add copy again

pinellolab · Mar 30, 2024 · 78193f7 · 78193f7
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diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml
@@ -19,6 +19,8 @@ jobs:
     - name: Build Documentation
       working-directory: docs
       run: sphinx-build . _build
+    - name: copy image files
+      run: cp -r docs/assets docs/_build/assets/
     - uses: actions/upload-pages-artifact@v3
       with:
         name: github-pages

diff --git a/docs/count.md b/docs/count.md
@@ -18,7 +18,7 @@ bean count --R1 R1.fq --R2 R2.fq -b A -f sgRNA_info_table.csv -r
 ```
 By default, `bean count[-samples]` assume R1 and R2 are trimmed off of the adapter sequence. You may need to adjust the command arguments according to your read structure. 
 
-   <img src="assets/sequence_struct.png" alt="Read structuren" width="600"/>  
+   <img src="/crispr-bean/assets/sequence_struct.png" alt="Read structuren" width="600"/>  
 
 See full detail [below](#full-parameters).
 

diff --git a/docs/filter.md b/docs/filter.md
@@ -16,7 +16,7 @@ You may want to adjust the flitering parameters to obtain optimal balance betwee
 # Translating alleles
 If you want to obtain **amino acid level variant** for coding sequence tiling screens, provide coding sequence positions which variants occuring within the coding sequence will be translated. *This is optional, but **highly recommended** to increase per-(coding)variant support.*  
 
-<img src="assets/translation.png" alt="Allele translation" width="500"/>  
+<img src="/crispr-bean/assets/translation.png" alt="Allele translation" width="500"/>  
 
 
 ```bash

diff --git a/docs/ldl_cds.md b/docs/ldl_cds.md
@@ -4,11 +4,11 @@ Tiling screen that tiles gRNA densely across locus or multiple loci, selected ba
 <table>
   <tr>
     <th>Library design</th>
-    <td>Tiling (gRNAs tile each locus densely)   <br> <img src="assets/tiling.png" alt="tiling library design" width="300"/> </td>
+    <td>Tiling (gRNAs tile each locus densely)   <br> <img src="/crispr-bean/assets/tiling.png" alt="tiling library design" width="300"/> </td>
   </tr>
   <tr>
     <th>Selection</th>
-    <td>Cells are sorted based on FACS signal quantiles  <br>  <img src="assets/[email protected]" alt="variant library design" width="300"/></td>
+    <td>Cells are sorted based on FACS signal quantiles  <br>  <img src="/crispr-bean//crispr-bean/assets/[email protected]" alt="variant library design" width="300"/></td>
   </tr>
 </table>
 

diff --git a/docs/ldl_var.md b/docs/ldl_var.md
@@ -1,14 +1,14 @@
-# Variant sorting screen tutorial
+## Variant sorting screen tutorial
 GWAS variant screen with per-variant gRNA tiling design, selected based on FACS signal quantiles.  
 
 <table>
   <tr>
     <th>Library design</th>
-    <td>Variant (gRNAs tile each target variant)   <br> <img src="assets/variant.png" alt="variant library design" width="600"/></td>
+    <td>Variant (gRNAs tile each target variant)   <br> <img src="/crispr-bean/assets/variant.png" alt="variant library design" width="600"/></td>
   </tr>
   <tr>
     <th>Selection</th>
-    <td>Cells are sorted based on FACS signal quantiles  <br>  <img src="assets/[email protected]" alt="variant library design" width="300"/></td>
+    <td>Cells are sorted based on FACS signal quantiles  <br>  <img src="/crispr-bean/assets/[email protected]" alt="variant library design" width="300"/></td>
   </tr>
 </table>
 

diff --git a/docs/profile.md b/docs/profile.md
@@ -5,4 +5,4 @@ bean profile my_sorting_screen.h5ad -o output_prefix `# Prefix for editing profi
 # Output
 Above command produces `prefix_editing_preference.[html,ipynb]` as editing preferences ([see example](../notebooks/profile_editing_preference.ipynb)).  
 
-<img src="assets/profile_output.png" alt="Allele translation" width="700" />  
+<img src="/crispr-bean/assets/profile_output.png" alt="Allele translation" width="700" />  
diff --git a/docs/prolif_gwas.md b/docs/prolif_gwas.md
@@ -1,14 +1,14 @@
-# Variant sorting screen tutorial
+## Variant survival screen tutorial
 GWAS variant screen with per-variant gRNA tiling design, selected based on FACS signal quantiles.  
 
