added dataset loading and removed continuous dataset part

Author: mariiabilous

21-MC_construction_discrete.Rmd

@@ -9,11 +9,6 @@ TO_CACHE <- FALSE
 ```
 
 
-```{r include=FALSE}
-source('./R/config.R')
-```
-
-
 ```{python true-import, echo = FALSE, result = FALSE, message = FALSE, warning = FALSE}
 # This is true import section that is executed, but not displayed as it simultaneously load MC2 and SEACells.
 # As MC2 and SEACells workflow displayed in separate files, while indeed they run in the same file/session (due to fact that in bookdown one and only one chapter per Rmd file)

30-commandline_tool.Rmd

@@ -0,0 +1,4 @@
+# Command line tool for MC construction
+
+Here is a command line tool to construct metacells using either tool (MC2, SuperCell or SEACells) from a provided dataset.
+

31-MC_construction_continuous.Rmd renamed to _31-MC_construction_continuous.Rmd

@@ -3,6 +3,7 @@ language:
   ui:
     chapter_name: "Chapter "
 new_session: yes
+before_chapter_script: './R/config.R'
 view: https://github.com/GfellerLab/Metacell_tutorial/blob/master/%s
 edit: https://github.com/GfellerLab/Metacell_tutorial/edit/master/%s
 output_dir: "docs"

32-MC_analysis_continuous.Rmd renamed to _32-MC_analysis_continuous.Rmd

@@ -8,9 +8,6 @@ For this, we will use a dataset of PBMCs from study. This dataset contains 30K c
 
 
 
-
-
-
 ```
 #> findfont: Font family ['Raleway'] not found. Falling back to DejaVu Sans.
 #> findfont: Font family ['Lato'] not found. Falling back to DejaVu Sans.
@@ -111,8 +108,8 @@ The first round of cell cleaning usually implies filltering out cell with very l
 
