.4         IRanges_2.24.1
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-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.11.0</span>
34 
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106 106 
       Boston University School of Medicine<br><a class="author_email" href="mailto:#"></a><a href="mailto:camp@bu.edu" class="email">camp@bu.edu</a>
107 107 
       </address>
108 108
109 
-            <h4 class="date">2022-03-31</h4>
109 
+            <h4 class="date">2022-04-30</h4>
110 110
111 111 
       <small class="dont-index">Source: <a href="https://github.com/campbio/celda/blob/master/vignettes/decontX.Rmd"><code>vignettes/decontX.Rmd</code></a></small>
112 112 
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@@ -145,19 +145,12 @@
145 145 
 <a href="#load-pbmc4k-data-from-10x" class="anchor"></a>Load PBMC4k data from 10X</h1>
146 146 
 <p>We will utilize the 10X PBMC 4K dataset as an example in this vignette. This data can be easily retrieved from the package <a href="http://bioconductor.org/packages/release/data/experiment/html/TENxPBMCData.html">TENxPBMCData</a>. Make sure the the column names are set before running decontX.</p>
147 147 
 <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
148 
-<code class="sourceCode R"><span class="co"># Install TENxPBMCData if is it not already</span>
149 
-<span class="kw">if</span> <span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/ns-load.html">requireNamespace</a></span><span class="op">(</span><span class="st">"TENxPBMCData"</span>, quietly <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span>
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-  <span class="kw">if</span> <span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/ns-load.html">requireNamespace</a></span><span class="op">(</span><span class="st">"BiocManager"</span>, quietly <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span>
151 
-    <span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span><span class="op">(</span><span class="st">"BiocManager"</span><span class="op">)</span>
152 
-  <span class="op">}</span>
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-  <span class="fu">BiocManager</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/BiocManager/man/install.html">install</a></span><span class="op">(</span><span class="st">"TENxPBMCData"</span><span class="op">)</span>
154 
-<span class="op">}</span>
155 
-
156 
-<span class="co"># Load PBMC data</span>
148 
+<code class="sourceCode R"><span class="co"># Load PBMC data</span>
157 149 
 <span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va">TENxPBMCData</span><span class="op">)</span>
158 150 
 <span class="va">sce</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/TENxPBMCData/man/TENxPBMCData.html">TENxPBMCData</a></span><span class="op">(</span><span class="st">"pbmc4k"</span><span class="op">)</span>
159 151 
 <span class="fu"><a href="https://rdrr.io/r/base/colnames.html">colnames</a></span><span class="op">(</span><span class="va">sce</span><span class="op">)</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html">paste</a></span><span class="op">(</span><span class="va">sce</span><span class="op">$</span><span class="va">Sample</span>, <span class="va">sce</span><span class="op">$</span><span class="va">Barcode</span>, sep <span class="op">=</span> <span class="st">"_"</span><span class="op">)</span>
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+<span class="fu"><a href="https://rdrr.io/r/base/colnames.html">rownames</a></span><span class="op">(</span><span class="va">sce</span><span class="op">)</span> <span class="op">&lt;-</span> <span class="fu">rowData</span><span class="op">(</span><span class="va">sce</span><span class="op">)</span><span class="op">$</span><span class="va">Symbol_TENx</span>
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+<span class="fu"><a href="https://rdrr.io/pkg/SingleCellExperiment/man/assays.html">counts</a></span><span class="op">(</span><span class="va">sce</span><span class="op">)</span> <span class="op">&lt;-</span> <span class="fu">as</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/pkg/SingleCellExperiment/man/assays.html">counts</a></span><span class="op">(</span><span class="va">sce</span><span class="op">)</span>, <span class="st">"dgCMatrix"</span><span class="op">)</span></code></pre></div>
161 154 
 </div>
162 155 
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163 156 
 <h1 class="hasAnchor">
... ... 
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357 350 
 ##  [1] scater_1.18.6               ggplot2_3.3.5
358 351 
 ##  [3] TENxPBMCData_1.8.0          HDF5Array_1.18.1
359 352 
 ##  [5] rhdf5_2.34.0                DelayedArray_0.16.2
360 
-##  [7] celda_1.11.0                Matrix_1.3-2
353 
+##  [7] celda_1.12.0                Matrix_1.3-2
361 354 
 ##  [9] SingleCellExperiment_1.12.0 SummarizedExperiment_1.20.0
362 355 
 ## [11] Biobase_2.50.0              GenomicRanges_1.42.0
363 356 
 ## [13] GenomeInfoDb_1.26.4         IRanges_2.24.1
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-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.11.0</span>
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 <pre><code>if (!requireNamespace("BiocManager", quietly = TRUE))
113 113 
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114 114 
 BiocManager::install("celda")</code></pre>
115 
-<p>To install the development version (R &gt;= 3.6) of <strong>celda</strong> from GitHub using <code>devtools</code>:</p>
115 
+<p>The latest stable version of <strong>celda</strong> can be installed from GitHub using <code>devtools</code>:</p>
116 116 
 <pre><code><a href="https://devtools.r-lib.org/">library(devtools)
117 117 
 install_github("campbio/celda")</a></code></pre>
118 
+<p>The development version of <strong>celda</strong> can also be installed from GitHub using <code>devtools</code>:</p>
119 
+<pre><code><a href="https://devtools.r-lib.org/">library(devtools)
120 
+install_github("campbio/celda@devel")</a></code></pre>
118 121 
 <p><strong>NOTE</strong> For MAC OSX users, <code><a href="https://devtools.r-lib.org/reference/remote-reexports.html">devtools::install_github()</a></code> requires installation of <strong>libgit2.</strong> This can be installed via homebrew:</p>
119 122 
 <pre><code>brew install libgit2</code></pre>
120 123 
 <p>Also, if you receive installation errors when Rcpp is being installed and compiled, try following the steps outlined here to solve the issue:</p>
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       <small>Source: <a href='https://github.com/campbio/celda/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
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+<h1 class="page-header" data-toc-text="1.12.0">
