RAM (version 1.2.1.3)

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

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.

Value

This function returns a barplot.

Details

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

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)