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<h3>
Steffen Möller pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/pigx-scrnaseq">Debian Med / pigx-scrnaseq</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/pigx-scrnaseq/-/commit/bfa5c0280f033e356fd31d35a63518e67ac6d2dd">bfa5c028</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-12-14T00:07:42+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.1.7+ds</pre>
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<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#21d719f539cf9a480ce1e27b5a63679059dfda15">
Snake_Dropseq.py
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<li class="file-stats">
<a href="#b33892fbddeffc3368077b4904ad0b3d562a7312">
VERSION
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<li class="file-stats">
<a href="#19359a61ae2446b51b549167b014da2fcf265768">
requirements.txt
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<li class="file-stats">
<a href="#2fae19cf43679d831fb0de1a4c19e9ec4589d915">
scripts/Sample_Sheet_Class.py
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<li class="file-stats">
<a href="#8b8c025c2cb41d9e35f386de8a8ebd3f5ce5ed3d">
<span class="new-file">
+
scripts/scrnaReport.Rmd
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</li>
<li class="file-stats">
<a href="#2cbb1531805dadad312d5ff126dd81256d74598b">
scripts/scrnaReport.Rmd.in
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<h4>Changes:</h4>
<li id="21d719f539cf9a480ce1e27b5a63679059dfda15">
<a href="https://salsa.debian.org/med-team/pigx-scrnaseq/-/commit/bfa5c0280f033e356fd31d35a63518e67ac6d2dd#21d719f539cf9a480ce1e27b5a63679059dfda15"><strong>Snake_Dropseq.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -153,7 +153,6 @@ for sample_name in SAMPLE_NAMES:</td>
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="python"> <span class="n" style="color: #333;">read_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">PATH_MAPPED</span><span class="p">,</span> <span class="n" style="color: #333;">sample_name</span><span class="p">,</span> <span class="n" style="color: #333;">genome</span><span class="p">,</span> <span class="n" style="color: #333;">sample_name</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'_2.fastq.gz'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="python"> <span class="n" style="color: #333;">FILTER_READS</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">read_file</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------- #</span></span>
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># MAPPING</span></span>
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<td class="diff-line-num old_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="python"><span class="n" style="color: #333;">MAP_scRNA</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">expand</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">PATH_MAPPED</span><span class="p">,</span> <span class="s" style="color: #d14;">"{name}"</span><span class="p">,</span> <span class="s" style="color: #d14;">"{genome}"</span><span class="p">,</span> <span class="s" style="color: #d14;">"{name}_Aligned.out.bam"</span><span class="p">),</span> <span class="n" style="color: #333;">genome</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">REFERENCE_NAMES</span><span class="p">,</span> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SAMPLE_NAMES</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -211,11 +210,9 @@ RULE_ALL = RULE_ALL + [LINK_REFERENCE_PRIMARY, LINK_GTF_PRIMARY]</td>
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">COMBINE_REFERENCE</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="python"> <span class="n" style="color: #333;">RULE_ALL</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">RULE_ALL</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">COMBINE_REFERENCE</span></span>
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<td class="diff-line-num old_line" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC214" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#RULE_ALL = RULE_ALL + DICT + REFFLAT + MAKE_STAR_INDEX + FASTQC + MERGE_FASTQ_TO_BAM + MERGE_BAM_PER_SAMPLE + MAP_scRNA + BAM_HISTOGRAM + FIND_READ_CUTOFF + READS_MATRIX + UMI + READ_STATISTICS + BIGWIG + UMI_LOOM + COMBINED_UMI_MATRICES + SCE_RDS_FILES + SEURAT_RDS_FILES + REPORT_FILES</span></span>
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="python"><span class="n" style="color: #333;">RULE_ALL</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">RULE_ALL</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">MAKE_STAR_INDEX</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">MERGE_TECHNICAL_REPLICATES</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">FILTER_READS</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">BAM_HISTOGRAM</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">FIND_CELL_NUMBER_CUTOFF</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">MAP_scRNA</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">SORT_BAM</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">INDEX_BAM</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">UMI_LOOM</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">COMBINED_LOOM_MATRICES</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">SCE_RDS_FILES</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">SEURAT_RDS_FILES</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">BIGWIG</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">READ_STATISTICS</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">REPORT_FILES</span></span>
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------- #</span></span>
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="python"><span class="n" style="color: #333;">rule</span> <span class="nb" style="color: #0086b3;">all</span><span class="p">:</span></span>
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218
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="python"> <span class="nb" style="color: #0086b3;">input</span><span class="p">:</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -392,6 +389,7 @@ if GENOME_SECONDARY_IND:</td>
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392
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389
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<pre style="margin: 0;"> <span id="LC389" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------------- #</span></span>
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390
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<pre style="margin: 0;"> <span id="LC390" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">fetch_fastq_technical_replicates</span><span class="p">(</span><span class="n" style="color: #333;">wc</span><span class="p">):</span></span>
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394
