How to download how to run how to interpret accessing data

1. Download and expand the demo data here: https://drive.google.com/file/d/1cBw8ZyY703Z1S5httWJ_J7OStgMZPOnQ/view?usp=sharing
   Downloading and expanding to your Downloads folder is fine. If on a Mac, you can copy the filepath by selecting the expanded file and pressing Cmd-Opt-C. Keep that copied.

   These are the results files from a recent run on an unaligned dataset, which can be found here (in case you want that as well):

   Demo study page

   https://www.ebi.ac.uk/metabolights/editor/MTBLS1
   spectral matrix (auto-generated spectral matrix file extracted from processed data from MTBLS1)

   http://ftp.ebi.ac.uk/pub/databases/metabolights/studies/mariana/spectral_matrices/MTBLS1_nmrML_missing_spectralMatrix.RDS

2. Run this to start the app (replacing the path to the expanded results directory):

   browse_evidence('path_you_copied') # e.g. '/Users/mjudge/Downloads/mtbls1_demo'

Instructions:

• use the heatmap or the search box to select a compound with high scores (or compound of interest)
• select a spectral region of the PCRS, as well as some samples (a subset of high-scoring samples is usually best for the stackplot)
• a stackplot will appear with evidence for the selected peak plotted in blue
• pan and zoom in the PCRS window to move around the spectrum, or use the vshift slide bar to adjust the spacing in the stackplot