 ```python
 ### The first round (high/low UMIs)
-properly_sampled_min_cell_total = {'cell_lines' : 5000, '3k_pbmc': 200}[proj_name] # setup for the dataset that will be used 
-properly_sampled_max_cell_total = {'cell_lines' : 110000, '3k_pbmc': 10000}[proj_name] # setup for the dataset that will be used 
+properly_sampled_min_cell_total = 200 # setup for the dataset that will be used 
+properly_sampled_max_cell_total = 10000 # setup for the dataset that will be used 
 ```
 
 
@@ -418,6 +415,7 @@ sc.tl.umap(ad)
 ### Metacell QC {-}
 
 
+### Save output {-}
 
 
 
@@ -586,7 +584,7 @@ model.initialize_archetypes()
 #> Initializing f and g...
 #> Selecting 10 cells from greedy initialization.
 #> 
-#>   0%|          | 0/20 [00:00<?, ?it/s]100%|##########| 20/20 [00:00<00:00, 460.83it/s]
+#>   0%|          | 0/20 [00:00<?, ?it/s]100%|##########| 20/20 [00:00<00:00, 469.56it/s]
 
 # Plot the initialization to ensure they are evenly spread
 SEACells.plot.plot_initialization(ad, model, plot_basis='X_umap') ## error, mb missing some modules
@@ -631,7 +629,7 @@ membership = model.get_hard_assignments()
 
 # aggregate metacells    
 mc_ad = SEACells.core.summarize_by_SEACell(ad, SEACells_label='SEACell', summarize_layer='raw')
-#>   0%|          | 0/52 [00:00<?, ?it/s] 81%|########  | 42/52 [00:00<00:00, 419.01it/s]100%|##########| 52/52 [00:00<00:00, 431.98it/s]
+#>   0%|          | 0/52 [00:00<?, ?it/s] 73%|#######3  | 38/52 [00:00<00:00, 374.72it/s]100%|##########| 52/52 [00:00<00:00, 391.38it/s]
 
 # make `membership` numeric
 d = {x: int(i)+1 for i, x in enumerate(mc_ad.obs_names)}

_bookdown.yml

@@ -0,0 +1,4 @@
+# Command line tool for MC construction
+
+Here is a command line tool to construct metacells using either tool (MC2, SuperCell or SEACells) from a provided dataset.
+

docs/21-MC_construction_discrete.md

@@ -145,6 +145,7 @@
 <li class="chapter" data-level="1.1" data-path="book-structure.html"><a href="book-structure.html"><i class="fa fa-check"></i><b>1.1</b> Book structure</a></li>
 <li class="chapter" data-level="1.2" data-path="installation-and-requirements.html"><a href="installation-and-requirements.html"><i class="fa fa-check"></i><b>1.2</b> Installation and requirements</a></li>
 <li class="chapter" data-level="1.3" data-path="render-book.html"><a href="render-book.html"><i class="fa fa-check"></i><b>1.3</b> Render book</a></li>
+<li class="chapter" data-level="1.4" data-path="get-data.html"><a href="get-data.html"><i class="fa fa-check"></i><b>1.4</b> Get data</a></li>
 </ul></li>
 <li class="chapter" data-level="2" data-path="the-metacell-concept.html"><a href="the-metacell-concept.html"><i class="fa fa-check"></i><b>2</b> The metacell concept</a>
 <ul>
@@ -159,6 +160,7 @@
 <li class="chapter" data-level="" data-path="mc2-python.html"><a href="mc2-python.html#running-mc2"><i class="fa fa-check"></i>Running MC2</a></li>
 <li class="chapter" data-level="" data-path="mc2-python.html"><a href="mc2-python.html#compute-latent-space-for-metacell-qc"><i class="fa fa-check"></i>Compute latent space for metacell QC</a></li>
 <li class="chapter" data-level="" data-path="mc2-python.html"><a href="mc2-python.html#metacell-qc"><i class="fa fa-check"></i>Metacell QC</a></li>
+<li class="chapter" data-level="" data-path="mc2-python.html"><a href="mc2-python.html#save-output"><i class="fa fa-check"></i>Save output</a></li>
 </ul></li>
 <li class="chapter" data-level="3.2" data-path="supercell-r.html"><a href="supercell-r.html"><i class="fa fa-check"></i><b>3.2</b> SuperCell (R)</a></li>
 <li class="chapter" data-level="3.3" data-path="seacells-python.html"><a href="seacells-python.html"><i class="fa fa-check"></i><b>3.3</b> SEACells (Python)</a>