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+<a href="#celda-v1120-2022-03-31" class="anchor"></a>celda v1.12.0 (2022-03-31)</h1>
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+<ul>
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+<li>Update to match Bioconductor 3.15 release version</li>
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+</ul>
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+</div>
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+    <div id="celda-v1111-2022-03-31" class="section level1">
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+<h1 class="page-header" data-toc-text="1.11.1">
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+<a href="#celda-v1111-2022-03-31" class="anchor"></a>celda v1.11.1 (2022-03-31)</h1>
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+<ul>
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+<li>Fixes to reports</li>
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+<li>Use smoothe splines for perplexity and RPC plots</li>
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+</ul>
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+</div>
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+    <div id="celda-v1110-2022-03-31" class="section level1">
142 157 
 <h1 class="page-header" data-toc-text="1.11.0">
143 
-<a href="#celda-v1110-2022-xx-xx" class="anchor"></a>celda v1.11.0 (2022-XX-XX)</h1>
158 
+<a href="#celda-v1110-2022-03-31" class="anchor"></a>celda v1.11.0 (2022-03-31)</h1>
144 159 
 <ul>
145 160 
 <li>Improvments to decontX vignette</li>
146 161 
 <li>Added ability to subsample to speed up perplexity calculations</li>
147 162 
 <li>Added ability to use batch parameter with the raw matrix in decontX</li>
148 163 
 </ul>
164 
+</div>
165 
+    <div id="celda-v1100-2021-12-28" class="section level1">
166 
+<h1 class="page-header" data-toc-text="1.10.0">
167 
+<a href="#celda-v1100-2021-12-28" class="anchor"></a>celda v1.10.0 (2021-12-28)</h1>
168 
+<ul>
169 
+<li>Update to match Bioconductor release version</li>
170 
+</ul>
149 171 
 </div>
150 172 
     <div id="celda-v193-2021-10-04" class="section level1">
151 173 
 <h1 class="page-header" data-toc-text="1.9.3">
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357 357 
     K <span class='op'>=</span> <span class='va'>celdaCSim</span><span class='op'>$</span><span class='va'>K</span>,
358 358 
     sampleLabel <span class='op'>=</span> <span class='va'>celdaCSim</span><span class='op'>$</span><span class='va'>sampleLabel</span>,
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360 
-</div><div class='output co'>#&gt; <span class='message'>--------------------------------------------------</span></div><div class='output co'>#&gt; <span class='message'>Starting Celda_C: Clustering cells.</span></div><div class='output co'>#&gt; <span class='message'>--------------------------------------------------</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:10:16 2022 .. Initializing 'z' in chain 1 with 'split' </span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:10:16 2022 .... Completed iteration: 1 | logLik: -1282027.27277705</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:10:16 2022 .... Completed iteration: 2 | logLik: -1282027.27277705</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:10:16 2022 .. Finished chain 1</span></div><div class='output co'>#&gt; <span class='message'>--------------------------------------------------</span></div><div class='output co'>#&gt; <span class='message'>Completed Celda_C. Total time: 0.1379719 secs</span></div><div class='output co'>#&gt; <span class='message'>--------------------------------------------------</span></div></pre>
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+</div><div class='output co'>#&gt; <span class='message'>--------------------------------------------------</span></div><div class='output co'>#&gt; <span class='message'>Starting Celda_C: Clustering cells.</span></div><div class='output co'>#&gt; <span class='message'>--------------------------------------------------</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:14:05 2022 .. Initializing 'z' in chain 1 with 'split' </span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:14:06 2022 .... Completed iteration: 1 | logLik: -1282027.27277705</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:14:06 2022 .... Completed iteration: 2 | logLik: -1282027.27277705</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:14:06 2022 .. Finished chain 1</span></div><div class='output co'>#&gt; <span class='message'>--------------------------------------------------</span></div><div class='output co'>#&gt; <span class='message'>Completed Celda_C. Total time: 0.149879 secs</span></div><div class='output co'>#&gt; <span class='message'>--------------------------------------------------</span></div></pre>
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402 402 
     L <span class='op'>=</span> <span class='va'>celdaCGSim</span><span class='op'>$</span><span class='va'>L</span>,
403 403 
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404 404 
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405 
-</div><div class='output co'>#&gt; <span class='message'>--------------------------------------------------</span></div><div class='output co'>#&gt; <span class='message'>Starting Celda_CG: Clustering cells and genes.</span></div><div class='output co'>#&gt; <span class='message'>--------------------------------------------------</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:10:17 2022 .. Initializing 'z' in chain 1 with 'split' </span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:10:17 2022 .. Initializing 'y' in chain 1 with 'split' </span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:10:19 2022 .... Completed iteration: 1 | logLik: -1215542.98684529</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:10:19 2022 .... Completed iteration: 2 | logLik: -1215541.0958389</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:10:19 2022 .... Completed iteration: 3 | logLik: -1215541.0958389</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:10:19 2022 .... Completed iteration: 4 | logLik: -1215542.98684529</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:10:19 2022 .... Completed iteration: 5 | logLik: -1215541.0958389</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:10:19 2022 .... Completed iteration: 6 | logLik: -1215541.0958389</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:10:19 2022 .... Completed iteration: 7 | logLik: -1215541.0958389</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:10:19 2022 .... Completed iteration: 8 | logLik: -1215541.0958389</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:10:19 2022 .... Completed iteration: 9 | logLik: -1215541.0958389</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:10:19 2022 .... Determining if any gene clusters should be split.