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<pre style="margin: 0;"> <span id="LC391" class="line" lang="python"> <span class="n" style="color: #333;">sample_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">wc</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">)</span></span>
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392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="python"></span>
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395
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<pre style="margin: 0;"> <span id="LC393" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">wc</span><span class="p">.</span><span class="nb" style="color: #0086b3;">type</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'R1'</span><span class="p">):</span></span>
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396
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394
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<pre style="margin: 0;"> <span id="LC394" class="line" lang="python"> <span class="n" style="color: #333;">input_fastq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SAMPLE_SHEET</span><span class="p">.</span><span class="n" style="color: #333;">fetch_barcode_path</span><span class="p">(</span><span class="n" style="color: #333;">sample_name</span><span class="p">)</span></span>
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397
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<pre style="margin: 0;"> <span id="LC395" class="line" lang="python"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -400,6 +398,7 @@ def fetch_fastq_technical_replicates(wc):</td>
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400
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398
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<pre style="margin: 0;"> <span id="LC398" class="line" lang="python"></span>
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401
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<pre style="margin: 0;"> <span id="LC399" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">input_fastq</span><span class="p">.</span><span class="n" style="color: #333;">__class__</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">:</span></span>
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402
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<pre style="margin: 0;"> <span id="LC400" class="line" lang="python"> <span class="n" style="color: #333;">input_fastq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">input_fastq</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC402" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span><span class="p">(</span><span class="n" style="color: #333;">input_fastq</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC403" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC404" class="line" lang="python"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -659,6 +658,11 @@ rule map_star:</td>
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<pre style="margin: 0;"> <span id="LC658" class="line" lang="python"> <span class="s" style="color: #d14;">'--soloFeatures'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">params</span><span class="p">.</span><span class="n" style="color: #333;">features</span><span class="p">),</span></span>
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660
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<pre style="margin: 0;"> <span id="LC659" class="line" lang="python"> <span class="s" style="color: #d14;">'--outSAMtype'</span><span class="p">,</span> <span class="s" style="color: #d14;">'BAM Unsorted'</span><span class="p">,</span></span>
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661
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<pre style="margin: 0;"> <span id="LC660" class="line" lang="python"> <span class="s" style="color: #d14;">'--readFilesCommand'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">params</span><span class="p">.</span><span class="n" style="color: #333;">zcat</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC661" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># CR/UR: raw (uncorrected) CellBarcode/UMI</span></span>
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<pre style="margin: 0;">+<span id="LC662" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># CY/UY: quality score for CellBarcode/UMI</span></span>
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<pre style="margin: 0;">+<span id="LC663" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># GX/GN: for gene ID/names</span></span>
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<pre style="margin: 0;">+<span id="LC664" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># sS/sQ: for sequence/quality combined CellBarcode and UMI; sM for barcode match status.</span></span>
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<pre style="margin: 0;">+<span id="LC665" class="line" lang="python"> <span class="s" style="color: #d14;">'--outSAMattributes NH HI nM AS CR UR GX GN sS sQ sM'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC666" class="line" lang="python"> <span class="n" style="color: #333;">join_params</span><span class="p">(</span><span class="s" style="color: #d14;">"STAR"</span><span class="p">,</span> <span class="n" style="color: #333;">PARAMS</span><span class="p">,</span> <span class="n" style="color: #333;">params</span><span class="p">.</span><span class="n" style="color: #333;">params_STAR</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC667" class="line" lang="python"> <span class="s" style="color: #d14;">'2>'</span><span class="p">,</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">log</span><span class="p">.</span><span class="n" style="color: #333;">logfile</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC668" class="line" lang="python"> <span class="p">])</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -686,7 +690,7 @@ rule sort_bam:</td>
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<pre style="margin: 0;"> <span id="LC690" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC691" class="line" lang="python"> <span class="n" style="color: #333;">run</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC692" class="line" lang="python"> <span class="n" style="color: #333;">command</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">' '</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span></span>
