chmAddPCA {NGCHM} | R Documentation |
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 |
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
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)
[Package NGCHM version 1.0.3 Index]