</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:10:20 2022 .... No additional splitting was performed.</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:10:20 2022 .... Determining if any cell clusters should be split.</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:10:20 2022 .... No additional splitting was performed.</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:10:20 2022 .... Completed iteration: 10 | logLik: -1215541.0958389</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:10:20 2022 .... Determining if any cell clusters should be split.</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:10:20 2022 .... No additional splitting was performed.</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:10:20 2022 .... Completed iteration: 11 | logLik: -1215541.0958389</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:10:20 2022 .. Finished chain 1</span></div><div class='output co'>#&gt; <span class='message'>--------------------------------------------------</span></div><div class='output co'>#&gt; <span class='message'>Completed Celda_CG. Total time: 3.212025 secs</span></div><div class='output co'>#&gt; <span class='message'>--------------------------------------------------</span></div></pre>
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+</div><div class='output co'>#&gt; <span class='message'>--------------------------------------------------</span></div><div class='output co'>#&gt; <span class='message'>Starting Celda_CG: Clustering cells and genes.</span></div><div class='output co'>#&gt; <span class='message'>--------------------------------------------------</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:14:06 2022 .. Initializing 'z' in chain 1 with 'split' </span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:14:06 2022 .. Initializing 'y' in chain 1 with 'split' </span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:14:09 2022 .... Completed iteration: 1 | logLik: -1215542.98684529</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:14:09 2022 .... Completed iteration: 2 | logLik: -1215541.0958389</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:14:09 2022 .... Completed iteration: 3 | logLik: -1215541.0958389</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:14:09 2022 .... Completed iteration: 4 | logLik: -1215542.98684529</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:14:09 2022 .... Completed iteration: 5 | logLik: -1215541.0958389</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:14:09 2022 .... Completed iteration: 6 | logLik: -1215541.0958389</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:14:09 2022 .... Completed iteration: 7 | logLik: -1215541.0958389</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:14:09 2022 .... Completed iteration: 8 | logLik: -1215541.0958389</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:14:09 2022 .... Completed iteration: 9 | logLik: -1215541.0958389</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:14:09 2022 .... Determining if any gene clusters should be split.</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:14:09 2022 .... No additional splitting was performed.</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:14:09 2022 .... Determining if any cell clusters should be split.</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:14:09 2022 .... No additional splitting was performed.</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:14:09 2022 .... Completed iteration: 10 | logLik: -1215541.0958389</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:14:09 2022 .... Determining if any cell clusters should be split.</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:14:09 2022 .... No additional splitting was performed.</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:14:09 2022 .... Completed iteration: 11 | logLik: -1215541.0958389</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:14:09 2022 .. Finished chain 1</span></div><div class='output co'>#&gt; <span class='message'>--------------------------------------------------</span></div><div class='output co'>#&gt; <span class='message'>Completed Celda_CG. Total time: 3.036642 secs</span></div><div class='output co'>#&gt; <span class='message'>--------------------------------------------------</span></div></pre>
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341 341 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
342 342 
     <pre class="examples"><div class='input'><span class='fu'><a href='https://rdrr.io/r/utils/data.html'>data</a></span><span class='op'>(</span><span class='va'>celdaGSim</span><span class='op'>)</span>
343 343 
 <span class='va'>sce</span> <span class='op'>&lt;-</span> <span class='fu'>celda_G</span><span class='op'>(</span><span class='va'>celdaGSim</span><span class='op'>$</span><span class='va'>counts</span>, L <span class='op'>=</span> <span class='va'>celdaGSim</span><span class='op'>$</span><span class='va'>L</span>, nchains <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span>
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-</div><div class='output co'>#&gt; <span class='message'>--------------------------------------------------</span></div><div class='output co'>#&gt; <span class='message'>Starting Celda_G: Clustering genes.</span></div><div class='output co'>#&gt; <span class='message'>--------------------------------------------------</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:10:20 2022 .. Initializing 'y' in chain 1 with 'split' </span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:10:22 2022 .... Completed iteration: 1 | logLik: -290669.046132139</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:10:22 2022 .... Completed iteration: 2 | logLik: -290669.046132139</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:10:22 2022 .... Completed iteration: 3 | logLik: -290669.046132139</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:10:22 2022 .... Completed iteration: 4 | logLik: -290669.046132139</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:10:22 2022 .... Completed iteration: 5 | logLik: -290669.046132139</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:10:22 2022 .... Completed iteration: 6 | logLik: -290669.046132139</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:10:22 2022 .... Completed iteration: 7 | logLik: -290669.046132139</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:10:22 2022 .... Completed iteration: 8 | logLik: -290669.046132139</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:10:22 2022 .... Completed iteration: 9 | logLik: -290669.046132139</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:10:22 2022 .... Determining if any gene clusters should be split.</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:10:22 2022 .... No additional splitting was performed.</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:10:22 2022 .... Completed iteration: 10 | logLik: -290669.046132139</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:10:22 2022 .... Completed iteration: 11 | logLik: -290669.046132139</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:10:22 2022 .. Finished chain 1</span></div><div class='output co'>#&gt; <span class='message'>--------------------------------------------------</span></div><div class='output co'>#&gt; <span class='message'>Completed Celda_G. Total time: 2.057198 secs</span></div><div class='output co'>#&gt; <span class='message'>--------------------------------------------------</span></div></pre>
