boxplot.biom: Summarize BIOM data in boxplots

In MG-RAST/matR: Metagenomics Analysis Tools

Description

Summarize distribution of a biom object in columnwise boxplots.

Usage

## S3 method for class 'biom'
boxplot(x, y=NULL, ..., map=NULL, columns=TRUE)

Arguments

x	an object (biom)
y	optionally, a second object for comparison (biom)
...	arguments to graphics::boxplot()
map	assignment of par variables to metadata fields (character)
columns	subselection of columns (integer, character, or logical)

Details

Complete technical documentation is forthcoming. For the current preliminary release, please refer to the examples provided.

Value

Complete technical documentation is forthcoming. For the current preliminary release, please refer to the examples provided.

Author(s)

Daniel T. Braithwaite and Kevin P. Keegan

See Also

graphics::boxplot, BIOM.utils::biom

Examples

####  simple use
xx2t <- transform (xx2, t_Log)
boxplot (xx2t, main="log transformed data", notch=FALSE)

####  plotting raw and normalized against each other
columns (xx2t, "material")
boxplot (xx2t, xx2, x.main="log of data", y.main="raw data", map=c(col="material"),
  col=c("freshwater"="darkorange", "hot spring"="slateblue", 
  "hot spring ; microbial mat"="chocolate4"), notch=FALSE)

####  label by metadata
columns (xx4, "sample_name")
boxplot (transform (xx4, t_Log), names="$$sample.data.sample_name", notch=FALSE)

####  two normalizations plotted against each other
xx2tt <- transform (xx2, t_Threshold=list(entry.min=5), t_Log)
boxplot (xx2t, xx2tt, notch=FALSE, x.main="log transformation", 
  y.main="low counts removed, then log transformation")

MG-RAST/matR documentation built on May 8, 2019, 3:21 p.m.