CovariatePlot: Plot trend lines of bacterial abundances against a continuous...
In katrikorpela/mare: Microbiota Analysis in R Easily

CovariatePlot

R Documentation

Plot trend lines of bacterial abundances against a continuous covariate

Description

The function plots the relative abundances of selected bacterial taxa against a continuous covariate.

Usage

CovariatePlot(meta, taxonomic.table, covariate, taxa, smooth.method = "loess", 
    readcount.cutoff = 0, select.by = NULL, select = NULL, pdf = F, logtrans = F, nozeros = F)

Arguments

`meta`	Name of the metadata file containing the covariate. Should be the name of a text file.
`taxonomic.table`	Name of the taxonomic table. Should be the name of a text file.
`covariate`	The covariate to plot against the bacterial taxa. Should be the name of a column in the metadata file.
`taxa`	A vector specifying the bacterial taxa that should be plotted.
`smooth.method`	Smoothing method to use. Options include 'lm' for a linear fit, and 'loess' for locally-weighted polynomial regression fit.
`readcount.cutoff`	Lowest acceptable read count per sample. Samples with fewer reads are ignored.
`select.by`	Name of a variable in the metadata file by which a subset will be selected for plotting.
`select`	Determines which value on the selection variable will be selected.
`pdf`	Should the figure be saved as pdf? If yes, specify TRUE.
`logtrans`	Should the bacterial abundances be log-transformed? TRUE or FALSE.
`logtrans`	Should zero values be omitted from the plot? TRUE or FALSE.

Author(s)

Katri Korpela

Examples

## Not run: 
#Plot the most abundant and prevalent genera against age, excluding samples with <2000 reads and 
#selecting only cases in treatment group 1.

CovariatePlot(meta = 'meta.txt',
              taxonomic.table = 'organised_genus_table.txt', 
              readcount.cutoff = 10000, 
              covariate = 'Age', 
              taxa = unlist(CommonTaxa(taxonomic.table = 'organised_genus_table.txt', 
              mean.abundance = 0.05, prevalence = 1)), 
              smooth.method = 'loess',
              select.by = 'Treatment', 
              select = '1')
	

## End(Not run)

katrikorpela/mare documentation built on July 17, 2022, 2:49 a.m.