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+</div><div class='output co'>#&gt; <span class='message'>--------------------------------------------------</span></div><div class='output co'>#&gt; <span class='message'>Starting Celda_G: Clustering genes.</span></div><div class='output co'>#&gt; <span class='message'>--------------------------------------------------</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:14:09 2022 .. Initializing 'y' in chain 1 with 'split' </span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:14:11 2022 .... Completed iteration: 1 | logLik: -290669.046132139</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:14:11 2022 .... Completed iteration: 2 | logLik: -290669.046132139</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:14:11 2022 .... Completed iteration: 3 | logLik: -290669.046132139</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:14:11 2022 .... Completed iteration: 4 | logLik: -290669.046132139</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:14:11 2022 .... Completed iteration: 5 | logLik: -290669.046132139</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:14:11 2022 .... Completed iteration: 6 | logLik: -290669.046132139</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:14:11 2022 .... Completed iteration: 7 | logLik: -290669.046132139</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:14:11 2022 .... Completed iteration: 8 | logLik: -290669.046132139</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:14:11 2022 .... Completed iteration: 9 | logLik: -290669.046132139</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:14:11 2022 .... Determining if any gene clusters should be split.</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:14:11 2022 .... No additional splitting was performed.</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:14:11 2022 .... Completed iteration: 10 | logLik: -290669.046132139</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:14:11 2022 .... Completed iteration: 11 | logLik: -290669.046132139</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:14:11 2022 .. Finished chain 1</span></div><div class='output co'>#&gt; <span class='message'>--------------------------------------------------</span></div><div class='output co'>#&gt; <span class='message'>Completed Celda_G. Total time: 2.014838 secs</span></div><div class='output co'>#&gt; <span class='message'>--------------------------------------------------</span></div></pre>
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 <span class='va'>sce</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/SingleCellExperiment/man/SingleCellExperiment.html'>SingleCellExperiment</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>counts <span class='op'>=</span> <span class='va'>s</span><span class='op'>$</span><span class='va'>observedCounts</span><span class='op'>)</span><span class='op'>)</span>
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-    <pre class="usage"><span class='fu'>plotGridSearchPerplexity</span><span class='op'>(</span><span class='va'>x</span>, altExpName <span class='op'>=</span> <span class='st'>"featureSubset"</span>, sep <span class='op'>=</span> <span class='fl'>1</span>, alpha <span class='op'>=</span> <span class='fl'>0.5</span><span class='op'>)</span>
149 
+    <pre class="usage"><span class='fu'>plotGridSearchPerplexity</span><span class='op'>(</span><span class='va'>x</span>, altExpName <span class='op'>=</span> <span class='st'>"featureSubset"</span>, sep <span class='op'>=</span> <span class='fl'>5</span>, alpha <span class='op'>=</span> <span class='fl'>0.5</span><span class='op'>)</span>
150 150
151 151 
 <span class='co'># S4 method for SingleCellExperiment</span>
152 
-<span class='fu'>plotGridSearchPerplexity</span><span class='op'>(</span><span class='va'>x</span>, altExpName <span class='op'>=</span> <span class='st'>"featureSubset"</span>, sep <span class='op'>=</span> <span class='fl'>1</span>, alpha <span class='op'>=</span> <span class='fl'>0.5</span><span class='op'>)</span>
152 
+<span class='fu'>plotGridSearchPerplexity</span><span class='op'>(</span><span class='va'>x</span>, altExpName <span class='op'>=</span> <span class='st'>"featureSubset"</span>, sep <span class='op'>=</span> <span class='fl'>5</span>, alpha <span class='op'>=</span> <span class='fl'>0.5</span><span class='op'>)</span>
153 153
154 154 
 <span class='co'># S4 method for celdaList</span>
155 
-<span class='fu'>plotGridSearchPerplexity</span><span class='op'>(</span><span class='va'>x</span>, sep <span class='op'>=</span> <span class='fl'>1</span>, alpha <span class='op'>=</span> <span class='fl'>0.5</span><span class='op'>)</span></pre>
155 
+<span class='fu'>plotGridSearchPerplexity</span><span class='op'>(</span><span class='va'>x</span>, sep <span class='op'>=</span> <span class='fl'>5</span>, alpha <span class='op'>=</span> <span class='fl'>0.5</span><span class='op'>)</span></pre>
156 156
157 157 
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
158 158 
     <table class="ref-arguments">
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       </button>
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       <span class="navbar-brand">
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41 41
42 42 
 <meta property="og:title" content="Visualize perplexity differences of a list of celda models — plotRPC" />
43 43 
 <meta property="og:description" content="Visualize perplexity differences of every model in a celdaList,
44 
- by unique K/L combinations. Line represents centered moving average with
45 
- windows of length n." />
44 
+ by unique K/L combinations." />
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48 47
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       </button>
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+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.12.0</span>
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80 79
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@@ -144,17 +143,16 @@
