image.biom: Display heatmap of BIOM data with optional dendrograms

In matR: Metagenomics Analysis Tools

Description

Display heatmap of a biom object with optional row and column dendrograms.

Usage

## S3 method for class 'biom'
image(x, ..., map=NULL, rows=TRUE, columns=TRUE, rerender=NULL)

Arguments

x	an object (biom)
...	arguments to gplots::heatmap.2()
map	assignment of par variables to metadata (character)
rows	subselection of rows (integer, character, or logical)
columns	subselection of columns (integer, character, or logical)
rerender	previous computation to reuse in this call (heatmap, dclust, list, or dist)

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.

Note

The function image() is declared S3 generic in the base package graphics. The method documented here does not apply any existing methods, however, but rather relies on entirely different libraries for computation and graphical rendering. See reference below.

Author(s)

Daniel T. Braithwaite and Kevin P. Keegan

See Also

gplots::heatmap.2, BIOM.utils::biom

Examples

####  simple heatmap; using log transformation makes interesting things more apparent
image (xx2)
xx2t <- transform (xx2, t_Log)
image (xx2t, labCol="$$project.id")

####  clustering analysis restricted to Archaea
image (xx2t, labCol="$$project.id", rows=rows(xx2t,"taxonomy1")=="Archaea")

####  clustering analysis restricted by significance test p values
p <- rowstats (xx2t, test="t-test-unpaired", groups="$$material") $ p.value
p [is.na(p)] <- p [is.nan(p)] <- FALSE
image (xx2t [rows = p < 0.05, ], labCol="$$material")

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 c71ee9)

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