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<pre style="margin: 0;">-<span id="LC689" class="line" lang="python"> <span class="s" style="color: #d14;"><span class="idiff left right">'samtools </span>sort'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC693" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">params</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">samtools</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">'</span>sort'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC694" class="line" lang="python"> <span class="s" style="color: #d14;">'-@'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">params</span><span class="p">.</span><span class="n" style="color: #333;">threads</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC695" class="line" lang="python"> <span class="s" style="color: #d14;">'-o'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">outfile</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC696" class="line" lang="python"> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="nb" style="color: #0086b3;">input</span><span class="p">.</span><span class="n" style="color: #333;">infile</span><span class="p">)</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -714,7 +718,7 @@ rule index_bam:</td>
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<pre style="margin: 0;"> <span id="LC718" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC719" class="line" lang="python"> <span class="n" style="color: #333;">run</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC720" class="line" lang="python"> <span class="n" style="color: #333;">command</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">' '</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span></span>
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<pre style="margin: 0;">-<span id="LC717" class="line" lang="python"> <span class="s" style="color: #d14;"><span class="idiff left right">'samtools </span>index'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC721" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">params</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">samtools</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">'</span>index'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC722" class="line" lang="python"> <span class="s" style="color: #d14;">'-b'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC723" class="line" lang="python"> <span class="s" style="color: #d14;">'-@'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">params</span><span class="p">.</span><span class="n" style="color: #333;">threads</span><span class="p">),</span></span>
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720
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724
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<pre style="margin: 0;"> <span id="LC724" class="line" lang="python"> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="nb" style="color: #0086b3;">input</span><span class="p">.</span><span class="n" style="color: #333;">infile</span><span class="p">),</span></span>
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<a href="https://salsa.debian.org/med-team/pigx-scrnaseq/-/commit/bfa5c0280f033e356fd31d35a63518e67ac6d2dd#b33892fbddeffc3368077b4904ad0b3d562a7312"><strong>VERSION</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">1.1.<span class="idiff left right">6</span></span></pre>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">1.1.<span class="idiff left right">7</span></span></pre>
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<a href="https://salsa.debian.org/med-team/pigx-scrnaseq/-/commit/bfa5c0280f033e356fd31d35a63518e67ac6d2dd#19359a61ae2446b51b549167b014da2fcf265768"><strong>requirements.txt</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/STAR" rel="nofollow noreferrer noopener" target="_blank">STAR</a></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/java" rel="nofollow noreferrer noopener" target="_blank">java</a></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/picard" rel="nofollow noreferrer noopener" target="_blank">picard</a></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/Drop-seq_tools-1.12" rel="nofollow noreferrer noopener" target="_blank">Drop-seq_tools-1.12</a> #see software at http://mccarrolllab.com/dropseq/</span>
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5
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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6
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/snakemake" rel="nofollow noreferrer noopener" target="_blank">snakemake</a>=4.0.0</span>
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7
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/python" rel="nofollow noreferrer noopener" target="_blank">python</a>=3.6*</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -11,8 +8,11 @@ pandas</td>
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11
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/yaml" rel="nofollow noreferrer noopener" target="_blank">yaml</a></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/snakemake" rel="nofollow noreferrer noopener" target="_blank">snakemake</a></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/fastqc" rel="nofollow noreferrer noopener" target="_blank">fastqc</a></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/flexbar" rel="nofollow noreferrer noopener" target="_blank">flexbar</a></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"><a href="https://pypi.python.org/pypi/jellyfish" rel="nofollow noreferrer noopener" target="_blank">jellyfish</a></span>
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14
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">#R dependencies</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">#argparser</span>
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">#dplyr</span>
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17
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">#dropbead</span>
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">#GenomicAlignments</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -24,6 +24,7 @@ fastqc</td>
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24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">#rtracklayer</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">#stringr</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">#yaml</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">#Seurat</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext">#cowplot</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext">#data.table</span>
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<a href="https://salsa.debian.org/med-team/pigx-scrnaseq/-/commit/bfa5c0280f033e356fd31d35a63518e67ac6d2dd#2fae19cf43679d831fb0de1a4c19e9ec4589d915"><strong>scripts/Sample_Sheet_Class.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -133,13 +133,13 @@ class experiment:</td>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># ----------------------------------------------------------------------- #</span></span>
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># pivots the sample_sheet by sample_name to get unique technical replicates</span></span>
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">merge_technical_replicates</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#print('Merging technical replicates ...')</span></span>