144 143
145 144 
     <div class="ref-description">
146 145 
     <p>Visualize perplexity differences of every model in a celdaList,
147 
- by unique K/L combinations. Line represents centered moving average with
148 
- windows of length <code>n</code>.</p>
146 
+ by unique K/L combinations.</p>
149 147 
     </div>
150 148
151 
-    <pre class="usage"><span class='fu'>plotRPC</span><span class='op'>(</span><span class='va'>x</span>, altExpName <span class='op'>=</span> <span class='st'>"featureSubset"</span>, sep <span class='op'>=</span> <span class='fl'>1</span>, n <span class='op'>=</span> <span class='fl'>10</span>, alpha <span class='op'>=</span> <span class='fl'>0.5</span><span class='op'>)</span>
149 
+    <pre class="usage"><span class='fu'>plotRPC</span><span class='op'>(</span><span class='va'>x</span>, altExpName <span class='op'>=</span> <span class='st'>"featureSubset"</span>, sep <span class='op'>=</span> <span class='fl'>5</span>, alpha <span class='op'>=</span> <span class='fl'>0.5</span><span class='op'>)</span>
152 150
153 151 
 <span class='co'># S4 method for SingleCellExperiment</span>
154 
-<span class='fu'>plotRPC</span><span class='op'>(</span><span class='va'>x</span>, altExpName <span class='op'>=</span> <span class='st'>"featureSubset"</span>, sep <span class='op'>=</span> <span class='fl'>1</span>, n <span class='op'>=</span> <span class='fl'>10</span>, alpha <span class='op'>=</span> <span class='fl'>0.5</span><span class='op'>)</span>
152 
+<span class='fu'>plotRPC</span><span class='op'>(</span><span class='va'>x</span>, altExpName <span class='op'>=</span> <span class='st'>"featureSubset"</span>, sep <span class='op'>=</span> <span class='fl'>5</span>, alpha <span class='op'>=</span> <span class='fl'>0.5</span><span class='op'>)</span>
155 153
156 154 
 <span class='co'># S4 method for celdaList</span>
157 
-<span class='fu'>plotRPC</span><span class='op'>(</span><span class='va'>x</span>, sep <span class='op'>=</span> <span class='fl'>1</span>, n <span class='op'>=</span> <span class='fl'>10</span>, alpha <span class='op'>=</span> <span class='fl'>0.5</span><span class='op'>)</span></pre>
155 
+<span class='fu'>plotRPC</span><span class='op'>(</span><span class='va'>x</span>, sep <span class='op'>=</span> <span class='fl'>5</span>, alpha <span class='op'>=</span> <span class='fl'>0.5</span><span class='op'>)</span></pre>
158 156
159 157 
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
160 158 
     <table class="ref-arguments">
... ... 
@@ -178,10 +176,6 @@ to use. Default "featureSubset".</p></td>
178 176 
       <th>sep</th>
179 177 
       <td><p>Numeric. Breaks in the x axis of the resulting plot.</p></td>
180 178 
     </tr>
181 
-    <tr>
182 
-      <th>n</th>
183 
-      <td><p>Integer. Width of the rolling window. Default 10.</p></td>
184 
-    </tr>
185 179 
     <tr>
186 180 
       <th>alpha</th>
187 181 
       <td><p>Numeric. Passed to geom_jitter. Opacity of the points.
... ... 
@@ -192,19 +186,19 @@ to more transparent colors.</p></td>
192 186
193 187 
     <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
194 188
195 
-    <p>A ggplot plot object showing perplexity diferences as a function of
189 
+    <p>A ggplot plot object showing perplexity differences as a function of
196 190 
  clustering parameters.</p>
197 191
198 192 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
199 193 
     <pre class="examples"><div class='input'><span class='fu'><a href='https://rdrr.io/r/utils/data.html'>data</a></span><span class='op'>(</span><span class='va'>sceCeldaCGGridSearch</span><span class='op'>)</span>
200 194 
 <span class='va'>sce</span> <span class='op'>&lt;-</span> <span class='fu'><a href='resamplePerplexity.html'>resamplePerplexity</a></span><span class='op'>(</span><span class='va'>sceCeldaCGGridSearch</span><span class='op'>)</span>
201 
-<span class='fu'>plotRPC</span><span class='op'>(</span><span class='va'>sce</span>, n <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span>
195 
+<span class='fu'>plotRPC</span><span class='op'>(</span><span class='va'>sce</span><span class='op'>)</span>
202 196 
 </div><div class='img'><img src='plotRPC-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/utils/data.html'>data</a></span><span class='op'>(</span><span class='va'>celdaCGSim</span>, <span class='va'>celdaCGGridSearchRes</span><span class='op'>)</span>
203 197 
 <span class='co'>## Run various combinations of parameters with 'celdaGridSearch'</span>
204 198 
 <span class='va'>celdaCGGridSearchRes</span> <span class='op'>&lt;-</span> <span class='fu'><a href='resamplePerplexity.html'>resamplePerplexity</a></span><span class='op'>(</span>
205 199 
   <span class='va'>celdaCGSim</span><span class='op'>$</span><span class='va'>counts</span>,
206 200 
   <span class='va'>celdaCGGridSearchRes</span><span class='op'>)</span>
207 
-<span class='fu'>plotRPC</span><span class='op'>(</span><span class='va'>celdaCGGridSearchRes</span>, n <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span>
201 
+<span class='fu'>plotRPC</span><span class='op'>(</span><span class='va'>celdaCGGridSearchRes</span><span class='op'>)</span>
208 202 
 </div><div class='img'><img src='plotRPC-2.png' alt='' width='700' height='433' /></div></pre>
209 203 
   </div>
210 204 
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
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-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.11.0</span>
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+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.12.0</span>
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-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.11.0</span>
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       </button>
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83 83 
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84 
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.11.0</span>
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+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.12.0</span>
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     </div>
87 87
... ... 
@@ -180,9 +180,7 @@
180 180 
   seed <span class='op'>=</span> <span class='fl'>12345</span>,
181 181 
   perplexity <span class='op'>=</span> <span class='cn'>TRUE</span>,
182 182 
   doResampling <span class='op'>=</span> <span class='cn'>FALSE</span>,
183 
-  doSubsampling <span class='op'>=</span> <span class='cn'>TRUE</span>,
184 183 
   numResample <span class='op'>=</span> <span class='fl'>5</span>,
185 
-  numSubsample <span class='op'>=</span> <span class='fl'>5000</span>,
186 184 
   logfile <span class='op'>=</span> <span class='cn'>NULL</span>,
187 185 
   verbose <span class='op'>=</span> <span class='cn'>TRUE</span>
188 186 
 <span class='op'>)</span>
... ... 
