HOMEChem: the molecular impact of life in an indoor environment.

Repository with pertinent files necessary to recreate main figures from HOMEChem paper (https://doi.org/10.26434/chemrxiv-2021-nk5cr)

Figure 1

b) & c)

Both of these panels are plotting metabolomics feature counts for 2 different annotated features (gamma-glutamyl-S-allylcysteine and tryptophan) using molecular cartography through ili. To recreate these panels, one simply needs to drag and drop a 3D_model.stl file and a metabolomics_feature_table.csv file into the ili chrome extension.
Follow this step-by-step description to recreate panels.

1. Open the ili chrome extension. Familiarize yourself with the GUI.
2. Drag and drop the 3D_model.stl file and let it load and render.
3. Drag and drop the ...metabolomics_feature_table.csv files (one for each timepoint) and let the application load and render.
4. Drag and drop ...feature_snapshot.json files to load the specific feature (gamma-glutamyl-S-allylcysteine or tryptophan) with the appropriate visualization settings to recreate figure panels.

e)

This pannel is plotting the sum of counts of Δm/z shifts ( Δm/z of 15.995 Da corresponding to the O atom , and 28.031 Da corresponding to C2H4) observed across the global molecular network of spectra in the study, subset by sample (surface) and timepoint (panel shows T2).
Follow this step-by-step description to recreate panel.

1. Open the ili chrome extension. Familiarize yourself with the GUI.
2. Drag and drop the 3D_model.stl file and let it load and render.
3. Drag and drop the T2_mz_shifts_counts_table.csv file and let the application load and render.
4. Drag and drop ...shift_snapshot.json files to load the specific Δm/z shift (O or C2H4) with the appropriate visualization settings to recreate figure panels.

Figure 2

a)

This panel shows three-dimensional embedding using singular value decomposition of co-occurrence probabilities, which are highest for microbial genera (arrows) pointing in the same direction as metabolites (dots). To recreate this panel one simply needs to drag and drop a biplot.qzv file into the qiime2 web visalizer
Follow this step-by-step description to recreate panel.

1. Open the qiime2 web-browser visualizer.
2. Drag and drop the mmvec_biplot.qzv file.
3. Drag and drop the mmvec_snapshot.json file to load the specific visualization settings that recreate the panel.

b)

This panel is plotting the normalized counts of sequencing reads taxonomically classsified to genus Paenibacillus. Similar to the other 3D plots, the visualization was creating with ili. To recreate this panel, one simply needs to drag and drop a 3D_model.stl file and a microbiome_feature_table.csv file into the ili chrome extension.
Follow this step-by-step description to recreate this panel.

1. Open the ili chrome extension. Familiarize yourself with the GUI.
2. Drag and drop the 3D_model.stl file and let it load and render.
3. Drag and drop the T2_microbiome_feature_table.csv file and let the application load and render.
4. Drag and drop g__Paenibacillus_snapshot.json file to load the specific feature with the appropriate visualization settings to recreate figure panel.