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># defines the sample descriptors</span></span>
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="python"> <span class="n" style="color: #333;">sample_sheet</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">pivot_table</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">SAMPLE_SHEET</span><span class="p">,</span> <span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'sample_name'</span><span class="p">,</span> <span class="n" style="color: #333;">aggfunc</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;"><span class="idiff left right">se</span>t</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="python"> <span class="n" style="color: #333;">sample_sheet</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">pivot_table</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">SAMPLE_SHEET</span><span class="p">,</span> <span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'sample_name'</span><span class="p">,</span> <span class="n" style="color: #333;">aggfunc</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;"><span class="idiff left right">lis</span>t</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="python"> <span class="n" style="color: #333;">sample_sheet</span><span class="p">[</span><span class="s" style="color: #d14;">'sample_name'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sample_sheet</span><span class="p">.</span><span class="n" style="color: #333;">index</span></span>
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="python"> <span class="n" style="color: #333;">column_names</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">SAMPLE_SHEET</span><span class="p">.</span><span class="n" style="color: #333;">columns</span><span class="p">))</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -148,13 +148,12 @@ class experiment:</td>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># checks whether all technical replicates have the same metadata</span></span>
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">cname</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">column_names</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="python"> <span class="n" style="color: #333;">cid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sample_sheet</span><span class="p">[</span><span class="n" style="color: #333;">cname</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">cid</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">):</span></span>
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153
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="s" style="color: #d14;">'Technical replicates have different metadata'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">cid</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]))</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">):</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="s" style="color: #d14;">'Technical replicates have different metadata'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># names for merged files</span></span>
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="python"> <span class="n" style="color: #333;">sample_sheet</span><span class="p">[</span><span class="s" style="color: #d14;">'barcode_merged'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sample_sheet</span><span class="p">[</span><span class="s" style="color: #d14;">'sample_name'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'_R1.fastq.gz'</span></span>
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157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="python"> <span class="n" style="color: #333;">sample_sheet</span><span class="p">[</span><span class="s" style="color: #d14;">'reads_merged'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sample_sheet</span><span class="p">[</span><span class="s" style="color: #d14;">'sample_name'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'_R2.fastq.gz'</span></span>
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="python"> <span class="n" style="color: #333;">sample_sheet</span><span class="p">[</span><span class="s" style="color: #d14;">'reads_merged'</span><span class="p">]</span> <span class="idiff left right"> </span><span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sample_sheet</span><span class="p">[</span><span class="s" style="color: #d14;">'sample_name'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'_R2.fastq.gz'</span></span>
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># names for mapped reads</span></span>
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="python"> <span class="n" style="color: #333;">sample_sheet</span><span class="p">[</span><span class="s" style="color: #d14;">'mapped_reads'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sample_sheet</span><span class="p">[</span><span class="s" style="color: #d14;">'sample_name'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'.bam'</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -192,8 +191,13 @@ class experiment:</td>
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="s" style="color: #d14;">'unindentified column selected: '</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">column</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="python"></span>
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194
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="python"> <span class="n" style="color: #333;">field</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sheet</span><span class="p">[</span><span class="n" style="color: #333;">sheet</span><span class="p">[</span><span class="s" style="color: #d14;">'sample_name'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">sample_name</span><span class="p">][</span><span class="n" style="color: #333;">column</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">field</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">__class__</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">:</span></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">field</span><span class="p">.</span><span class="n" style="color: #333;">__class__</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">:</span></span>
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196
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196
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="python"> <span class="n" style="color: #333;">field</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">field</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">field</span><span class="p">,</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">Series</span><span class="p">):</span></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="python"> <span class="n" style="color: #333;">field</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">field</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="python"></span>
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197