 <table>
   <tr>
     <th>Library design</th>
-    <td>Variant (gRNAs tile each target variant)   <br> <img src="assets/variant.png" alt="variant library design" width="600"/></td>
+    <td>Variant (gRNAs tile each target variant)   <br> <img src="/crispr-bean/assets/variant.png" alt="variant library design" width="600"/></td>
   </tr>
   <tr>
     <th>Selection</th>
-    <td>Cells are sorted based on FACS signal quantiles  <br>  <img src="assets/proliferation.png" alt="variant library design" width="300"/></td>
+    <td>Cells are sorted based on FACS signal quantiles  <br>  <img src="/crispr-bean/assets/proliferation.png" alt="variant library design" width="300"/></td>
   </tr>
 </table>
 

diff --git a/docs/prolif_gwas.rst b/docs/prolif_gwas.rst
@@ -1,4 +1,4 @@
-GWAS variant library
+Proliferation screen with GWAS library
 ***********************
 .. mdinclude:: profile_gwas.md
 

diff --git a/docs/qc.md b/docs/qc.md
@@ -17,7 +17,7 @@ bean qc \
 
 `bean qc` supports following quality control and masks samples with low quality. Specifically:  
 
-<img src="assets/qc_output.png" alt="Allele translation" width="900"/>  
+<img src="/crispr-bean/assets/qc_output.png" alt="Allele translation" width="900"/>  
 
 * Plots guide coverage and the uniformity of coverage
 * Guide count correlation between samples

diff --git a/docs/reporterscreen.md b/docs/reporterscreen.md
@@ -1,6 +1,6 @@
 BEAN stores mapped gRNA and allele counts in `ReporterScreen` object which is compatible with [AnnData](https://anndata.readthedocs.io/en/latest/index.html).  
 
-<img src="assets/data_structure_v2.png" alt="ReporterScreen object structure" width="700" />
+<img src="/crispr-bean/assets/data_structure_v2.png" alt="ReporterScreen object structure" width="700" />
 
   * `.guides`: guide information provided in input (`gRNA_library.csv` in above example)
   * `.samples`: sample information provided in input (`sample_list.csv` in above example)

diff --git a/docs/run.md b/docs/run.md
@@ -6,7 +6,7 @@ BEAN uses Bayesian network to incorporate gRNA editing outcome to provide poster
 
 For the full detail, see the method section of the [BEAN manuscript](https://www.medrxiv.org/content/10.1101/2023.09.08.23295253v1).
 
-<img src="assets/bean.gif" alt="model" width="700"/>   
+<img src="/crispr-bean/assets/bean.gif" alt="model" width="700"/>   
 
 <br></br>
 
@@ -45,7 +45,7 @@ See full list of parameters [below](#full-parameters).
 
 
 # Output
-<img src="assets/model_output.png" alt="model" width="700"/>
+<img src="/crispr-bean/assets/model_output.png" alt="model" width="700"/>
 
 Above command produces
 * `output_prefix/bean_element_result.[model_type].csv` with following columns:

diff --git a/docs/tutorials/ldl_cds.md b/docs/tutorials/ldl_cds.md
@@ -4,11 +4,11 @@ Tiling screen that tiles gRNA densely across locus or multiple loci, selected ba
 <table>
   <tr>
     <th>Library design</th>
-    <td>Tiling (gRNAs tile each locus densely)   <br> <img src="assets/tiling.png" alt="tiling library design" width="300"/> </td>
+    <td>Tiling (gRNAs tile each locus densely)   <br> <img src="/crispr-bean/assets/tiling.png" alt="tiling library design" width="300"/> </td>
   </tr>
   <tr>
     <th>Selection</th>
-    <td>Cells are sorted based on FACS signal quantiles  <br>  <img src="assets/[email protected]" alt="variant library design" width="300"/></td>
+    <td>Cells are sorted based on FACS signal quantiles  <br>  <img src="/crispr-bean//crispr-bean/assets/[email protected]" alt="variant library design" width="300"/></td>
   </tr>
 </table>
 

diff --git a/docs/tutorials/ldl_var.md b/docs/tutorials/ldl_var.md
@@ -1,14 +1,14 @@
-# Variant sorting screen tutorial
+## Variant sorting screen tutorial
 GWAS variant screen with per-variant gRNA tiling design, selected based on FACS signal quantiles.  
 
 <table>
   <tr>
     <th>Library design</th>
-    <td>Variant (gRNAs tile each target variant)   <br> <img src="assets/variant.png" alt="variant library design" width="600"/></td>
+    <td>Variant (gRNAs tile each target variant)   <br> <img src="/crispr-bean/assets/variant.png" alt="variant library design" width="600"/></td>
   </tr>
   <tr>
     <th>Selection</th>
-    <td>Cells are sorted based on FACS signal quantiles  <br>  <img src="assets/[email protected]" alt="variant library design" width="300"/></td>
+    <td>Cells are sorted based on FACS signal quantiles  <br>  <img src="/crispr-bean/assets/[email protected]" alt="variant library design" width="300"/></td>
   </tr>
 </table>