NGCHM | R Documentation |
NGCHM provides tools for defining the contents of a new NGCHM, and for compiling and installing it on a NGCHM server.
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.
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.
chmNew()
chmAdd()
chmExportToFile()
chmExportToPDF()
chmSetCollection()
chmInstall()
ngchm
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)
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