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201
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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198
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202
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="python"> <span class="n" style="color: #333;">field</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">field</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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199
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203
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/pigx-scrnaseq/-/commit/bfa5c0280f033e356fd31d35a63518e67ac6d2dd#8b8c025c2cb41d9e35f386de8a8ebd3f5ce5ed3d"><strong>scripts/scrnaReport.Rmd</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">---</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">title: "PiGx-scRNAseq Report"</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">author: "BIMSB Bioinformatics Platform"</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">date: "`r date()`"</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">output:</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> html_document:</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> df_print: paged</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">params:</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> sceRds_file:</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> read_stats: NULL</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> output_file: 'test.scRNA.html'</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> workdir: './'</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> path_mapped: NULL</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">---</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">```{r setup, include=FALSE}</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">knitr::opts_chunk$set(echo = TRUE, message = FALSE, warning = FALSE)</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">knitr::opts_knit$set(root.dir = params$workdir)</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">```</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">```{r libraries, include=FALSE}</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">suppressPackageStartupMessages({</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> library(cowplot)</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> library(SingleCellExperiment)</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> library(data.table)</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> library(dplyr)</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> library(pheatmap)</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> library(DT)</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> library(ggplot2)</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">})</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">```</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"># Description</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">PiGx scRNAseq</span>
</pre>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">This report was generated with PiGx-scRNAseq version 1.1.6.</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"></span>
</pre>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"># Input Settings</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">```{r printInputSettings}</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">sceRds_file = params$sceRds_file</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">workdir = params$workdir</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">output_file = params$output_file</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">inputParameterDesc = c('RDS format file containing a SingleCellExperiment object',</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"> 'Working directory',</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"> 'Path to HTML report output'</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"> )</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">inputParameterValues = c(sceRds_file,</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"> workdir,</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"> output_file)</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">inputSettings = data.frame(parameters = inputParameterDesc,</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext"> values = inputParameterValues,</span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext"> stringsAsFactors = FALSE)</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">DT::datatable(data = inputSettings,</span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext"> extensions = 'FixedColumns',</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext"> options = list(fixedColumns = TRUE,</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"> scrollX = TRUE,</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"> pageLength = length(inputParameterValues),</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext"> dom = 't'))</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">```</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext"></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">```{r read-sce-object, include=FALSE, echo=FALSE}</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">sce = readRDS(file = sceRds_file)</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">```</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext"></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">```{r input, include=FALSE, echo=FALSE}</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">read_statistics = do.call(rbind, lapply(params$read_stats, read.table, header=TRUE))</span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext">```</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext"></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext"></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext"># Sample Statistics</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext"></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext">The following set of figures provide the basic statistics about the quality of the single cell data sets.</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext"></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext">### Total number of reads per sample</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext"></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext">The plot displays the numbers of mapped reads (in millions) for total (green bars) and uniquely-mapped UMI (orange bars) for each sample.