top.groups.plot: Plot the Top Taxon Groups

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

Description

These functions consume two OTU tables, along with (optionally) a file name and a parameter top. They create a box plot of the top number of OTUs (for plot.top.number), or all OTUs with relative abundance above top percent (for plot.top.percent) at the taxonomic ranks phylum, class, order, family, and genus.

Usage

group.top.number(data, top=10, ranks=c("p","c","o","f","g"),
                 drop.unclassified=FALSE, cex.x=NULL,
                 main=NULL,file=NULL, ext=NULL, height=8, 
                 width=16, bw=FALSE, ggplot2=TRUE)
group.top.percent(data, top=10, ranks=c("p","c","o","f","g"),
                  drop.unclassified=FALSE, cex.x=NULL,
                  main=NULL, file=NULL, ext=NULL, height=8,
                  width=16, bw=FALSE, ggplot2=TRUE)

Arguments

data	a list of OTU tables.
top	the number of OTUs to select (for top.number), or the minimum relative abundance threshold to use for selecting OTUs (for top.percent).
ranks	a vector of the taxonomic ranks. See also RAM.rank.formatting
drop.unclassified	logical. Should OTUs labelled "unclassified" or missing classification at the given taxonomic rank be excluded?
cex.x	optional. The size of the x axis names.
main	the title of the plot
file	the file path where the image should be created (see ?RAM.plotting).
ext	the file type to be used; one of "pdf", "png", "tiff", "bmp", "jpg", or "svg".
height	the height of the image to be created (in inches).
width	the width of the image to be created (in inches).
bw	logical. Should the image be created in black and white?
ggplot2	logical. Should the ggplot2 package be used to produce the plot, or should the base graphics be used? (see ?RAM.plotting).

Note

Please be aware that the 'whiskers' in the plot may differ depending on the setting of ggplot2. Please see geom_boxplot boxplot, and boxplot.stats for more information on how the whiskers are calculated.

Author(s)

Wen Chen and Joshua Simpson.

See Also

RAM.plotting

Examples

## Not run: 
data(ITS1, ITS2)
# plots the top 10 OTUs (by default) at five ranks
group.top.percent(data=list(ITS1=ITS1, ITS2=ITS2), top=10)
# plots all OTUs w/ relative abundance > 10% (as specified) at
# five ranks and saves the result as a .tiff file
# (only using ITS1 data)
group.top.percent(data=list(ITS1=ITS1, ITS2=ITS2), top=10,
                 file="my/file/path", ext="tiff")
## End(Not run)

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