group.Taxa.box: Boxplot Of Taxa In Each Level of A Metadata Variable

In RAM: R for Amplicon-Sequencing-Based Microbial-Ecology

Description

This function do a boxplot to show the distribution of selected taxa in each level of a given metadata variable

Usage

group.Taxa.box(data, is.OTU=TRUE, rank="g", 
               taxa="", meta, meta.factor="",      
               cex.y=5, cex.x=5, cex.main=10,
               RAM.theme=NULL, col.pal=NULL, main="", 
               file=NULL, ext=NULL, height=8, width=16)

Arguments

data	a list of otu tables or taxonomic abundance matrices. See also RAM.input.formatting.
is.OTU	logical. If an OTU table was provided, is.OTU should be set as TRUE; otherwise, it should be set as FALSE.
rank	a single taxonomic rank. See also RAM.rank.formatting
taxa	a vector containing taxa names for plotting.
meta	the metadata table to be used (must have same samples as data.
meta.factor	a character string. Must be one of the metadata variables.
cex.y	size of y axis tick labels.
cex.x	size of x axis tick labels.
cex.main	size of title.
RAM.theme	customized ggplot_theme in RAM. See also ?theme_ggplot.
col.pal	color palettes to be used.
main	a character string. The title of the plot, default is an empty string.
file	filename to save the plot.
ext	filename extension, the type of image to be saved to.
width	an integer, width of the plot.
height	an integer, height of the plot.

Value

This function returns a boxplot of the distribution of seleted taxa within each level of a given metadata variable.

Author(s)

Wen Chen.

Examples

data(ITS1, ITS2, meta)
taxa <- c("Fusarium", "Alternaria", "Cladosporium")
group.Taxa.box(data=list(ITS1=ITS1, ITS2=ITS2), 
               is.OTU=TRUE, rank="g", 
               taxa=taxa, meta=meta, meta.factor="City")
## Not run: 
taxa.1 <- c("Fusarium", "Alternaria", "Cladosporium", 
            "Verticillium", "Kondoa")
group.Taxa.box(data=list(ITS1=ITS1, ITS2=ITS2), 
               is.OTU=TRUE, rank="g", 
               taxa=taxa.1, meta=meta, meta.factor="City")

## End(Not run)

Example output

Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.5-3
Loading required package: ggplot2
sh: 1: cannot create /dev/null: Permission denied
sh: 1: cannot create /dev/null: Permission denied
Using City, sample as id variables
Using City, sample as id variables
Using City, sample as id variables
Using City, sample as id variables
Using City, sample as id variables
Using City, sample as id variables
Using City, sample as id variables
Using City, sample as id variables
Warning messages:
1: In group.Taxa.box(data = list(ITS1 = ITS1, ITS2 = ITS2), is.OTU = TRUE,  :
  1 taxa are not in the ITS1 dataset
2: In group.Taxa.box(data = list(ITS1 = ITS1, ITS2 = ITS2), is.OTU = TRUE,  :
  1 taxa are not in the ITS2 dataset

RAM documentation built on May 2, 2019, 3:04 p.m.