@@ -188,38 +190,12 @@
 </ul></li>
 <li class="chapter" data-level="4.4" data-path="weighted-analysis.html"><a href="weighted-analysis.html"><i class="fa fa-check"></i><b>4.4</b> Sample-weighted analysis</a></li>
 </ul></li>
-<li class="chapter" data-level="5" data-path="MC-continuous.html"><a href="MC-continuous.html"><i class="fa fa-check"></i><b>5</b> Construction of metacells (for ‘continuous’ data)</a>
+<li class="chapter" data-level="5" data-path="command-line-tool-for-mc-construction.html"><a href="command-line-tool-for-mc-construction.html"><i class="fa fa-check"></i><b>5</b> Command line tool for MC construction</a></li>
+<li class="chapter" data-level="6" data-path="comparison-of-metacells-usage-for-a-discrete-and-continuous-data.html"><a href="comparison-of-metacells-usage-for-a-discrete-and-continuous-data.html"><i class="fa fa-check"></i><b>6</b> Comparison of metacells usage for a discrete and continuous data</a>
 <ul>
-<li class="chapter" data-level="5.1" data-path="mc2-python-1.html"><a href="mc2-python-1.html"><i class="fa fa-check"></i><b>5.1</b> MC2 (Python)</a>
-<ul>
-<li class="chapter" data-level="" data-path="mc2-python-1.html"><a href="mc2-python-1.html#running-mc2-1"><i class="fa fa-check"></i>Running MC2</a></li>
-<li class="chapter" data-level="" data-path="mc2-python-1.html"><a href="mc2-python-1.html#compute-latent-space-for-metacell-qc-1"><i class="fa fa-check"></i>Compute latent space for metacell QC</a></li>
-<li class="chapter" data-level="" data-path="mc2-python-1.html"><a href="mc2-python-1.html#metacell-qc-2"><i class="fa fa-check"></i>Metacell QC</a></li>
-</ul></li>
-<li class="chapter" data-level="5.2" data-path="supercell-r-1.html"><a href="supercell-r-1.html"><i class="fa fa-check"></i><b>5.2</b> SuperCell (R)</a></li>
-<li class="chapter" data-level="5.3" data-path="seacells-python-1.html"><a href="seacells-python-1.html"><i class="fa fa-check"></i><b>5.3</b> SEACells (Python)</a></li>
-</ul></li>
-<li class="chapter" data-level="6" data-path="downstream-analysis-of-metacells-for-a-continuous-dataset.html"><a href="downstream-analysis-of-metacells-for-a-continuous-dataset.html"><i class="fa fa-check"></i><b>6</b> Downstream analysis of metacells (for a continuous dataset)</a>
-<ul>
-<li class="chapter" data-level="6.1" data-path="standard-analysis-r-1.html"><a href="standard-analysis-r-1.html"><i class="fa fa-check"></i><b>6.1</b> Standard analysis (R)</a>
-<ul>
-<li class="chapter" data-level="6.1.1" data-path="standard-analysis-r-1.html"><a href="standard-analysis-r-1.html#dimensionality-reduction-2"><i class="fa fa-check"></i><b>6.1.1</b> Dimensionality reduction</a></li>
-<li class="chapter" data-level="6.1.2" data-path="standard-analysis-r-1.html"><a href="standard-analysis-r-1.html#clustering-2"><i class="fa fa-check"></i><b>6.1.2</b> Clustering</a></li>
-<li class="chapter" data-level="6.1.3" data-path="standard-analysis-r-1.html"><a href="standard-analysis-r-1.html#differential-expression-analysis-2"><i class="fa fa-check"></i><b>6.1.3</b> Differential expression analysis</a></li>
-</ul></li>
-<li class="chapter" data-level="6.2" data-path="standard-analysis-Py-cont.html"><a href="standard-analysis-Py-cont.html"><i class="fa fa-check"></i><b>6.2</b> Standard analysis (Python)</a>
-<ul>
-<li class="chapter" data-level="6.2.1" data-path="standard-analysis-Py-cont.html"><a href="standard-analysis-Py-cont.html#dimensionality-reduction-3"><i class="fa fa-check"></i><b>6.2.1</b> Dimensionality reduction</a></li>
-<li class="chapter" data-level="6.2.2" data-path="standard-analysis-Py-cont.html"><a href="standard-analysis-Py-cont.html#clustering-3"><i class="fa fa-check"></i><b>6.2.2</b> Clustering</a></li>
