Starting MOFA chapter

Plant-Food-Research-Open · Jan 24, 2024 · dbca1d4 · dbca1d4
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diff --git a/_quarto.yml b/_quarto.yml
@@ -20,6 +20,7 @@ book:
       chapters:
       - spls.qmd
       - so2pls.qmd
+      - mofa.qmd
     - part: "Supervised integration"
       chapters:
       - diablo.qmd

diff --git a/_targets.R b/_targets.R
@@ -504,6 +504,39 @@ list(
     )
   ),
 
+  ##===============##
+  ## MOFA pipeline ----
+  ##===============##
+
+  ## Creating MOFA input
+  tar_target(
+    mofa_input,
+    get_input_mofa(
+      mo_presel_supervised,
+      options_list = list(
+        data_options = list(scale_views = TRUE),
+        model_options = list( likelihoods = c(
+          "snps" = "poisson",
+          "rnaseq" = "gaussian",
+          "metabolome" = "gaussian"
+        )
+        ),
+        training_options = list(seed = 43)
+      ),
+      only_common_samples = TRUE
+    )
+  ),
+
+  ## Training MOFA model
+  tar_target(
+    mofa_trained,
+    run_mofa(
+      mofa_input,
+      save_data = TRUE,
+      use_basilisk = TRUE
+    )
+  ),
+
   ##========================##
   ## Results interpretation ----
   ##========================##

diff --git a/_targets/meta/meta b/_targets/meta/meta
@@ -2,9 +2,9 @@ name|type|data|command|depend|seed|path|time|size|bytes|format|repository|iterat
 data_geno|stem|6c35052b46564eaa|2f6d6fac438e0c68|8846e09db8d257d5|-676849289||t19737.0760777314s|c999686471cd2bf1|1616600|rds|local|vector|||1.47||
 data_metabo|stem|d373e47b182755db|91ad6cfa4064ca3b|a8b88e2a622ece40|-1296975954||t19737.0760063898s|6044e0195a090f92|19248|rds|local|vector|||1.715||
 data_transcripto|stem|3f48590934bb1333|5d10bc167155482a|69f2986da2408dad|196911606||t19737.076051425s|a0d23620354f1de9|6494110|rds|local|vector|||1.74||
-dataset_file_geno|stem|af97a53623d6e7de|3d7a8f99ddc05036|ef46db3751d8e999|1960638429|/powerplant/workspace/hrpoab/RENV_CACHE/v5/R-4.2/x86_64-pc-linux-gnu/moiraine/0.0.0.9000/ea944811306c200792f0808f5fa53cec/moiraine/extdata/genomics_dataset.csv|t19745.9853896047s|20566495b664ffb4|6850822|file|local|vector|||0||
-dataset_file_metabo|stem|175ac2cf6405fbad|877816dafd820145|ef46db3751d8e999|1190506623|/powerplant/workspace/hrpoab/RENV_CACHE/v5/R-4.2/x86_64-pc-linux-gnu/moiraine/0.0.0.9000/ea944811306c200792f0808f5fa53cec/moiraine/extdata/metabolomics_dataset.csv|t19745.9853898302s|c4e0ec1268286261|35815|file|local|vector|||0||
-dataset_file_transcripto|stem|71a95dd921de2179|3f2f9666068c76c2|ef46db3751d8e999|-658525691|/powerplant/workspace/hrpoab/RENV_CACHE/v5/R-4.2/x86_64-pc-linux-gnu/moiraine/0.0.0.9000/ea944811306c200792f0808f5fa53cec/moiraine/extdata/transcriptomics_dataset.csv|t19745.9853901212s|92b17bfefe92cde3|10702704|file|local|vector|||0||
+dataset_file_geno|stem|af97a53623d6e7de|7d4279445b0f2f30|ef46db3751d8e999|1960638429|/powerplant/workspace/hrpoab/RENV_CACHE/v5/R-4.2/x86_64-pc-linux-gnu/moiraine/0.0.0.9000/c5fcba1231fe0ad084ba7ffc17cfc3e0/moiraine/extdata/genomics_dataset.csv|t19746.1427907402s|20566495b664ffb4|6850822|file|local|vector|||0.001||
