BatchScale: Scale taxonomy summary plots (output of...

In econtijoch/Biomass-Workflow: Microbial Density Data Generation and Analysis Tools

Description

Scale taxonomy summary plots (output of summarize_taxa_through_plots.py of QIIME) by biomass

Usage

BatchScale(biomass_file, taxonomy_directory, OutputPrefix = "Scaled",
  XAxisLabel = "Timepoint", YAxisLabel = "ug DNA per mg Fecal Pellet",
  OutputDirectory = ".", batchName = "Sample", ...)

Arguments

biomass_file	input file that contains biomass data for each x-axis category of your summary plots
taxonomy_directory	path to directory that contains output of the QIIME funciton call
OutputPrefix	OPTIONAL: a string to append to the beginning of output files (default = 'Scaled')
XAxisLabel	OPTIONAL: a string to label x-axis of plots (default = 'Timepoint')
YAxisLabel	OPTIONAL: a string to label y-axis of plots (default = 'ug DNA per mg Fecal Pellet')
OutputDirectory	OPTIONAL: path to output directory (by default './')
batchName	OPTIONAL: string to label batch of plots (default = 'Sample')
...	Optional arguments

Value

a list that contains within it: a list of the scale taxonomy plots (at the various levels), and the scaled plots

econtijoch/Biomass-Workflow documentation built on May 15, 2019, 7:59 p.m.