boxplot.biom: Summarize BIOM data in boxplots

In 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")

Example output

Loading required package: MGRASTer
MGRASTer (0.9 02e288)
Loading required package: BIOM.utils
BIOM.utils (0.9 dbcb27)
matR: metagenomics analysis tools for R (0.9.1)
                   sample.data.material
mgm4440411.3                 freshwater
mgm4440412.3                 freshwater
mgm4440413.3                 freshwater
mgm4440414.3                 freshwater
mgm4440422.3                 freshwater
mgm4440423.3                 freshwater
mgm4440424.3                 freshwater
mgm4440439.3                 freshwater
mgm4440440.3                 freshwater
mgm4441095.3                 hot spring
mgm4441096.3                 hot spring
mgm4442583.3                 hot spring
mgm4443679.3                 freshwater
mgm4443680.3                 freshwater
mgm4443681.3                 freshwater
mgm4443682.3                 freshwater
mgm4443683.3                 freshwater
mgm4443684.3                 freshwater
mgm4443746.3 hot spring ; microbial mat
mgm4443747.3 hot spring ; microbial mat
mgm4443749.3 hot spring ; microbial mat
mgm4443750.3 hot spring ; microbial mat
mgm4443762.3 hot spring ; microbial mat
             env_package.data.sample_name library.data.sample_name
mgm4575333.3                          AR3                      AR3
mgm4575334.3                          BZ1                      BZ1
mgm4575335.3                          CL1                      CL1
mgm4575336.3                          DF1                      DF1
mgm4575337.3                        EB017                    EB017
mgm4575338.3                        EB019                    EB019
mgm4575339.3                        EB020                    EB020
mgm4575340.3                        EB021                    EB021
mgm4575341.3                        EB024                    EB024
mgm4575342.3                        EB026                    EB026
mgm4575343.3                          KP1                      KP1
mgm4575344.3                          MD3                      MD3
mgm4575345.3                          PE6                      PE6
mgm4575346.3                          SF2                      SF2
mgm4575347.3                          SV1                      SV1
mgm4575348.3                          TL1                      TL1
             sample.data.sample_name
mgm4575333.3                     AR3
mgm4575334.3                     BZ1
mgm4575335.3                     CL1
mgm4575336.3                     DF1
mgm4575337.3                   EB017
mgm4575338.3                   EB019
mgm4575339.3                   EB020
mgm4575340.3                   EB021
mgm4575341.3                   EB024
mgm4575342.3                   EB026
mgm4575343.3                     KP1
mgm4575344.3                     MD3
mgm4575345.3                     PE6
mgm4575346.3                     SF2
mgm4575347.3                     SV1
mgm4575348.3                     TL1
Warning message:
In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL'

matR documentation built on May 2, 2019, 6:53 a.m.