</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext"></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext">```{r TotalReads, results='asis', echo = FALSE}</span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext">read_statistics %>%</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext"> dplyr::filter(mapped %in% c('reads.total','map.uniq')) %>%</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext"> mutate(mapped = case_when(</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext"> mapped == 'reads.total' ~ 'total UMI',</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext"> mapped == 'map.uniq' ~ 'uniquely mapped UMI'</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext"> )) %>%</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext"> ggplot(aes(sample, cnts, fill=mapped)) +</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext"> geom_bar(stat='identity', position='dodge') +</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext"> xlab('Sample') +</span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext"> ylab('Number of mapped reads (in milions)') +</span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext"> scale_fill_brewer(name='Mapped reads', palette='Set2') +</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext"> theme(axis.text.x = element_text(angle = 45, hjust = 1))</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext">```</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext"></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext"></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext">### Number of cell barcodes</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext"></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext">The figure shows the total number of reads mapping to exons per sample.</span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext"></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext">```{r Read_Statistics}</span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext">read_statistics %>%</span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext"> filter(mapped == 'nCellBarcodes') %>%</span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext"> filter(type == 'Gene') %>%</span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext"> ggplot(aes(sample, cnts)) +</span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext"> geom_bar(stat='identity') +</span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext"> theme(axis.text.x=element_text(angle=45, hjust=1)) +</span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext"> xlab('Sample Name') +</span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext"> ylab('Number of detected cells') +</span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext"> scale_fill_manual(values=c('black','lightgray'))</span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext">```</span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext"></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext">### Number of UMI</span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext"></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext">The figure shows the total number of detected UMIs per sample.</span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext"></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext">```{r exon_reads}</span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext">read_statistics %>%</span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext"> filter(mapped == 'nUMIs') %>%</span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext"> ggplot(aes(sample, cnts)) +</span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext"> geom_bar(stat='identity') +</span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext"> theme(axis.text.x=element_text(angle=45, hjust=1)) +</span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="plaintext"> xlab('Sample Name') +</span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext"> ylab('Number of detected UMI') +</span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="plaintext"> scale_fill_manual(values=c('black','lightgray'))</span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="plaintext">```</span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="plaintext"></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="plaintext">### Read Distribution in Genomic Features</span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext"></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="plaintext">The plot displays the numbers of mapped reads (in millions) categorized by annotation (as indicated by the legend) for each sample.</span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="plaintext"></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext">```{r ReadDistribution, results='asis', echo = FALSE}</span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="plaintext">read_statistics %>%</span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="plaintext"> mutate(type = as.character(type)) %>%</span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="plaintext"> mutate(type = case_when(</span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="plaintext"> type == 'GeneFull' ~ 'gene',</span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="plaintext"> type == 'Gene' ~ 'exon',</span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="plaintext"> TRUE ~ type</span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="plaintext"> )) %>%</span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="plaintext"> dplyr::filter(type %in% c('exon','gene','mapped')) %>%</span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="plaintext"> dplyr::filter(mapped %in% c('map.total','nUMIs')) %>%</span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="plaintext"> reshape2::dcast(sample ~ type, value.var='cnts') %>%</span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="plaintext"> mutate(intron = gene - exon) %>%</span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="plaintext"> mutate(other = mapped - gene) %>%</span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="plaintext"> dplyr::select(sample, other, exon, intron) %>%</span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="plaintext"> reshape2::melt() %>%</span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="plaintext"> mutate(sample = factor(sample, ordered=TRUE, levels=unique(sample))) %>%</span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="plaintext"> mutate(value = value * 1e-6) %>%</span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="plaintext"> ggplot(aes(sample, value, fill=variable)) +</span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="plaintext"> geom_bar(stat='identity') +</span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="plaintext"> xlab('Sample') +</span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="plaintext"> ylab('Number of mapped reads (in milions)') +</span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="plaintext"> scale_fill_brewer(name = 'Annotation', palette='Set2') +</span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="plaintext"> theme(axis.text.x = element_text(angle = 45, hjust = 1))</span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="plaintext">```</span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="plaintext"></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="plaintext"></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="plaintext">```{r cell-stats}</span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="plaintext">plotCellStats = function(df, x, y, label_x, label_y, title) {</span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="plaintext"> p = ggplot(df, aes_string(x=x, y=y)) +</span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="plaintext"> geom_boxplot() +</span>
