group.diversity: Boxplot To Compare Diversity Indices Among Groups

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

Description

This function first use OTU.diversity to calculate the diversity indices for each sample and then do a boxplot to compare the selected indices among different groups.

Usage

group.diversity(data, meta, factors="", indices="",
                diversity.info=FALSE,
                x.axis=NULL, compare=NULL,
                facet=NULL, facet.y=TRUE, facet.x.cex=NULL,
                facet.y.cex=NULL, scale.free=NULL,
                xlab=NULL, ylab=NULL,
                legend.title=NULL, legend.labels=NULL,
                file=NULL, ext=NULL, width=8, height=8)

Arguments

data	a list, containing otu tables. See also RAM.input.formatting
meta	the metadata table to be used (must have same samples as data.
factors	a character vector. Must be variables in the metadata
indices	a character vector. Must be one or more of the following: "spec", "sim", "invsim", "shan", "sim_even", "shan_even", "sim_trudiv", "shan_trudiv", "chao", "ACE". See also OTU.diversity, true.diversity, evenness, and diversity.
diversity.info	logical. Whether the diversity indices have calculated and included in the metadata table. The diversity indices should be processed by OTU.diversity for the same otu tables and metadata table.
x.axis	optional. If NULL, will use the first variable in factors; otherwise, must be one factor in the metadata or 'SampleID'
compare	optional. If NULL, will use the first variable in factors; otherwise, must be one factor in the metadata
facet	optional. If provided, must be one factor in the metadata or 'SampleID'
facet.y	logical, whether the facet being used as strip text of y axis or x axis.
facet.x.cex	optional, an integer, the font size of the stip.text.x in ggplot
facet.y.cex	optional, an integer, the font size of the strip.text.y in ggplot.
scale.free	optional. Whether use free scale for y axis.
xlab	optional. If not provided, the x.axis will be used as the title of the x axis, otherwise, will use the provided string.
ylab	optional. If not provided, "value" will be used as the title of the y axis, otherwise, will use the provided string.
legend.title	optional. If not provided, compare will be used as the title of the legend, otherwise, will use the provided string.
legend.labels	optional. If not provided, will use the levels of compare for the legends, otherwise, will use the provided vector of strings. The length of the provided vector of strings must equals to the levels of compare.
file	the filename to save the plot.
ext	the extention (file type) of the plot to saved.
width	the width of the plot to be saved.
height	the heigth of the plot to be saved.

Value

This function returns a boxplot to compared selected diversity indices among different groups.

Author(s)

Wen Chen.

See Also

OTU.diversity, true.diversity, evenness and diversity

Examples

data(ITS1, ITS2, meta)
## Not run: 
RAM.theme<-RAM.color()
group.diversity(data=list(ITS1=ITS1, ITS2=ITS2), meta=meta,
                factors=c("Crop", "City"),
                indices=c("sim_trudiv", "shan_trudiv"),
                x.axis="Crop", compare="Harvestmethod",
                facet="City", facet.y=FALSE) + RAM.theme

## End(Not run)

Example output

Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.4-4
Loading required package: ggplot2
sh: 1: cannot create /dev/null: Permission denied
sh: 1: cannot create /dev/null: Permission denied
Warning messages:
1: `axis.ticks.margin` is deprecated. Please set `margin` property  of `axis.text` instead 
2: `panel.margin` is deprecated. Please use `panel.spacing` property instead 
Using City, Crop, Harvestmethod, SampleID as id variables

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