fabilab · YingX97 · Oct 23, 2024 · Oct 23, 2024 · Oct 23, 2024 · Oct 23, 2024
diff --git a/.github/workflows/r_test.yml b/.github/workflows/r_test.yml
@@ -21,6 +21,21 @@ jobs:
     - name: Setup Pandoc
       uses: r-lib/actions/setup-pandoc@v2
 
+    - name: Install dependencies (Ubuntu)
+      if: runner.os == 'Linux'
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y tidy
+        sudo apt-get install -y texlive-full
+
+    - name: Install dependencies (macOS)
+      if: runner.os == 'macOS'
+      run: |
+        brew install tidy-html5
+        Rscript -e "if (!require('tinytex')) install.packages('tinytex')"
+        Rscript -e "tinytex::install_tinytex(force = TRUE)"
+        Rscript -e "tinytex::tlmgr_install(c('latex-bin', 'inconsolata'))"
+
     - name: Install R dependencies
       uses: r-lib/actions/setup-r-dependencies@v2
       with:
@@ -33,4 +48,31 @@ jobs:
       with:
         error-on: '"note"'
         working-directory: R/atlasapprox
-
+
+    - name: Build package (Windows)
+      if: runner.os == 'Windows'
+      shell: cmd
+      run: |
+        R.exe CMD build .
+      working-directory: R/atlasapprox
+
+    - name: Run CRAN check (Windows)
+      if: runner.os == 'Windows'
+      shell: cmd
+      run: |
+        R.exe CMD check --no-manual --as-cran atlasapprox_0.1.0.tar.gz
+      working-directory: R/atlasapprox
+
+    - name: Build R package (other systems)
+      if: runner.os != 'Windows'
+      shell: bash
+      run: |
+        R CMD build .
+      working-directory: R/atlasapprox
+
+    - name: Run R CMD check --as-cran
+      if: runner.os != 'Windows'
+      shell: bash
+      run: |
+        R CMD check --as-cran atlasapprox_*.tar.gz
+      working-directory: R/atlasapprox
diff --git a/R/atlasapprox/.Rbuildignore b/R/atlasapprox/.Rbuildignore
@@ -8,4 +8,5 @@
 ^\.Rcheck$
 ^.*\.Rcheck$
 ^doc$
-^Meta$
+^Meta$
+^\.Rproj\.user$
diff --git a/R/atlasapprox/DESCRIPTION b/R/atlasapprox/DESCRIPTION
@@ -2,16 +2,16 @@ Package: atlasapprox
 Title: Cell Atlas Approximations
 Version: 0.1.0
 Authors@R: 
-    person("Fabio", "Zanini", , "fabio.zanini@unsw.edu.au", role = c("aut", "cre"),
-           comment = c(ORCID = "0000-0001-7097-8539"))
-Author: Fabio Zanini <fabio.zanini@unsw.edu.au>
-Maintainer: Fabio Zanini <fabio.zanini@unsw.edu.au>
-Description: This package provides an interface in R to cell atlas approximations.
-    See the vignette under "Get started" for instructions, or the reference documentation
-    for specific functions. Other interfaces at https://atlasapprox.readthedocs.io.
+    c(
+      person("Fabio", "Zanini", , "fabio.zanini@unsw.edu.au", role = "aut",
+             comment = c(ORCID = "0000-0001-7097-8539")),
+      person("Ying", "Xu", , "ying.xu3@unsw.edu.au", role = c("aut", "cre"))
+    )
+Maintainer: Ying Xu <ying.xu3@unsw.edu.au>
+Description: Provides an interface in R to cell atlas approximations. See the vignette under "Getting started" for instructions. You can also explore the reference documentation for specific functions. Additional interfaces and resources are available at <https://atlasapprox.readthedocs.io>.
 License: MIT + file LICENSE
-URL: https://atlasapprox.readthedocs.io/R, https://github.com/fabilab/atlasapprox
-BugReports: https://github.com/fabilab/atlasapprox/issues
+URL: https://atlasapprox.readthedocs.io/en/latest/R/index.html, https://github.com/fabilab/cell_atlas_approximations_API
+BugReports: https://github.com/fabilab/cell_atlas_approximations_API/issues
 Imports:
     httr
 Suggests:
@@ -22,4 +22,4 @@ Config/testthat/edition: 3
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2
-VignetteBuilder: knitr
+VignetteBuilder: knitr
diff --git a/R/atlasapprox/README.md b/R/atlasapprox/README.md
@@ -1,5 +1,5 @@
 # R
-The R interface can be used to access the atlas approximation API from R. It uses caching to speed up multiple requests so it is generally as fast or faster than using the [REST API](../index.html) directly.
+The R interface can be used to access the atlas approximation API from R. It uses caching to speed up multiple requests so it is generally as fast or faster than using the [REST API](https://atlasapprox.readthedocs.io/en/latest/rest/index.html) directly.
 
