NGCHM-package: Next Generation Clustered Heat Map (NGCHM) Construction...

NGCHMR Documentation

Next Generation Clustered Heat Map (NGCHM) Construction Library

Description

NGCHM provides tools for defining the contents of a new NGCHM, and for compiling and installing it on a NGCHM server.

Details

Typical usage (see example) is to create a base NGCHM using chmNew; extend it with at least one ngchmLayer; typically extend it further with an additional ngchmLayer, row and column dendrograms, classification bars, and popup menu entries; compile and install it on an available ngchmServer.

Initialization

When first loaded the NGCHM library reads configuration files in the directories specified by the NGCHMCONFIGPATH environment variable. This is a colon (:) separated list of directory names. If not set it defaults to /etc/ngchm:/usr/local/ngchm:/opt/ngchm:$HOME/.ngchm. See NGCHM-initialization for details.

See Also

chmNew()

chmAdd()

chmExportToFile()

chmExportToPDF()

chmSetCollection()

chmInstall()

ngchm

Examples

data(TCGA.GBM.EXPR)
chm1 <- chmNew('gbm', TCGA.GBM.EXPR[1:50,1:50], rowAxisType='bio.gene.hugo', colAxisType='bio.tcga.barcode.sample.vial.portion.analyte.aliquot');
## Not run: chmExportToFile(chm1, 'gbm.ngchm');
chmExportToPDF(chm1, 'gbm.pdf');

## End(Not run)

mat <- matrix(rnorm(100),nrow=10)
rownames(mat) <- sprintf ("ABCA%d", 1:10)
colnames(mat) <- sprintf ("Sample%d", 1:10)
chm <- chmNew ('my-chm', mat)
## Not run: chmSetCollection ('//server/collection')
chmInstall (chm)

## End(Not run)

bmbroom/NGCHMR documentation built on April 18, 2022, 6:52 p.m.