+dataset_file_metabo|stem|175ac2cf6405fbad|2cea41e52ddc05f6|ef46db3751d8e999|1190506623|/powerplant/workspace/hrpoab/RENV_CACHE/v5/R-4.2/x86_64-pc-linux-gnu/moiraine/0.0.0.9000/c5fcba1231fe0ad084ba7ffc17cfc3e0/moiraine/extdata/metabolomics_dataset.csv|t19746.1427922693s|c4e0ec1268286261|35815|file|local|vector|||0||
+dataset_file_transcripto|stem|71a95dd921de2179|a25d3eca0f4a1f07|ef46db3751d8e999|-658525691|/powerplant/workspace/hrpoab/RENV_CACHE/v5/R-4.2/x86_64-pc-linux-gnu/moiraine/0.0.0.9000/c5fcba1231fe0ad084ba7ffc17cfc3e0/moiraine/extdata/transcriptomics_dataset.csv|t19746.1427963896s|92b17bfefe92cde3|10702704|file|local|vector|||0||
 dataset_names_pca|stem|b7dcb1f702f808d7|cbd5b838d68f1692|ed471008ce8c9ddc|-1982688821||t19739.9580991333s|abbdb7fe746336f0|76|rds|local|vector||dataset_names_pca_266715e9*dataset_names_pca_90c252f2*dataset_names_pca_a29776a2|0||
 diablo_design_matrix|stem|29c6a413f89d3f67|348c9ac4eba4001a|9bfafd062325ed6e|1135312759||t19744.9620132827s|82d1d1c4d23d6aba|150|rds|local|vector|||0.001||
 diablo_final_run|stem|b299f53f75cc3c4f|23964c06fd68be70|ee3fac541fa5e2dd|-1601141966||t19744.9989792927s|99991ea38374c569|1124171|rds|local|vector|||0.178||
@@ -24,8 +24,8 @@ diablo_pls_runs_list_4f48d450|branch|3a05360ad3f5dae7|077baa4499ed4701|347c6916a
 diablo_tune_plot|stem|b615a21be99179e9|8cf07375c3b3d80f|f4985a8965dde29e|-311548008||t19744.9990244999s|c965ce08dcbcf633|1386462|rds|local|vector|||3.082||
 diablo_tune_res|stem|3c54bb7e00a94d6c|2e74485360175d64|50019954d23c4902|1659021768||t19744.9989759177s|2dabcffb297d71a5|8626|rds|local|vector|||3113.796||
 fmetadata_file_geno|stem|0d4f9d1abe758d58|8ac42325af16f9cc|0fce92a88a7882f5|987449262|/powerplant/workspace/hrpoab/RENV_CACHE/v5/R-4.2/x86_64-pc-linux-gnu/moiraine/0.0.0.9000/a0cb1ab1c9bfde027266aa5d81f33617/moiraine/extdata/genomics_features_info.csv|t19737.0751431053s|e86eccc6c1038d8e|1462543|file|local|vector|||0.007||
-fmetadata_file_metabo|stem|ce74bd2201a2d6ed|3db26d4ee54840b9|ef46db3751d8e999|-1426493726|/powerplant/workspace/hrpoab/RENV_CACHE/v5/R-4.2/x86_64-pc-linux-gnu/moiraine/0.0.0.9000/ea944811306c200792f0808f5fa53cec/moiraine/extdata/metabolomics_features_info.csv|t19745.9853898654s|9cb4cce6003c5d85|13765|file|local|vector|||0||
-fmetadata_file_transcripto|stem|5b0c736c6e2b1870|ef036d9b9ad4c5c9|ef46db3751d8e999|1741435395|/powerplant/workspace/hrpoab/RENV_CACHE/v5/R-4.2/x86_64-pc-linux-gnu/moiraine/0.0.0.9000/ea944811306c200792f0808f5fa53cec/moiraine/extdata/bos_taurus_gene_model.gff3|t19745.9853887737s|3c1bc2cfc685286e|47182268|file|local|vector|||1.918||
+fmetadata_file_metabo|stem|ce74bd2201a2d6ed|a30aa8baa67fb264|ef46db3751d8e999|-1426493726|/powerplant/workspace/hrpoab/RENV_CACHE/v5/R-4.2/x86_64-pc-linux-gnu/moiraine/0.0.0.9000/c5fcba1231fe0ad084ba7ffc17cfc3e0/moiraine/extdata/metabolomics_features_info.csv|t19746.1427926081s|9cb4cce6003c5d85|13765|file|local|vector|||3.875||
