• Description

  • This script is used for correlation analysis between taxa abundance and phenotypic data, and visulization.

  • There are two types of environmental, clinical or phenotypic data, numerical and binary variables.

  • For numerical variables, simply correlation such as spearman or pearson coefficient was caculated.

  • For binary variables, they can be as factors or groups for wilcox test, then the W-statistics and p-value can be acquired and visualized.

• Dependencies

  • "vegan","ggplot2","psych", "pheatmap", "plyr", "optparse"

• Example

  See example file

  Rscript corr.stat.plot.r --help
  

  Rscript corr.stat.plot.r --taxa_abund cag.abundance.matrix.xls --pheno clinical_data.xls --taxa_info map.txt --outdir output 1>1.log 2>2.log