Add notebook which integrates metag, metap, metab data

.github/workflows/notebook_check_r.yml

@@ -31,6 +31,10 @@ jobs:
       name: Set up R
       uses: r-lib/actions/setup-r@v2
 
+    - name: dependencies on Linux
+      if: runner.os == 'Linux'
+      run: sudo apt-get install -y make libicu-dev libxml2-dev libssl-dev pandoc librdf0-dev libnode-dev libcurl4-gnutls-dev
+
     - id: r-dependencies
       name: Install r dependencies
       run: |
@@ -39,6 +43,11 @@ jobs:
         R -e 'install.packages("IRkernel")'
         R -e 'IRkernel::installspec()'
 
+    - id: execute-integration
+      name: Execute integration notebook
+      run: |
+        jupyter nbconvert --execute --to notebook --inplace omics_types_integration/R/integration_notebook.ipynb
+
     - id: execute-bioscales
       name: Execute bioscales notebook
       run: |

README.md

@@ -7,6 +7,7 @@ Notebooks that are ready for use and exploration.
 - [Bio-Scales Biogeochemical MetaData](https://github.com/microbiomedata/nmdc_notebooks/tree/main/bioscales_biogeochemical_metadata)
 - [NEON Soil Microbial Community Composition](https://github.com/microbiomedata/nmdc_notebooks/tree/main/taxonomic_dist_by_soil_layer)
 - [Natural Organic Matter Composition by Sample Type](https://github.com/microbiomedata/nmdc_notebooks/tree/main/NOM_visualizations)
+- [Omics Types Data Integration](https://github.com/microbiomedata/nmdc_notebooks/tree/main/NOM_visualizations/omics_types_integration)
 
 
 ## Overview 

libraries.R

@@ -9,4 +9,10 @@ library(lubridate)
 library(GGally)
 library(stringr)
 library(ggExtra)
-library(readr)
+library(readr)
+library(purrr)
+library(tibble)
+library(jsonlite)
+library(KEGGREST)
+library(circlize)
+library(pathview)

omics_types_integration/README.md

@@ -0,0 +1,11 @@
+# Integrating Different Types of Omics Data
+
+This folder includes two notebooks (in R and Python) that illustrate how metagenomic, metaproteomic, and metabolomic data from the same sample can be retrieved from the [NMDC-runtime API](https://api.microbiomedata.org/docs) and integrated using KEGG annotations.
+
+## R 
+### TODO update links once the branch is merged into main
+- [Static rendered Jupyter notebook](https://nbviewer.org/github/microbiomedata/nmdc_notebooks/blob/91-create-notebook-integrating-metag-metap-metab-data-r/omics_types_integration/R/integration_notebook.ipynb). This is the recommended way to interact with the notebook. _Viewing only, not editable_
+- [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/microbiomedata/nmdc_notebooks/blob/91-create-notebook-integrating-metag-metap-metab-data-r/omics_types_integration/R/integration_notebook.ipynb). **Running this notebook in the colab interactive environment is not recommended due to long API calls** _You need a google account to use this option_
+
+## Python
+Coming soon!