group.Taxa.bar: Barplot Of Taxa Distribution In Groups

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

Description

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

Usage

group.Taxa.bar(data, is.OTU=TRUE, rank="g", taxa="",
               meta, meta.factor="", func="sum", cex.y=5, 
               cex.x=5, cex.main=10, bar.width=NULL, 
               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.
func	function to be used to aggregate count data, e.g. "sum" or "mean", default is "sum"
cex.y	size of y axis tick labels.
cex.x	size of x axis tick labels.
cex.main	size of title.
bar.width	width of bars
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.

Details

To use customized color palettes, must pass a vector of color names or hexadecimals. See examples for detail.

Value

This function returns a barplot.

Author(s)

Wen Chen

Examples

data(ITS1, ITS2, meta)
taxa <- c("Fusarium", "Alternaria", "Cladosporium")
group.Taxa.bar(data=list(ITS1=ITS1, ITS2=ITS2), is.OTU=TRUE,
               rank="g", taxa=taxa, meta=meta, 
               meta.factor="City", cex.y=5, cex.x=5, 
               bar.width=1, RAM.theme=RAM.color())
## Not run: 
# change default color schemes
col <- c("dodgerblue1", "darkcyan")
taxa.1 <- c("Fusarium", "Alternaria", "Cladosporium", 
            "Verticillium", "Kondoa")
group.Taxa.bar(data=list(ITS1=ITS1, ITS2=ITS2), is.OTU=TRUE,
               rank="g", taxa=taxa.1, meta=meta, 
               meta.factor="City", cex.y=5, cex.x=5, 
               bar.width=1, RAM.theme=NULL, col.pal=col)
group.Taxa.bar(data=list(ITS1=ITS1, ITS2=ITS2), is.OTU=TRUE,
               rank="g", taxa=taxa.1, meta=meta, 
               meta.factor="City", cex.y=5, cex.x=5, 
               bar.width=1, RAM.theme=NULL,
               col.pal=col, func="mean")
# change ggplot theme
group.Taxa.bar(data=list(ITS1=ITS1, ITS2=ITS2), is.OTU=TRUE,
               rank="g", taxa=taxa.1, meta=meta, 
               meta.factor="City", cex.y=5, cex.x=5, 
               bar.width=1, col.pal=col, RAM.theme=RAM.border())
# save the plot
group.Taxa.bar(data=list(ITS1=ITS1, ITS2=ITS2), is.OTU=TRUE,
               rank="g", taxa=taxa.1, meta=meta, 
               meta.factor="City", cex.y=5, cex.x=5, 
               bar.width=1, RAM.theme=NULL,
               col.pal=col,main="", file="path/to/filename.pdf",
               ext="pdf", height=8, width=16)

## End(Not run)

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