chmAddPCA: Add PCA coordinates to an NG-CHM.

In MD-Anderson-Bioinformatics/NGCHM-R: Next Generation Clustered Heat Maps

Add PCA coordinates to an NG-CHM.

Description

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.
## Not run: 
  # 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)

## End(Not run)

MD-Anderson-Bioinformatics/NGCHM-R documentation built on April 1, 2024, 12:34 p.m.