 ## Requirements
 You need the following R packages:

diff --git a/R/atlasapprox/_pkgdown.yml b/R/atlasapprox/_pkgdown.yml
@@ -12,7 +12,6 @@ template:
     border-radius: 0.5rem
     btn-border-radius: 0.25rem
 
-
 navbar:
   structure:
     left:

diff --git a/R/atlasapprox/man/GetAverage.Rd b/R/atlasapprox/man/GetAverage.Rd
diff --git a/R/atlasapprox/man/GetMarkers.Rd b/R/atlasapprox/man/GetMarkers.Rd
diff --git a/R/atlasapprox/vignettes/atlasapprox.Rmd b/R/atlasapprox/vignettes/atlasapprox.Rmd
@@ -9,7 +9,6 @@ vignette: >
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---
-
 Cell atlases such as Tabula Muris and Tabula Sapiens are multi-organ single cell omics data sets describing entire organisms. A cell atlas approximation is a lossy and lightweight compression of a cell atlas that can be streamed via the internet.
 
 This project enables biologists, doctors, and data scientist to quickly find answers for questions such as:
@@ -137,7 +136,7 @@ print(similar_genes)
 `atlasapprox` relies upon available cell atlases kindly released for public use:
 
 - [A. queenslandica - Sebé-Pedrós et al 2018](https://www.nature.com/articles/s41559-018-0575-6)
-- A. thaliana: [Shahan et al 2022](https://www.sciencedirect.com/science/article/pii/S1534580722000338) [root], [Xu et al 2024](https://doi.org/10.1101/2024.03.04.583414) [shoot]
+- A. thaliana: [Shahan et al 2022](https://doi.org/10.1016/j.devcel.2022.01.008) [root], [Xu et al 2024](https://doi.org/10.1101/2024.03.04.583414) [shoot]
 - [C. elegans - Cao et al. 2017](https://www.science.org/doi/10.1126/science.aam8940)
 - [C. gigas - Piovani et al 2023](https://doi.org/10.1126/sciadv.adg6034)
 - [C. hemisphaerica - Chari et al. 2021](https://www.science.org/doi/10.1126/sciadv.abh1683)
@@ -147,24 +146,24 @@ print(similar_genes)
 - [H. miamia - Hulett et al. 2023](https://www.nature.com/articles/s41467-023-38016-4)
 - H. sapiens: [ATAC - Zhang et al. Ren](https://doi.org/10.1016/j.cell.2021.10.024), [RNA - Tabula Sapiens](https://www.science.org/doi/10.1126/science.abl4896)
 - [H. vulgaris - Sieert et al 2019](https://doi.org/10.1126/science.aav9314)
-- [I. pulchra - Duruz et al. 2020](https://academic.oup.com/mbe/article/38/5/1888/6045962)
+- [I. pulchra - Duruz et al. 2020](https://doi.org/10.1093/molbev/msaa333)
 - [L. minuta - Abramson et al. 2022](https://doi.org/10.1093/plphys/kiab564)
 - [M. leidyi - Sebé-Pedrós et al 2018](https://www.nature.com/articles/s41559-018-0575-6)
 - [M. murinus - Tabula Microcebus](https://www.biorxiv.org/content/10.1101/2021.12.12.469460v2)
 - [M. musculus - Tabula Muris Senis 2020](https://www.nature.com/articles/s41586-020-2496-1)
 - [N. vectensis - Steger et al 2022](https://doi.org/10.1016/j.celrep.2022.111370)
 - [O. sativa - Zhang et al 2021](https://doi.org/10.1038/s41467-021-22352-4)
 - [P. crozieri - Piovani et al 2023](https://doi.org/10.1126/sciadv.adg6034)
-- [P. dumerilii - Achim et al 2017](https://academic.oup.com/mbe/article/35/5/1047/4823215)
+- [P. dumerilii - Achim et al 2017](https://doi.org/10.1093/molbev/msx336)
 - [S. lacustris - Musser et al. 2021](https://www.science.org/doi/10.1126/science.abj2949)
 - [S. mansoni - Li et al. 2021](https://www.nature.com/articles/s41467-020-20794-w)
 - [S. mediterranea - Plass et al. 2018](https://doi.org/10.1126/science.aaq1723)
-- [S. pistillata - Levi et al. 2021](https://www.sciencedirect.com/science/article/pii/S0092867421004402)
+- [S. pistillata - Levi et al. 2021](https://doi.org/10.1016/j.cell.2021.04.005)
 - [S. purpuratus - Paganos et al 2021](https://doi.org/10.7554/eLife.70416)
 - [T. adhaerens - Sebé-Pedrós et al 2018](https://www.nature.com/articles/s41559-018-0575-6)
 - [T. aestivum - Zhang et al 2023](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-023-02908-x)
 - [X. laevis - Liao et al. 2022](https://www.nature.com/articles/s41467-022-31949-2)
-- Z. mays: [Marand et al 2021](https://www.cell.com/cell/pdf/S0092-8674(21)00493-1.pdf) [seedling], [Xu et al 2024](https://doi.org/10.1101/2024.03.04.583414) [eartip]
+- Z. mays: [Marand et al 2021](https://doi.org/10.1016/j.cell.2021.04.014) [seedling], [Xu et al 2024](https://doi.org/10.1101/2024.03.04.583414) [eartip]
 