-<li class="chapter" data-level="6.2.3" data-path="standard-analysis-Py-cont.html"><a href="standard-analysis-Py-cont.html#differential-expression-analysis-3"><i class="fa fa-check"></i><b>6.2.3</b> Differential expression analysis</a></li>
-</ul></li>
-<li class="chapter" data-level="6.3" data-path="weighted-analysis-cont.html"><a href="weighted-analysis-cont.html"><i class="fa fa-check"></i><b>6.3</b> Sample-weighted analysis</a></li>
-</ul></li>
-<li class="chapter" data-level="7" data-path="comparison-of-metacells-usage-for-a-discrete-and-continuous-data.html"><a href="comparison-of-metacells-usage-for-a-discrete-and-continuous-data.html"><i class="fa fa-check"></i><b>7</b> Comparison of metacells usage for a discrete and continuous data</a>
-<ul>
-<li class="chapter" data-level="7.1" data-path="continuous-metacells-have-lower-purity.html"><a href="continuous-metacells-have-lower-purity.html"><i class="fa fa-check"></i><b>7.1</b> Continuous metacells have lower purity</a></li>
+<li class="chapter" data-level="6.1" data-path="continuous-metacells-have-lower-purity.html"><a href="continuous-metacells-have-lower-purity.html"><i class="fa fa-check"></i><b>6.1</b> Continuous metacells have lower purity</a></li>
 </ul></li>
-<li class="chapter" data-level="8" data-path="data-integration-with-metacells.html"><a href="data-integration-with-metacells.html"><i class="fa fa-check"></i><b>8</b> Data integration with metacells</a></li>
+<li class="chapter" data-level="7" data-path="data-integration-with-metacells.html"><a href="data-integration-with-metacells.html"><i class="fa fa-check"></i><b>7</b> Data integration with metacells</a></li>
 <li class="divider"></li>
 <li><a href="https://github.com/rstudio/bookdown" target="blank">Published with bookdown</a></li>
 

docs/30-commandline_tool.md

@@ -145,6 +145,7 @@
 <li class="chapter" data-level="1.1" data-path="book-structure.html"><a href="book-structure.html"><i class="fa fa-check"></i><b>1.1</b> Book structure</a></li>
 <li class="chapter" data-level="1.2" data-path="installation-and-requirements.html"><a href="installation-and-requirements.html"><i class="fa fa-check"></i><b>1.2</b> Installation and requirements</a></li>
 <li class="chapter" data-level="1.3" data-path="render-book.html"><a href="render-book.html"><i class="fa fa-check"></i><b>1.3</b> Render book</a></li>
+<li class="chapter" data-level="1.4" data-path="get-data.html"><a href="get-data.html"><i class="fa fa-check"></i><b>1.4</b> Get data</a></li>
 </ul></li>
 <li class="chapter" data-level="2" data-path="the-metacell-concept.html"><a href="the-metacell-concept.html"><i class="fa fa-check"></i><b>2</b> The metacell concept</a>
 <ul>
@@ -159,6 +160,7 @@
 <li class="chapter" data-level="" data-path="mc2-python.html"><a href="mc2-python.html#running-mc2"><i class="fa fa-check"></i>Running MC2</a></li>
 <li class="chapter" data-level="" data-path="mc2-python.html"><a href="mc2-python.html#compute-latent-space-for-metacell-qc"><i class="fa fa-check"></i>Compute latent space for metacell QC</a></li>
 <li class="chapter" data-level="" data-path="mc2-python.html"><a href="mc2-python.html#metacell-qc"><i class="fa fa-check"></i>Metacell QC</a></li>
+<li class="chapter" data-level="" data-path="mc2-python.html"><a href="mc2-python.html#save-output"><i class="fa fa-check"></i>Save output</a></li>
 </ul></li>
 <li class="chapter" data-level="3.2" data-path="supercell-r.html"><a href="supercell-r.html"><i class="fa fa-check"></i><b>3.2</b> SuperCell (R)</a></li>
 <li class="chapter" data-level="3.3" data-path="seacells-python.html"><a href="seacells-python.html"><i class="fa fa-check"></i><b>3.3</b> SEACells (Python)</a>

