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fix table style
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@Yunuuuu
Yunuuuu committed Jan 22, 2024
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56 changes: 52 additions & 4 deletions README.html
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Expand Up @@ -717,7 +717,55 @@ <h1 id="eheat">eheat</h1>
</tr>
</tbody>
</table>
<p>Other non-lazied operations: | Operations | BPCells | BPCellsArray | Note | | —————– | —————- | ———————— | —————- | | row/col summarize | matrix_stats | matrix_stats | | | row summarize | rowSums,rowMeans | rowSums,rowMeans,rowVars | | | col summarize | colSums,colMeans | colSums,colMeans,colVars | | | Multiplication | %<em>% | %</em>% | For some methods | | Crossproduct | | crossprod | For some methods | | svd | svds | SpectraParam | |</p>
<p>Other non-lazied operations:</p>
<table>
<thead>
<tr class="header">
<th>Operations</th>
<th>BPCells</th>
<th>BPCellsArray</th>
<th>Note</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td>row/col summarize</td>
<td>matrix_stats</td>
<td>matrix_stats</td>
<td></td>
</tr>
<tr class="even">
<td>row summarize</td>
<td>rowSums,rowMeans</td>
<td>rowSums,rowMeans,rowVars</td>
<td></td>
</tr>
<tr class="odd">
<td>col summarize</td>
<td>colSums,colMeans</td>
<td>colSums,colMeans,colVars</td>
<td></td>
</tr>
<tr class="even">
<td>Multiplication</td>
<td>%*%</td>
<td>%*%</td>
<td>For some methods</td>
</tr>
<tr class="odd">
<td>Crossproduct</td>
<td></td>
<td>crossprod</td>
<td>For some methods</td>
</tr>
<tr class="even">
<td>svd</td>
<td>svds</td>
<td>SpectraParam</td>
<td></td>
</tr>
</tbody>
</table>
<h2 id="matrix-storage-format">Matrix Storage Format</h2>
<p>BPCells provide three format: 1. Directory of files 2. Hdf5 file 3. R object Details see: <a href="https://bnprks.github.io/BPCells/articles/web-only/bitpacking-format.html">https://bnprks.github.io/BPCells/articles/web-only/bitpacking-format.html</a></p>
<p><code>BPCellsArray</code> only implement the Directory of files format, which is used across the package of <code>BPCells</code>.</p>
Expand Down Expand Up @@ -821,7 +869,7 @@ <h2 id="matrix-storage-format">Matrix Storage Format</h2>
<span id="cb5-8"><a href="#cb5-8" aria-hidden="true"></a><span class="co">#&gt; Storage order: column major</span></span>
<span id="cb5-9"><a href="#cb5-9" aria-hidden="true"></a><span class="co">#&gt; </span></span>
<span id="cb5-10"><a href="#cb5-10" aria-hidden="true"></a><span class="co">#&gt; Queued Operations:</span></span>
<span id="cb5-11"><a href="#cb5-11" aria-hidden="true"></a><span class="co">#&gt; 1. Load compressed matrix from directory /tmp/RtmpAq3VNF/BPCells26870138835a2e</span></span></code></pre></div>
<span id="cb5-11"><a href="#cb5-11" aria-hidden="true"></a><span class="co">#&gt; 1. Load compressed matrix from directory /tmp/RtmpJiXxC7/BPCells26938c5c1875ae</span></span></code></pre></div>
<p>If you do delayed operations with this assay, the class may be changed, that’s because all of BPCells operations are lazy, no real work is performed on the matrix until the result needs to be returned as an R object or written to disk. You can coerce it into a dense matrix or <code>dgCMatrix</code> to get a actual R object.</p>
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb6-1"><a href="#cb6-1" aria-hidden="true"></a><span class="kw">assay</span>(sce, <span class="st">&quot;counts&quot;</span>)[<span class="dv">1</span><span class="op">:</span><span class="dv">10</span>, <span class="dv">1</span><span class="op">:</span><span class="dv">10</span>]</span>
<span id="cb6-2"><a href="#cb6-2" aria-hidden="true"></a><span class="co">#&gt; 10 x 10 DelayedMatrix object with class BPCellsSubsetMatrix</span></span>
Expand All @@ -833,7 +881,7 @@ <h2 id="matrix-storage-format">Matrix Storage Format</h2>
<span id="cb6-8"><a href="#cb6-8" aria-hidden="true"></a><span class="co">#&gt; Storage order: column major</span></span>
<span id="cb6-9"><a href="#cb6-9" aria-hidden="true"></a><span class="co">#&gt; </span></span>
<span id="cb6-10"><a href="#cb6-10" aria-hidden="true"></a><span class="co">#&gt; Queued Operations:</span></span>
<span id="cb6-11"><a href="#cb6-11" aria-hidden="true"></a><span class="co">#&gt; 1. Load compressed matrix from directory /tmp/RtmpAq3VNF/BPCells26870138835a2e</span></span>
<span id="cb6-11"><a href="#cb6-11" aria-hidden="true"></a><span class="co">#&gt; 1. Load compressed matrix from directory /tmp/RtmpJiXxC7/BPCells26938c5c1875ae</span></span>
<span id="cb6-12"><a href="#cb6-12" aria-hidden="true"></a><span class="co">#&gt; 2. Select rows: 1, 2 ... 10 and cols: 1, 2 ... 10</span></span>
<span id="cb6-13"><a href="#cb6-13" aria-hidden="true"></a><span class="kw">as.matrix</span>(<span class="kw">assay</span>(sce, <span class="st">&quot;counts&quot;</span>)[<span class="dv">1</span><span class="op">:</span><span class="dv">10</span>, <span class="dv">1</span><span class="op">:</span><span class="dv">10</span>])</span>
<span id="cb6-14"><a href="#cb6-14" aria-hidden="true"></a><span class="co">#&gt; Cell_001 Cell_002 Cell_003 Cell_004 Cell_005 Cell_006 Cell_007</span></span>
Expand Down Expand Up @@ -887,7 +935,7 @@ <h2 id="matrix-storage-format">Matrix Storage Format</h2>
<span id="cb8-9"><a href="#cb8-9" aria-hidden="true"></a><span class="co">#&gt; Storage order: column major</span></span>
<span id="cb8-10"><a href="#cb8-10" aria-hidden="true"></a><span class="co">#&gt; </span></span>
<span id="cb8-11"><a href="#cb8-11" aria-hidden="true"></a><span class="co">#&gt; Queued Operations:</span></span>
<span id="cb8-12"><a href="#cb8-12" aria-hidden="true"></a><span class="co">#&gt; 1. Load compressed matrix from directory /tmp/RtmpAq3VNF/BPCells26870138835a2e</span></span>
<span id="cb8-12"><a href="#cb8-12" aria-hidden="true"></a><span class="co">#&gt; 1. Load compressed matrix from directory /tmp/RtmpJiXxC7/BPCells26938c5c1875ae</span></span>
<span id="cb8-13"><a href="#cb8-13" aria-hidden="true"></a><span class="co">#&gt; 2. Scale columns by 0.984, 1.05 ... 1</span></span>
<span id="cb8-14"><a href="#cb8-14" aria-hidden="true"></a><span class="co">#&gt; 3. Transform log1p</span></span>
<span id="cb8-15"><a href="#cb8-15" aria-hidden="true"></a><span class="co">#&gt; 4. Scale by 1.44</span></span></code></pre></div>
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23 changes: 13 additions & 10 deletions README.md
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Expand Up @@ -40,13 +40,16 @@ Here is a summarized delayed operations in BPCells:
| log(1+x) | `log1p`,`log1p_slow` | `log1p`,`log1p_slow` |
| Power | `pow_slow`,`^` | `pow_slow`,`^` |

