Add PCA coordinates to an NG-CHM.

Add PCA coordinates as hidden covariate bars to an axis of an NG-CHM. One hidden covariate bar is added for each PCA coordinate (up to ndim coordinates). Coordinates are given names 'BASENAME.coordinate.N', where BASENAME is specified by the parameter basename (default "PC") and N ranges from 1 to the number of added covariate bars.

Usage

chmAddPCA(hm, axis, prc, basename = "PC", ndim = 2)

Arguments

hm

The NGCHM to add the coordinates to.

axis

The NGCHM axis ("row" or "column") to add the coordinates to.

prc

Principal component coordinates (output of stats::prcomp()) for the specified NGCHM axis.

basename

The prefix to use for the coordinate names.

ndim

The maximum number of coordinates to add.

Value

The NGCHM with added coordinates.

See also

chmAddTSNE()

chmAddUMAP()

chmAddUWOT()

chmAddReducedDim()

Examples

# Examples using `chmNew()` require git to be installed.
if (FALSE) { # \dontrun{
  # If the NGCHMDemoData package is installed, use it to demo usage
  if (requireNamespace("NGCHMDemoData", quietly = TRUE)) {
   data(TCGA.GBM.EXPR, package = "NGCHMDemoData")
    prc <- prcomp(TCGA.GBM.EXPR[1:50, 1:50])
    hm <- chmNew("gbm", TCGA.GBM.EXPR[1:50, 1:50])
    hm <- chmAddPCA(hm, "column", prc)
  }
  # Small example not requiring NGCHMDemoData
  matrix <- matrix(rnorm(100),
    nrow = 10, ncol = 10,
    dimnames = list(paste0("r", 1:10), paste0("c", 1:10))
  )
  prc <- prcomp(matrix)
  hm <- chmNew("Demo PCA", matrix)
  hm <- chmAddPCA(hm, "column", prc)
} # }