matR (version 0.9.1)

boxplot.biom: Summarize BIOM data in boxplots

Description

Summarize distribution of a biom object in columnwise boxplots.

Usage

# S3 method for 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)

Value

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

Details

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

See Also

graphics::boxplot, BIOM.utils::biom

Examples

# NOT RUN {
####  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")
# }