 We are grateful to all authors above for their help and committment to open science.
 

diff --git a/R/atlasapprox/vignettes/atlasapprox.html b/R/atlasapprox/vignettes/atlasapprox.html
@@ -390,14 +390,12 @@ <h2>Available organisms or species</h2>
 available organisms:</p>
 <pre class="r"><code>organisms &lt;- GetOrganisms()
 print(organisms)</code></pre>
-<pre><code>##  [1] &quot;a_queenslandica&quot; &quot;a_thaliana&quot;      &quot;c_elegans&quot;       &quot;c_gigas&quot;        
-##  [5] &quot;c_hemisphaerica&quot; &quot;d_melanogaster&quot;  &quot;d_rerio&quot;         &quot;f_vesca&quot;        
-##  [9] &quot;h_miamia&quot;        &quot;h_sapiens&quot;       &quot;h_vulgaris&quot;      &quot;i_pulchra&quot;      
-## [13] &quot;l_minuta&quot;        &quot;m_leidyi&quot;        &quot;m_murinus&quot;       &quot;m_musculus&quot;     
-## [17] &quot;n_vectensis&quot;     &quot;o_sativa&quot;        &quot;p_crozieri&quot;      &quot;p_dumerilii&quot;    
-## [21] &quot;s_lacustris&quot;     &quot;s_mansoni&quot;       &quot;s_mediterranea&quot;  &quot;s_pistillata&quot;   
-## [25] &quot;s_purpuratus&quot;    &quot;t_adhaerens&quot;     &quot;t_aestivum&quot;      &quot;x_laevis&quot;       
-## [29] &quot;z_mays&quot;</code></pre>
+<pre><code>##  [1] &quot;a_queenslandica&quot; &quot;a_thaliana&quot;      &quot;c_elegans&quot;       &quot;c_gigas&quot;         &quot;c_hemisphaerica&quot;
+##  [6] &quot;d_melanogaster&quot;  &quot;d_rerio&quot;         &quot;f_vesca&quot;         &quot;h_miamia&quot;        &quot;h_sapiens&quot;      
+## [11] &quot;h_vulgaris&quot;      &quot;i_pulchra&quot;       &quot;l_minuta&quot;        &quot;m_leidyi&quot;        &quot;m_murinus&quot;      
+## [16] &quot;m_musculus&quot;      &quot;n_vectensis&quot;     &quot;o_sativa&quot;        &quot;p_crozieri&quot;      &quot;p_dumerilii&quot;    
+## [21] &quot;s_lacustris&quot;     &quot;s_mansoni&quot;       &quot;s_mediterranea&quot;  &quot;s_pistillata&quot;    &quot;s_purpuratus&quot;   
+## [26] &quot;t_adhaerens&quot;     &quot;t_aestivum&quot;      &quot;x_laevis&quot;        &quot;z_mays&quot;</code></pre>
 </div>
 <div id="organs-in-a-single-organism" class="section level2">
 <h2>Organs in a single organism</h2>
@@ -406,10 +404,10 @@ <h2>Organs in a single organism</h2>
 available:</p>
 <pre class="r"><code>human_organs &lt;- GetOrgans(organism = &#39;h_sapiens&#39;)
 print(human_organs)</code></pre>
-<pre><code>##  [1] &quot;bladder&quot;   &quot;blood&quot;     &quot;colon&quot;     &quot;eye&quot;       &quot;fat&quot;       &quot;gut&quot;      
-##  [7] &quot;heart&quot;     &quot;kidney&quot;    &quot;liver&quot;     &quot;lung&quot;      &quot;lymphnode&quot; &quot;mammary&quot;  
