/Class_Plot

Customized ChemRICH Plot for UCSD use.

Primary LanguageHTML

Class_Plot

Customized ChemRICH Plot for UCSD use.

Example Plot

Reference:

[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

Plot Intepretation

  • 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

input

  • 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]

output

  • 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]

To Run

  • Put input files into folder input_files
  • "RScript main.R"