docs/404.html

@@ -145,6 +145,7 @@
 <li class="chapter" data-level="1.1" data-path="book-structure.html"><a href="book-structure.html"><i class="fa fa-check"></i><b>1.1</b> Book structure</a></li>
 <li class="chapter" data-level="1.2" data-path="installation-and-requirements.html"><a href="installation-and-requirements.html"><i class="fa fa-check"></i><b>1.2</b> Installation and requirements</a></li>
 <li class="chapter" data-level="1.3" data-path="render-book.html"><a href="render-book.html"><i class="fa fa-check"></i><b>1.3</b> Render book</a></li>
+<li class="chapter" data-level="1.4" data-path="get-data.html"><a href="get-data.html"><i class="fa fa-check"></i><b>1.4</b> Get data</a></li>
 </ul></li>
 <li class="chapter" data-level="2" data-path="the-metacell-concept.html"><a href="the-metacell-concept.html"><i class="fa fa-check"></i><b>2</b> The metacell concept</a>
 <ul>
@@ -159,6 +160,7 @@
 <li class="chapter" data-level="" data-path="mc2-python.html"><a href="mc2-python.html#running-mc2"><i class="fa fa-check"></i>Running MC2</a></li>
 <li class="chapter" data-level="" data-path="mc2-python.html"><a href="mc2-python.html#compute-latent-space-for-metacell-qc"><i class="fa fa-check"></i>Compute latent space for metacell QC</a></li>
 <li class="chapter" data-level="" data-path="mc2-python.html"><a href="mc2-python.html#metacell-qc"><i class="fa fa-check"></i>Metacell QC</a></li>
+<li class="chapter" data-level="" data-path="mc2-python.html"><a href="mc2-python.html#save-output"><i class="fa fa-check"></i>Save output</a></li>
 </ul></li>
 <li class="chapter" data-level="3.2" data-path="supercell-r.html"><a href="supercell-r.html"><i class="fa fa-check"></i><b>3.2</b> SuperCell (R)</a></li>
 <li class="chapter" data-level="3.3" data-path="seacells-python.html"><a href="seacells-python.html"><i class="fa fa-check"></i><b>3.3</b> SEACells (Python)</a>
@@ -188,38 +190,12 @@
 </ul></li>
 <li class="chapter" data-level="4.4" data-path="weighted-analysis.html"><a href="weighted-analysis.html"><i class="fa fa-check"></i><b>4.4</b> Sample-weighted analysis</a></li>
 </ul></li>
-<li class="chapter" data-level="5" data-path="MC-continuous.html"><a href="MC-continuous.html"><i class="fa fa-check"></i><b>5</b> Construction of metacells (for ‘continuous’ data)</a>
+<li class="chapter" data-level="5" data-path="command-line-tool-for-mc-construction.html"><a href="command-line-tool-for-mc-construction.html"><i class="fa fa-check"></i><b>5</b> Command line tool for MC construction</a></li>
+<li class="chapter" data-level="6" data-path="comparison-of-metacells-usage-for-a-discrete-and-continuous-data.html"><a href="comparison-of-metacells-usage-for-a-discrete-and-continuous-data.html"><i class="fa fa-check"></i><b>6</b> Comparison of metacells usage for a discrete and continuous data</a>
 <ul>
-<li class="chapter" data-level="5.1" data-path="mc2-python-1.html"><a href="mc2-python-1.html"><i class="fa fa-check"></i><b>5.1</b> MC2 (Python)</a>
-<ul>
-<li class="chapter" data-level="" data-path="mc2-python-1.html"><a href="mc2-python-1.html#running-mc2-1"><i class="fa fa-check"></i>Running MC2</a></li>
-<li class="chapter" data-level="" data-path="mc2-python-1.html"><a href="mc2-python-1.html#compute-latent-space-for-metacell-qc-1"><i class="fa fa-check"></i>Compute latent space for metacell QC</a></li>
-<li class="chapter" data-level="" data-path="mc2-python-1.html"><a href="mc2-python-1.html#metacell-qc-2"><i class="fa fa-check"></i>Metacell QC</a></li>
-</ul></li>
-<li class="chapter" data-level="5.2" data-path="supercell-r-1.html"><a href="supercell-r-1.html"><i class="fa fa-check"></i><b>5.2</b> SuperCell (R)</a></li>