@@ -206,9 +204,7 @@
206 204 
   seed <span class='op'>=</span> <span class='fl'>12345</span>,
207 205 
   perplexity <span class='op'>=</span> <span class='cn'>TRUE</span>,
208 206 
   doResampling <span class='op'>=</span> <span class='cn'>FALSE</span>,
209 
-  doSubsampling <span class='op'>=</span> <span class='cn'>TRUE</span>,
210 207 
   numResample <span class='op'>=</span> <span class='fl'>5</span>,
211 
-  numSubsample <span class='op'>=</span> <span class='fl'>5000</span>,
212 208 
   logfile <span class='op'>=</span> <span class='cn'>NULL</span>,
213 209 
   verbose <span class='op'>=</span> <span class='cn'>TRUE</span>
214 210 
 <span class='op'>)</span>
... ... 
@@ -232,9 +228,7 @@
232 228 
   seed <span class='op'>=</span> <span class='fl'>12345</span>,
233 229 
   perplexity <span class='op'>=</span> <span class='cn'>TRUE</span>,
234 230 
   doResampling <span class='op'>=</span> <span class='cn'>FALSE</span>,
235 
-  doSubsampling <span class='op'>=</span> <span class='cn'>TRUE</span>,
236 231 
   numResample <span class='op'>=</span> <span class='fl'>5</span>,
237 
-  numSubsample <span class='op'>=</span> <span class='fl'>5000</span>,
238 232 
   logfile <span class='op'>=</span> <span class='cn'>NULL</span>,
239 233 
   verbose <span class='op'>=</span> <span class='cn'>TRUE</span>
240 234 
 <span class='op'>)</span></pre>
... ... 
@@ -344,23 +338,12 @@ If FALSE, then perplexity can be calculated later with
344 338 
       <td><p>Boolean. If <code>TRUE</code>, then each cell in the counts
345 339 
 matrix will be resampled according to a multinomial distribution to introduce
346 340 
 noise before calculating perplexity. Default <code>FALSE</code>.</p></td>
347 
-    </tr>
348 
-    <tr>
349 
-      <th>doSubsampling</th>
350 
-      <td><p>Boolean. If <code>TRUE</code>, then a subset of cells from
351 
-the original counts matrix will be randomly selected. Default <code>TRUE</code>.</p></td>
352 341 
     </tr>
353 342 
     <tr>
354 343 
       <th>numResample</th>
355 344 
       <td><p>Integer. The number of times to resample the counts matrix
356 
-for evaluating perplexity if <code>doSubsampling</code> is set to <code>TRUE</code>.
345 
+for evaluating perplexity if <code>doResampling</code> is set to <code>TRUE</code>.
357 346 
 Default <code>5</code>.</p></td>
358 
-    </tr>
359 
-    <tr>
360 
-      <th>numSubsample</th>
361 
-      <td><p>Integer. The number of cells to sample from the
362 
-the counts matrix if <code>doSubsampling</code> is set to <code>TRUE</code>.
363 
-Default <code>5000</code>.</p></td>
364 347 
     </tr>
365 348 
     <tr>
366 349 
       <th>logfile</th>
... ... 
@@ -390,36 +373,36 @@ Default <code>5000</code>.</p></td>
390 373 
 <span class='co'>## Create models that range from K = 3 to K = 7 by recursively splitting</span>
391 374 
 <span class='co'>## cell populations into two to produce \link{celda_C} cell clustering models</span>
392 375 
 <span class='va'>sce</span> <span class='op'>&lt;-</span> <span class='fu'>recursiveSplitCell</span><span class='op'>(</span><span class='va'>sceCeldaCG</span>, initialK <span class='op'>=</span> <span class='fl'>3</span>, maxK <span class='op'>=</span> <span class='fl'>7</span><span class='op'>)</span>
393 
-</div><div class='output co'>#&gt; <span class='message'>==================================================</span></div><div class='output co'>#&gt; <span class='message'>Starting recursive cell population splitting.</span></div><div class='output co'>#&gt; <span class='message'>==================================================</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:11:32 2022 .. Initializing with 3 populations</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:11:32 2022 .. Current cell population 4 | logLik: -1225755.01101897</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:11:32 2022 .. Current cell population 5 | logLik: -1213677.60126784</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:11:32 2022 .. Current cell population 6 | logLik: -1213903.59449854</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:11:32 2022 .. Current cell population 7 | logLik: -1214081.54311397</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:11:32 2022 .. Calculating perplexity</span></div><div class='output co'>#&gt; <span class='message'>==================================================</span></div><div class='output co'>#&gt; <span class='message'>Completed recursive cell population splitting. Total time: 0.285394 secs</span></div><div class='output co'>#&gt; <span class='message'>==================================================</span></div><div class='input'>
376 
+</div><div class='output co'>#&gt; <span class='message'>==================================================</span></div><div class='output co'>#&gt; <span class='message'>Starting recursive cell population splitting.</span></div><div class='output co'>#&gt; <span class='message'>==================================================</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:15:13 2022 .. Initializing with 3 populations</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:15:13 2022 .. Current cell population 4 | logLik: -1225755.01101897</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:15:13 2022 .. Current cell population 5 | logLik: -1213677.60126784</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:15:13 2022 .. Current cell population 6 | logLik: -1213903.59449854</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:15:13 2022 .. Current cell population 7 | logLik: -1214081.54311397</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:15:13 2022 .. Calculating perplexity</span></div><div class='output co'>#&gt; <span class='message'>==================================================</span></div><div class='output co'>#&gt; <span class='message'>Completed recursive cell population splitting. Total time: 0.2865281 secs</span></div><div class='output co'>#&gt; <span class='message'>==================================================</span></div><div class='input'>
394 377 
 <span class='co'>## Alternatively, first identify features modules using</span>
395 378 
 <span class='co'>## \link{recursiveSplitModule}</span>
396 379 
 <span class='va'>moduleSplit</span> <span class='op'>&lt;-</span> <span class='fu'><a href='recursiveSplitModule.html'>recursiveSplitModule</a></span><span class='op'>(</span><span class='va'>sceCeldaCG</span>, initialL <span class='op'>=</span> <span class='fl'>3</span>, maxL <span class='op'>=</span> <span class='fl'>15</span><span class='op'>)</span>
397 
