Customized ChemRICH Plot for UCSD use.
[Barupal, D.K. and Fiehn, O., 2017. Chemical Similarity Enrichment Analysis (ChemRICH) as alternative to biochemical pathway mapping for metabolomic datasets Scientific Report 2017. (https://www.nature.com/articles/s41598-017-15231-w)
github: https://github.com/barupal/ChemRICH
- x-axis : median of the feature xlogp in the class
- y-axis : negative log of the class p-value
- color code : fold change ratio, i.e. ratio of feature of the class increased
- Feature Annotation File: [see input_files/test_plot.txt]
- T test result : [see input_files/t_test.csv]
- fold change result : [see input_files/fold_change.csv]
- static plot : [see plots/Plot_Classes_impact_plot.png]
- interactive plot : [see plots/Plot_Classes_interactive.html]
- table for plot : [see intermediate_files/fold_change.csv]
- table of features included in the plot : [see intermediate_files/features_included_in_plots.csv]
- table of features from input annotation file paired with xlogp: [see intermediate_files/with_xlogp.csv]
- Put input files into folder input_files
- "RScript main.R"