+fmetadata_file_transcripto|stem|5b0c736c6e2b1870|a74fcb94350f3144|ef46db3751d8e999|1741435395|/powerplant/workspace/hrpoab/RENV_CACHE/v5/R-4.2/x86_64-pc-linux-gnu/moiraine/0.0.0.9000/c5fcba1231fe0ad084ba7ffc17cfc3e0/moiraine/extdata/bos_taurus_gene_model.gff3|t19746.1427898467s|3c1bc2cfc685286e|47182268|file|local|vector|||0||
 fmetadata_geno|stem|6e05fc065a44eb05|6063db1a29e2c1f0|adbbfaf18ae42144|1845751809||t19737.9062294664s|7228e160b348b511|410111|rds|local|vector|||0.222||
 fmetadata_metabo|stem|2fa264d9731315ae|6530e474805c7677|40a14803581cc40c|-1710108544||t19737.9062248138s|ebd621d71b90c5fd|5459|rds|local|vector|||0.879||
 fmetadata_transcripto|stem|452e3b635689568a|588e73874bd5990b|af559c33c19b2822|650025152||t19737.9129876928s|90da4f7e51eb50af|869252|rds|local|vector|||17.12||
@@ -52,6 +52,8 @@ mo_set_complete|stem|d79178dd6687be97|d76a85ef218e0cef|952f06b34b51e191|17398688
 mo_set_de|stem|2b7e2ace37c0bed5|50f81c565a9dc6aa|1d4929f8d72b5561|1698094396||t19739.0034448046s|fa7930e7b638c680|37442539|rds|local|vector|||0.167|rnaseq dataset 1594 feature IDs missing from df dataframe.|
 mo_set_transformed|stem|28334a82bdfebaa7|1a49152e06c5222d|6f732476e2857317|385723480||t19739.9580970037s|5c19986154657d81|57773059|rds|local|vector|||0.252||
 mo_set_with_names|stem|e64ebcd89ddb70bd|b88cddcfa5d2a267|6eebd2f68cb73320|-1640374052||t19738.0568285842s|593ace30823e21f2|36753195|rds|local|vector|||0.114||
+mofa_input|stem|55da511de7664cd8|a8548080dfc5818e|b1ff01b4e620143d|1284502458||t19746.154401993s|e22ca446e6bece21|837460|rds|local|vector|||0.324|Dataset snps is to be modelled with a poisson likelihood, but is not integer. Transforming to integer.|
+mofa_trained|stem|b38f267e60c1989a|ec971dccb1086e60|91cc7bf157eacf61|1854191013||t19746.1563374787s|29bcdeb5af24197c|966299|rds|local|vector|||166.175|No output filename provided. Using tmpRtmpHWxlYdmofa_20240124164221.hdf5 to store the trained model.. Factors 1 are strongly correlated with the total number of expressed features for at least one of your omics. Such factors appear when there are differences in the total levels between your samples, sometimes because of poor normalisation in the preprocessing steps.|
 omicspls_input|stem|488cc165105ef587|5103f8e1eb31dfb4|3fe933389d7e1821|1468063698||t19746.0144579806s|8dac9e868840a7ff|957717|rds|local|vector|||0.009||
 pca_mats_list|pattern|c831051151e4add2|72b302a65c0920ed||1078442447||||12164806|rds|local|list||pca_mats_list_302d7473*pca_mats_list_84d36937*pca_mats_list_64d37e6c|0.09||
 pca_mats_list_302d7473|branch|e839c68784be56c5|72b302a65c0920ed|0f98021e133aac1d|-46563577||t19739.9581108254s|1b793e6da03f6fbf|1616638|rds|local|list|pca_mats_list||0.072||
@@ -67,7 +69,7 @@ set_geno|stem|b9a63471a2bae355|6d0f65ce2b5dfcc3|53cc5826dcb4a6d2|1285324786||t19
 set_metabo|stem|0d94569ea56d374d|c474bc703c42933a|608f12a275630935|1932753424||t19738.0474809317s|ed98fcecc594d702|29765|rds|local|vector|||0.06|5 samples in samples metadata not in dataset, will be removed from metadata.|
 set_transcripto|stem|a34ee2565470dabc|ab4282af2718b58e|4a163e482e11d826|1396440415||t19738.0475239992s|5602925ca953b1da|7190802|rds|local|vector|||0.972|7272 features in feature metadata not in dataset, will be removed from metadata.. 1 samples in samples metadata not in dataset, will be removed from metadata.|