-</div><div class='output co'>#&gt; <span class='message'>==================================================</span></div><div class='output co'>#&gt; <span class='message'>Starting recursive module splitting.</span></div><div class='output co'>#&gt; <span class='message'>==================================================</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:11:32 2022 .. Collapsing to 100 temporary cell populations</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:11:33 2022 .. Initializing with 3 modules</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:11:33 2022 .. Created module 4 | logLik: -1241379.90928455</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:11:33 2022 .. Created module 5 | logLik: -1235212.7977535</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:11:34 2022 .. Created module 6 | logLik: -1232789.9817561</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:11:34 2022 .. Created module 7 | logLik: -1227246.66090571</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:11:34 2022 .. Created module 8 | logLik: -1223898.757694</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:11:34 2022 .. Created module 9 | logLik: -1221848.26936098</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:11:34 2022 .. Created module 10 | logLik: -1220147.96681948</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:11:34 2022 .. Created module 11 | logLik: -1220818.37022325</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:11:34 2022 .. Created module 12 | logLik: -1221489.07685946</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:11:34 2022 .. Created module 13 | logLik: -1222032.53497571</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:11:34 2022 .. Created module 14 | logLik: -1222712.17543857</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:11:34 2022 .. Created module 15 | logLik: -1223268.97596756</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:11:34 2022 .. Calculating perplexity</span></div><div class='output co'>#&gt; <span class='message'>==================================================</span></div><div class='output co'>#&gt; <span class='message'>Completed recursive module splitting. Total time: 2.224735 secs</span></div><div class='output co'>#&gt; <span class='message'>==================================================</span></div><div class='input'><span class='fu'><a href='plotGridSearchPerplexity.html'>plotGridSearchPerplexity</a></span><span class='op'>(</span><span class='va'>moduleSplit</span><span class='op'>)</span>
380 
+</div><div class='output co'>#&gt; <span class='message'>==================================================</span></div><div class='output co'>#&gt; <span class='message'>Starting recursive module splitting.</span></div><div class='output co'>#&gt; <span class='message'>==================================================</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:15:13 2022 .. Collapsing to 100 temporary cell populations</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:15:14 2022 .. Initializing with 3 modules</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:15:14 2022 .. Created module 4 | logLik: -1241379.90928455</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:15:14 2022 .. Created module 5 | logLik: -1235212.7977535</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:15:14 2022 .. Created module 6 | logLik: -1232789.9817561</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:15:14 2022 .. Created module 7 | logLik: -1227246.66090571</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:15:14 2022 .. Created module 8 | logLik: -1223898.757694</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:15:14 2022 .. Created module 9 | logLik: -1221848.26936098</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:15:15 2022 .. Created module 10 | logLik: -1220147.96681948</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:15:15 2022 .. Created module 11 | logLik: -1220818.37022325</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:15:15 2022 .. Created module 12 | logLik: -1221489.07685946</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:15:15 2022 .. Created module 13 | logLik: -1222032.53497571</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:15:15 2022 .. Created module 14 | logLik: -1222712.17543857</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:15:15 2022 .. Created module 15 | logLik: -1223268.97596756</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:15:15 2022 .. Calculating perplexity</span></div><div class='output co'>#&gt; <span class='message'>==================================================</span></div><div class='output co'>#&gt; <span class='message'>Completed recursive module splitting. Total time: 2.031379 secs</span></div><div class='output co'>#&gt; <span class='message'>==================================================</span></div><div class='input'><span class='fu'><a href='plotGridSearchPerplexity.html'>plotGridSearchPerplexity</a></span><span class='op'>(</span><span class='va'>moduleSplit</span><span class='op'>)</span>
398 381 
 </div><div class='img'><img src='recursiveSplitCell-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='va'>moduleSplitSelect</span> <span class='op'>&lt;-</span> <span class='fu'><a href='subsetCeldaList.html'>subsetCeldaList</a></span><span class='op'>(</span><span class='va'>moduleSplit</span>, <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>L <span class='op'>=</span> <span class='fl'>10</span><span class='op'>)</span><span class='op'>)</span>
399 382
400 383 
 <span class='co'>## Then use module labels for initialization in \link{recursiveSplitCell} to</span>
401 384 
 <span class='co'>## produce \link{celda_CG} bi-clustering models</span>
402 385 
 <span class='va'>cellSplit</span> <span class='op'>&lt;-</span> <span class='fu'>recursiveSplitCell</span><span class='op'>(</span><span class='va'>sceCeldaCG</span>,
403 386 
   initialK <span class='op'>=</span> <span class='fl'>3</span>, maxK <span class='op'>=</span> <span class='fl'>7</span>, yInit <span class='op'>=</span> <span class='fu'><a href='celdaModules.html'>celdaModules</a></span><span class='op'>(</span><span class='va'>moduleSplitSelect</span><span class='op'>)</span><span class='op'>)</span>
404 
