NGCHM {NGCHM}

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.

Note:

• chmNew() requires git to be installed.

• chmExportToFile(), chmExportToHTML(), and chmExportToPDF() require Java 11 and the NGCHMSupportFiles package. The NGCHMSupportFiles package can be installed with:
  
  install.packages('NGCHMDemoData',
repos = c('https://md-anderson-bioinformatics.r-universe.dev',
'https://cloud.r-project.org'))

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

# Examples using `chmNew()` require git to be installed.
# The NGCHMSupportFiles package is required by chmExportToFile and chmExportToPDF
# The NGCHMDemoData package is used to create a demo NGCHM
## Not run: 
  if (requireNamespace("NGCHMSupportFiles", quietly = TRUE)) {
    if (requireNamespace("NGCHMDemoData", quietly = TRUE)) {
      library(NGCHMSupportFiles)
      library(NGCHMDemoData)
      data(TCGA.GBM.EXPR, package = "NGCHMDemoData")
      chm1 <- chmNew("gbm", TCGA.GBM.EXPR[1:50, 1:50],
        rowAxisType = "bio.gene.hugo",
        colAxisType = "bio.tcga.barcode.sample.vial.portion.analyte.aliquot"
      )
      chmExportToFile(chm1, tempfile("gbm", fileext = ".ngchm"))
      chmExportToPDF(chm1, tempfile("gbm", fileext = ".pdf"))
    }
  }
  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)
  chmSetCollection("//server/collection")
  chmInstall(chm)

## End(Not run)