-<li class="chapter" data-level="5.3" data-path="seacells-python-1.html"><a href="seacells-python-1.html"><i class="fa fa-check"></i><b>5.3</b> SEACells (Python)</a></li>
-</ul></li>
-<li class="chapter" data-level="6" data-path="downstream-analysis-of-metacells-for-a-continuous-dataset.html"><a href="downstream-analysis-of-metacells-for-a-continuous-dataset.html"><i class="fa fa-check"></i><b>6</b> Downstream analysis of metacells (for a continuous dataset)</a>
-<ul>
-<li class="chapter" data-level="6.1" data-path="standard-analysis-r-1.html"><a href="standard-analysis-r-1.html"><i class="fa fa-check"></i><b>6.1</b> Standard analysis (R)</a>
-<ul>
-<li class="chapter" data-level="6.1.1" data-path="standard-analysis-r-1.html"><a href="standard-analysis-r-1.html#dimensionality-reduction-2"><i class="fa fa-check"></i><b>6.1.1</b> Dimensionality reduction</a></li>
-<li class="chapter" data-level="6.1.2" data-path="standard-analysis-r-1.html"><a href="standard-analysis-r-1.html#clustering-2"><i class="fa fa-check"></i><b>6.1.2</b> Clustering</a></li>
-<li class="chapter" data-level="6.1.3" data-path="standard-analysis-r-1.html"><a href="standard-analysis-r-1.html#differential-expression-analysis-2"><i class="fa fa-check"></i><b>6.1.3</b> Differential expression analysis</a></li>
-</ul></li>
-<li class="chapter" data-level="6.2" data-path="standard-analysis-Py-cont.html"><a href="standard-analysis-Py-cont.html"><i class="fa fa-check"></i><b>6.2</b> Standard analysis (Python)</a>
-<ul>
-<li class="chapter" data-level="6.2.1" data-path="standard-analysis-Py-cont.html"><a href="standard-analysis-Py-cont.html#dimensionality-reduction-3"><i class="fa fa-check"></i><b>6.2.1</b> Dimensionality reduction</a></li>
-<li class="chapter" data-level="6.2.2" data-path="standard-analysis-Py-cont.html"><a href="standard-analysis-Py-cont.html#clustering-3"><i class="fa fa-check"></i><b>6.2.2</b> Clustering</a></li>
-<li class="chapter" data-level="6.2.3" data-path="standard-analysis-Py-cont.html"><a href="standard-analysis-Py-cont.html#differential-expression-analysis-3"><i class="fa fa-check"></i><b>6.2.3</b> Differential expression analysis</a></li>
-</ul></li>
-<li class="chapter" data-level="6.3" data-path="weighted-analysis-cont.html"><a href="weighted-analysis-cont.html"><i class="fa fa-check"></i><b>6.3</b> Sample-weighted analysis</a></li>
-</ul></li>
-<li class="chapter" data-level="7" data-path="comparison-of-metacells-usage-for-a-discrete-and-continuous-data.html"><a href="comparison-of-metacells-usage-for-a-discrete-and-continuous-data.html"><i class="fa fa-check"></i><b>7</b> Comparison of metacells usage for a discrete and continuous data</a>
-<ul>
-<li class="chapter" data-level="7.1" data-path="continuous-metacells-have-lower-purity.html"><a href="continuous-metacells-have-lower-purity.html"><i class="fa fa-check"></i><b>7.1</b> Continuous metacells have lower purity</a></li>
+<li class="chapter" data-level="6.1" data-path="continuous-metacells-have-lower-purity.html"><a href="continuous-metacells-have-lower-purity.html"><i class="fa fa-check"></i><b>6.1</b> Continuous metacells have lower purity</a></li>
 </ul></li>
-<li class="chapter" data-level="8" data-path="data-integration-with-metacells.html"><a href="data-integration-with-metacells.html"><i class="fa fa-check"></i><b>8</b> Data integration with metacells</a></li>
+<li class="chapter" data-level="7" data-path="data-integration-with-metacells.html"><a href="data-integration-with-metacells.html"><i class="fa fa-check"></i><b>7</b> Data integration with metacells</a></li>
 <li class="divider"></li>
 <li><a href="https://github.com/rstudio/bookdown" target="blank">Published with bookdown</a></li>