-## [13] &quot;marrow&quot;    &quot;muscle&quot;    &quot;pancreas&quot;  &quot;prostate&quot;  &quot;salivary&quot;  &quot;skin&quot;     
-## [19] &quot;spleen&quot;    &quot;thymus&quot;    &quot;tongue&quot;    &quot;trachea&quot;   &quot;uterus&quot;</code></pre>
+<pre><code>##  [1] &quot;bladder&quot;   &quot;blood&quot;     &quot;colon&quot;     &quot;eye&quot;       &quot;fat&quot;       &quot;gut&quot;       &quot;heart&quot;    
+##  [8] &quot;kidney&quot;    &quot;liver&quot;     &quot;lung&quot;      &quot;lymphnode&quot; &quot;mammary&quot;   &quot;marrow&quot;    &quot;muscle&quot;   
+## [15] &quot;pancreas&quot;  &quot;prostate&quot;  &quot;salivary&quot;  &quot;skin&quot;      &quot;spleen&quot;    &quot;thymus&quot;    &quot;tongue&quot;   
+## [22] &quot;trachea&quot;   &quot;uterus&quot;</code></pre>
 </div>
 <div id="cell-types-within-an-organ" class="section level2">
 <h2>Cell types within an organ</h2>
@@ -513,10 +511,10 @@ <h2>Gene expression</h2>
 <pre class="r"><code>genes &lt;- GetFeatures(organism = &#39;h_sapiens&#39;)
 # To show just the first 20 genes
 print(head(genes, 20))</code></pre>
-<pre><code>##  [1] &quot;A1BG&quot;        &quot;A1BG-AS1&quot;    &quot;A1CF&quot;        &quot;A2M&quot;         &quot;A2M-AS1&quot;    
-##  [6] &quot;A2ML1&quot;       &quot;A2ML1-AS1&quot;   &quot;A2ML1-AS2&quot;   &quot;A2MP1&quot;       &quot;A3GALT2&quot;    
-## [11] &quot;A4GALT&quot;      &quot;A4GNT&quot;       &quot;AAAS&quot;        &quot;AACS&quot;        &quot;AACSP1&quot;     
-## [16] &quot;AADAC&quot;       &quot;AADACL2&quot;     &quot;AADACL2-AS1&quot; &quot;AADACL3&quot;     &quot;AADACL4&quot;</code></pre>
+<pre><code>##  [1] &quot;A1BG&quot;        &quot;A1BG-AS1&quot;    &quot;A1CF&quot;        &quot;A2M&quot;         &quot;A2M-AS1&quot;     &quot;A2ML1&quot;      
+##  [7] &quot;A2ML1-AS1&quot;   &quot;A2ML1-AS2&quot;   &quot;A2MP1&quot;       &quot;A3GALT2&quot;     &quot;A4GALT&quot;      &quot;A4GNT&quot;      
+## [13] &quot;AAAS&quot;        &quot;AACS&quot;        &quot;AACSP1&quot;      &quot;AADAC&quot;       &quot;AADACL2&quot;     &quot;AADACL2-AS1&quot;
+## [19] &quot;AADACL3&quot;     &quot;AADACL4&quot;</code></pre>
 </div>
 <div id="markers" class="section level2">
 <h2>Markers</h2>
@@ -580,9 +578,9 @@ <h2>Data sources</h2>
 <ul>
 <li><a href="https://www.nature.com/articles/s41559-018-0575-6">A.
 queenslandica - Sebé-Pedrós et al 2018</a></li>
-<li>A. thaliana: <a href="https://www.sciencedirect.com/science/article/pii/S1534580722000338">Shahan
-et al 2022</a> [root], <a href="https://doi.org/10.1101/2024.03.04.583414">Xu et al 2024</a>
-[shoot]</li>