 smetadata_all|stem|ab53a5d6797cc718|6b4aea71b616cb74|a19772ceb5ec11de|-937728991||t19737.9793081304s|f1652d5360365c83|4520|rds|local|vector|||0.784||
-smetadata_file_all|stem|334b548c7e00bff1|c9c52210ba4d01d4|ef46db3751d8e999|1816987930|/powerplant/workspace/hrpoab/RENV_CACHE/v5/R-4.2/x86_64-pc-linux-gnu/moiraine/0.0.0.9000/ea944811306c200792f0808f5fa53cec/moiraine/extdata/samples_info.csv|t19745.9853899s|70b525cc81b75a3d|7970|file|local|vector|||0.001||
+smetadata_file_all|stem|334b548c7e00bff1|687aeeaa89695065|ef46db3751d8e999|1816987930|/powerplant/workspace/hrpoab/RENV_CACHE/v5/R-4.2/x86_64-pc-linux-gnu/moiraine/0.0.0.9000/c5fcba1231fe0ad084ba7ffc17cfc3e0/moiraine/extdata/samples_info.csv|t19746.1427929686s|70b525cc81b75a3d|7970|file|local|vector|||0||
 so2pls_cv|stem|01c3e0f6ea779863|21e77ca6aee4664c|2fe8bf94339f8db8|1111841932||t19746.0262490569s|58772b208bb3c33b|420|rds|local|vector|||341.124||
 so2pls_cv_adj|stem|462835eb42a1a462|fd93850ca6adee40|0f6ca247cd6a95ea|710052968||t19746.0222975888s|71e695e858e0833c|250|rds|local|vector|||474.616||
 so2pls_cv_adj_plot|stem|048bba2eb50ed68a|9e2bdae32bcd502a|60b2a8e2ed9491fe|-2142098915||t19746.026251263s|4a215a353ab56115|130449|rds|local|vector|||0.109||

diff --git a/docs/index.html b/docs/index.html
@@ -209,6 +209,11 @@ <h1 class="quarto-secondary-nav-title">The moiraine R package user manual</h1>
   <div class="sidebar-item-container"> 
   <a href="./so2pls.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">9</span>&nbsp; <span class="chapter-title">Integration with sO2PLS</span></a>
   </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./mofa.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">10</span>&nbsp; <span class="chapter-title">Integration with MOFA</span></a>
+  </div>
 </li>
       </ul>
 </li>
@@ -222,7 +227,7 @@ <h1 class="quarto-secondary-nav-title">The moiraine R package user manual</h1>
       <ul id="quarto-sidebar-section-3" class="collapse list-unstyled sidebar-section depth1 show">
 <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="./diablo.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">10</span>&nbsp; <span class="chapter-title">Integration with DIABLO</span></a>
+  <a href="./diablo.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">11</span>&nbsp; <span class="chapter-title">Integration with DIABLO</span></a>
   </div>
 </li>
       </ul>
@@ -237,7 +242,7 @@ <h1 class="quarto-secondary-nav-title">The moiraine R package user manual</h1>
       <ul id="quarto-sidebar-section-4" class="collapse list-unstyled sidebar-section depth1 show">
 <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="./interpretation.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">11</span>&nbsp; <span class="chapter-title">Interpreting the integration results</span></a>
+  <a href="./interpretation.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">12</span>&nbsp; <span class="chapter-title">Interpreting the integration results</span></a>
   </div>
 </li>
       </ul>