• Description:

  This analysis tool was develeped for KEGG enrichment analysis according to the published article "Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life".

• Dependencies of R packages

  optparse, ggplot2

• For pathway enrichment caculation:

  Rscript caculate_reporter_score.R --group group.list --abund KO.rela.xls --type pathway --outdir pathway

• For module enrichment caculation:

  Rscript caculate_reporter_score.R --group group.list --abund KO.rela.xls --type module --outdir module

  This command will generate two files "stat.ko.res.xls" and "reporter_score.xls". More result interprations, please see the published article.

• Visualization:

  Rscript plot_reporter.score.R pathway/reporter_score.xls pathway/

  Rscript plot_reporter.score.R module/reporter_score.xls module/