+<li>A. thaliana: <a href="https://doi.org/10.1016/j.devcel.2022.01.008">Shahan et al
+2022</a> [root], <a href="https://doi.org/10.1101/2024.03.04.583414">Xu
+et al 2024</a> [shoot]</li>
 <li><a href="https://www.science.org/doi/10.1126/science.aam8940">C.
 elegans - Cao et al. 2017</a></li>
 <li><a href="https://doi.org/10.1126/sciadv.adg6034">C. gigas - Piovani
@@ -602,8 +600,8 @@ <h2>Data sources</h2>
 Sapiens</a></li>
 <li><a href="https://doi.org/10.1126/science.aav9314">H. vulgaris -
 Sieert et al 2019</a></li>
-<li><a href="https://academic.oup.com/mbe/article/38/5/1888/6045962">I.
-pulchra - Duruz et al. 2020</a></li>
+<li><a href="https://doi.org/10.1093/molbev/msaa333">I. pulchra - Duruz
+et al. 2020</a></li>
 <li><a href="https://doi.org/10.1093/plphys/kiab564">L. minuta -
 Abramson et al. 2022</a></li>
 <li><a href="https://www.nature.com/articles/s41559-018-0575-6">M.
@@ -618,16 +616,16 @@ <h2>Data sources</h2>
 Zhang et al 2021</a></li>
 <li><a href="https://doi.org/10.1126/sciadv.adg6034">P. crozieri -
 Piovani et al 2023</a></li>
-<li><a href="https://academic.oup.com/mbe/article/35/5/1047/4823215">P.
-dumerilii - Achim et al 2017</a></li>
+<li><a href="https://doi.org/10.1093/molbev/msx336">P. dumerilii - Achim
+et al 2017</a></li>
 <li><a href="https://www.science.org/doi/10.1126/science.abj2949">S.
 lacustris - Musser et al. 2021</a></li>
 <li><a href="https://www.nature.com/articles/s41467-020-20794-w">S.
 mansoni - Li et al. 2021</a></li>
 <li><a href="https://doi.org/10.1126/science.aaq1723">S. mediterranea -
 Plass et al. 2018</a></li>
-<li><a href="https://www.sciencedirect.com/science/article/pii/S0092867421004402">S.
-pistillata - Levi et al. 2021</a></li>
+<li><a href="https://doi.org/10.1016/j.cell.2021.04.005">S. pistillata -
+Levi et al. 2021</a></li>
 <li><a href="https://doi.org/10.7554/eLife.70416">S. purpuratus -
 Paganos et al 2021</a></li>
 <li><a href="https://www.nature.com/articles/s41559-018-0575-6">T.
@@ -636,8 +634,8 @@ <h2>Data sources</h2>
 aestivum - Zhang et al 2023</a></li>
 <li><a href="https://www.nature.com/articles/s41467-022-31949-2">X.
 laevis - Liao et al. 2022</a></li>
-<li>Z. mays: <a href="https://www.cell.com/cell/pdf/S0092-8674(21)00493-1.pdf">Marand et
-al 2021</a> [seedling], <a href="https://doi.org/10.1101/2024.03.04.583414">Xu et al 2024</a>
+<li>Z. mays: <a href="https://doi.org/10.1016/j.cell.2021.04.014">Marand
+et al 2021</a> [seedling], <a href="https://doi.org/10.1101/2024.03.04.583414">Xu et al 2024</a>
 [eartip]</li>
 </ul>
 <p>We are grateful to all authors above for their help and committment
-Original file line number
+Diff line change
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