matR (version 0.9)

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

Description

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

Usage

"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)

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

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")