</pre>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="plaintext"> labs(x = label_x, y = label_y, title = title) +</span>
</pre>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="plaintext"> theme(plot.title = element_text(hjust = 0.5),</span>
</pre>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="plaintext"> axis.text.x = element_text(angle = 45, hjust = 1))</span>
</pre>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="plaintext"> return(p)</span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="plaintext">}</span>
</pre>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="plaintext"></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="plaintext">plotDesc = list('nGene' = c('Sample',</span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="plaintext"> 'Number of detected genes',</span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="plaintext"> 'Number of detected genes per cell'),</span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="plaintext"> 'max_gene' = c('Sample',</span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="plaintext"> 'Maximum gene expression per cell',</span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="plaintext"> 'Maximum gene expression'),</span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="plaintext"> 'mean_expr' = c('Sample',</span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="plaintext"> 'Average gene expression',</span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="plaintext"> 'Average gene expression per cell\nfor genes with >0 UMI'))</span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="plaintext"></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="plaintext"></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="plaintext">cellStatsPlots = lapply(names(plotDesc), function(y){</span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="plaintext"> p = plotCellStats(</span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="plaintext"> df = as.data.frame(colData(sce)),</span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="plaintext"> x = 'sample_name',</span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="plaintext"> y = y,</span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="plaintext"> label_x = plotDesc[[y]][1],</span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="plaintext"> label_y = plotDesc[[y]][2],</span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="plaintext"> title = plotDesc[[y]][3])</span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="plaintext"> return(p)</span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="plaintext">})</span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="plaintext">names(cellStatsPlots) = paste(lapply(plotDesc, function(x) x[2]))</span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="plaintext">```</span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="plaintext"></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="plaintext">### Cell Statistics{.tabset}</span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="plaintext"></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="plaintext">These are boxplots of cell statistics.</span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="plaintext"></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="plaintext">__Number of detected genes__ displays the distributions of numbers of detected genes per cell.</span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="plaintext">__Maximum gene expression per cell__ displays the distributions of maximum gene expression per cell.</span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="plaintext">__Average gene expression__ displays the distributions of average gene expression for genes with at least 1 UMI per cell.</span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="plaintext"></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="plaintext">```{r cellStatsPlots, results='asis', echo = FALSE}</span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="plaintext">for (i in 1:length(cellStatsPlots)) {</span>
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="plaintext"> cat("### ",names(cellStatsPlots)[i],"\n")</span>
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="plaintext"> print(cellStatsPlots[[i]])</span>
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="plaintext"> cat('\n\n')</span>
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="plaintext">}</span>
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="plaintext">```</span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="plaintext"></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="plaintext"># Session Information</span>
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="plaintext">```{r sessionInfo}</span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="plaintext">sessionInfo()</span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="plaintext">```</span></pre>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -103,8 +103,8 @@ The figure shows the total number of detected cells per sample.</td>
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103
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="plaintext">```{r Read_Statistics}</span>
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104
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104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="plaintext">read_statistics %>%</span>
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105
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105
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="plaintext"> filter(mapped == 'nCellBarcodes') %>%</span>
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106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="plaintext"> filter(type == '<span class="idiff left right">exon</span>') %>%</span>
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107
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="plaintext"> ggplot(aes(sample, cnts<span class="idiff left right">, fill=mapped</span>)) +</span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext"> filter(type == '<span class="idiff left right">Gene</span>') %>%</span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext"> ggplot(aes(sample, cnts)) +</span>