Other non-lazied operations: | Operations | BPCells | BPCellsArray |
Note | | —————– | —————- | ———————— | —————- | | row/col summarize |
matrix\_stats | matrix\_stats | | | row summarize | rowSums,rowMeans |
rowSums,rowMeans,rowVars | | | col summarize | colSums,colMeans |
colSums,colMeans,colVars | | | Multiplication | %*% | %*% | For some
methods | | Crossproduct | | crossprod | For some methods | | svd | svds
| SpectraParam | |
Other non-lazied operations:

| Operations | BPCells | BPCellsArray | Note |
| ----------------- | ---------------- | ------------------------ | ---------------- |
| row/col summarize | matrix\_stats | matrix\_stats | |
| row summarize | rowSums,rowMeans | rowSums,rowMeans,rowVars | |
| col summarize | colSums,colMeans | colSums,colMeans,colVars | |
| Multiplication | %\*% | %\*% | For some methods |
| Crossproduct | | crossprod | For some methods |
| svd | svds | SpectraParam | |

## Matrix Storage Format

Expand Down Expand Up @@ -175,7 +178,7 @@ assay(sce, "counts")
#> Storage order: column major
#>
#> Queued Operations:
#> 1. Load compressed matrix from directory /tmp/RtmpAq3VNF/BPCells26870138835a2e
#> 1. Load compressed matrix from directory /tmp/RtmpJiXxC7/BPCells26938c5c1875ae
```

If you do delayed operations with this assay, the class may be changed,
Expand All @@ -195,7 +198,7 @@ assay(sce, "counts")[1:10, 1:10]
#> Storage order: column major
#>
#> Queued Operations:
#> 1. Load compressed matrix from directory /tmp/RtmpAq3VNF/BPCells26870138835a2e
#> 1. Load compressed matrix from directory /tmp/RtmpJiXxC7/BPCells26938c5c1875ae
#> 2. Select rows: 1, 2 ... 10 and cols: 1, 2 ... 10
as.matrix(assay(sce, "counts")[1:10, 1:10])
#> Cell_001 Cell_002 Cell_003 Cell_004 Cell_005 Cell_006 Cell_007
Expand Down Expand Up @@ -260,7 +263,7 @@ assay(sce, "logcounts")
#> Storage order: column major
#>
#> Queued Operations:
#> 1. Load compressed matrix from directory /tmp/RtmpAq3VNF/BPCells26870138835a2e
#> 1. Load compressed matrix from directory /tmp/RtmpJiXxC7/BPCells26938c5c1875ae
#> 2. Scale columns by 0.984, 1.05 ... 1
#> 3. Transform log1p
#> 4. Scale by 1.44
Expand Down
1 change: 1 addition & 0 deletions vignettes/BPCellsArray.Rmd
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Expand Up @@ -48,6 +48,7 @@ Here is a summarized delayed operations in BPCells:


Other non-lazied operations:

| Operations | BPCells | BPCellsArray | Note |
| ----------------- | ---------------- | ------------------------ | ---------------- |
| row/col summarize | matrix_stats | matrix_stats | |
Expand Down

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