-</div><div class='output co'>#&gt; <span class='message'>==================================================</span></div><div class='output co'>#&gt; <span class='message'>Starting recursive cell population splitting.</span></div><div class='output co'>#&gt; <span class='message'>==================================================</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:11:35 2022 .. Collapsing to 10 modules</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:11:35 2022 .. Initializing with 3 populations</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:11:35 2022 .. Current cell population 4 | logLik: -1225286.49558716</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:11:35 2022 .. Current cell population 5 | logLik: -1212955.15575681</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:11:36 2022 .. Current cell population 6 | logLik: -1212982.74290613</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:11:36 2022 .. Current cell population 7 | logLik: -1213005.40337891</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:11:36 2022 .. Calculating perplexity</span></div><div class='output co'>#&gt; <span class='message'>==================================================</span></div><div class='output co'>#&gt; <span class='message'>Completed recursive cell population splitting. Total time: 1.023948 secs</span></div><div class='output co'>#&gt; <span class='message'>==================================================</span></div><div class='input'><span class='fu'><a href='plotGridSearchPerplexity.html'>plotGridSearchPerplexity</a></span><span class='op'>(</span><span class='va'>cellSplit</span><span class='op'>)</span>
387 
+</div><div class='output co'>#&gt; <span class='message'>==================================================</span></div><div class='output co'>#&gt; <span class='message'>Starting recursive cell population splitting.</span></div><div class='output co'>#&gt; <span class='message'>==================================================</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:15:15 2022 .. Collapsing to 10 modules</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:15:15 2022 .. Initializing with 3 populations</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:15:16 2022 .. Current cell population 4 | logLik: -1225286.49558716</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:15:16 2022 .. Current cell population 5 | logLik: -1212955.15575681</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:15:16 2022 .. Current cell population 6 | logLik: -1212982.74290613</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:15:16 2022 .. Current cell population 7 | logLik: -1213005.40337891</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:15:16 2022 .. Calculating perplexity</span></div><div class='output co'>#&gt; <span class='message'>==================================================</span></div><div class='output co'>#&gt; <span class='message'>Completed recursive cell population splitting. Total time: 0.936219 secs</span></div><div class='output co'>#&gt; <span class='message'>==================================================</span></div><div class='input'><span class='fu'><a href='plotGridSearchPerplexity.html'>plotGridSearchPerplexity</a></span><span class='op'>(</span><span class='va'>cellSplit</span><span class='op'>)</span>
405 388 
 </div><div class='img'><img src='recursiveSplitCell-2.png' alt='' width='700' height='433' /></div><div class='input'><span class='va'>sce</span> <span class='op'>&lt;-</span> <span class='fu'><a href='subsetCeldaList.html'>subsetCeldaList</a></span><span class='op'>(</span><span class='va'>cellSplit</span>, <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>K <span class='op'>=</span> <span class='fl'>5</span>, L <span class='op'>=</span> <span class='fl'>10</span><span class='op'>)</span><span class='op'>)</span>
406 389 
 <span class='fu'><a href='https://rdrr.io/r/utils/data.html'>data</a></span><span class='op'>(</span><span class='va'>celdaCGSim</span>, <span class='va'>celdaCSim</span><span class='op'>)</span>
407 390 
 <span class='co'>## Create models that range from K = 3 to K = 7 by recursively splitting</span>
408 391 
 <span class='co'>## cell populations into two to produce \link{celda_C} cell clustering models</span>
409 392 
 <span class='va'>sce</span> <span class='op'>&lt;-</span> <span class='fu'>recursiveSplitCell</span><span class='op'>(</span><span class='va'>celdaCSim</span><span class='op'>$</span><span class='va'>counts</span>, initialK <span class='op'>=</span> <span class='fl'>3</span>, maxK <span class='op'>=</span> <span class='fl'>7</span><span class='op'>)</span>
410 
-</div><div class='output co'>#&gt; <span class='message'>==================================================</span></div><div class='output co'>#&gt; <span class='message'>Starting recursive cell population splitting.</span></div><div class='output co'>#&gt; <span class='message'>==================================================</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:11:36 2022 .. Initializing with 3 populations</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:11:36 2022 .. Current cell population 4 | logLik: -1341630.1679001</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:11:36 2022 .. Current cell population 5 | logLik: -1327506.91718317</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:11:36 2022 .. Current cell population 6 | logLik: -1315227.54586167</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:11:36 2022 .. Current cell population 7 | logLik: -1304393.65802293</span></div><div class='output co'>#&gt; <span class='message'>Thu Mar 31 11:11:36 2022 .. Calculating perplexity</span></div><div class='output co'>#&gt; <span class='message'>==================================================</span></div><div class='output co'>#&gt; <span class='message'>Completed recursive cell population splitting. Total time: 0.2181861 secs</span></div><div class='output co'>#&gt; <span class='message'>==================================================</span></div><div class='input'>
393 
+</div><div class='output co'>#&gt; <span class='message'>==================================================</span></div><div class='output co'>#&gt; <span class='message'>Starting recursive cell population splitting.</span></div><div class='output co'>#&gt; <span class='message'>==================================================</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:15:17 2022 .. Initializing with 3 populations</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:15:17 2022 .. Current cell population 4 | logLik: -1341630.1679001</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:15:17 2022 .. Current cell population 5 | logLik: -1327506.91718317</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:15:17 2022 .. Current cell population 6 | logLik: -1315227.54586167</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:15:17 2022 .. Current cell population 7 | logLik: -1304393.65802293</span></div><div class='output co'>#&gt; <span class='message'>Sat Apr 30 15:15:17 2022 .. Calculating perplexity</span></div><div class='output co'>#&gt; <span class='message'>==================================================</span></div><div class='out