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108
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108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="plaintext"> geom_bar(stat='identity') +</span>
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109
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="plaintext"> theme(axis.text.x=element_text(angle=45, hjust=1)) +</span>
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110
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="plaintext"> xlab('Sample Name') +</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -119,8 +119,8 @@ The figure shows the total number of detected UMIs per sample.</td>
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119
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119
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="plaintext">```{r exon_reads}</span>
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120
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120
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="plaintext">read_statistics %>%</span>
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121
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121
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="plaintext"> filter(mapped == 'nUMIs') %>%</span>
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122
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="plaintext"> filter(type == '<span class="idiff left right">exon</span>') %>%</span>
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123
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="plaintext"> ggplot(aes(sample, cnts<span class="idiff left right">, fill=mapped</span>)) +</span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext"> filter(type == '<span class="idiff left right">Gene</span>') %>%</span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext"> ggplot(aes(sample, cnts)) +</span>
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124
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124
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="plaintext"> geom_bar(stat='identity') +</span>
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125
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125
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="plaintext"> theme(axis.text.x=element_text(angle=45, hjust=1)) +</span>
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126
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="plaintext"> xlab('Sample Name') +</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -142,11 +142,11 @@ read_statistics %>%</td>
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142
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="plaintext"> )) %>%</span>
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143
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="plaintext"> dplyr::filter(type %in% c('exon','gene','mapped')) %>%</span>
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144
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="plaintext"> dplyr::filter(mapped %in% c('map.total','nUMIs')) %>%</span>
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145
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="plaintext"> dcast(sample ~ type, value.var='cnts') %>%</span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="plaintext"> <span class="idiff left right">reshape2::</span>dcast(sample ~ type, value.var='cnts') %>%</span>
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146
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146
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="plaintext"> mutate(intron = gene - exon) %>%</span>
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147
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147
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="plaintext"> mutate(other = mapped - gene) %>%</span>
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<td class="diff-line-num old_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
148
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148
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="plaintext"> dplyr::select(sample, other, exon, intron) %>%</span>
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149
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="plaintext"> melt() %>%</span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="plaintext"> <span class="idiff left right">reshape2::</span>melt() %>%</span>
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150
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="plaintext"> mutate(sample = factor(sample, ordered=TRUE, levels=unique(sample))) %>%</span>
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151
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151
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="plaintext"> mutate(value = value * 1e-6) %>%</span>
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152
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152
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="plaintext"> ggplot(aes(sample, value, fill=variable)) +</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -164,7 +164,7 @@ plotCellStats = function(df, x, y, label_x, label_y, title) {</td>
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164
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164
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="plaintext"> geom_boxplot() +</span>
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165
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165
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="plaintext"> labs(x = label_x, y = label_y, title = title) +</span>
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166
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166
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="plaintext"> theme(plot.title = element_text(hjust = 0.5),</span>
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167
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="plaintext"> axis.text.x = element_text(angle = <span class="idiff left right">90</span>, hjust = 1))</span>
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="plaintext"> axis.text.x = element_text(angle = <span class="idiff left right">45</span>, hjust = 1))</span>
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168
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168
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="plaintext"> return(p)</span>
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169
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169
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="plaintext">}</span>
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170
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="plaintext"></span>
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