chmAddUMAP: Add UMAP coordinates to an NG-CHM.

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

Add UMAP coordinates to an NG-CHM.

Description

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

Usage

chmAddUMAP(hm, axis, umap, basename = "UMAP")

Arguments

hm	The NGCHM to add the coordinates to.
axis	The NGCHM axis ("row" or "column") to add the coordinates to.
umap	TSNE coordinates (output of umap::umap()) for the specified NGCHM axis.
basename	The prefix to use for the coordinate names.

Value

The NGCHM with added coordinates.

See Also

chmAddPCA()

chmAddTSNE()

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")
    mat <- TCGA.GBM.EXPR[1:50, 1:50]
    umc <- umap::umap(t(mat))
    hm <- chmNew("gbm", mat)
    hm <- chmAddUMAP(hm, "column", umc)
  }
  # Small example not requiring NGCHMDemoData
  matrix <- matrix(rnorm(100),
    nrow = 10, ncol = 10,
    dimnames = list(paste0("r", 1:10), paste0("c", 1:10))
  )
  umc <- umap::umap(t(matrix), n_neighbors = 8)
  hm <- chmNew("Demo UMAP", matrix)
  hm <- chmAddUMAP(hm, "column", umc)

## End(Not run)

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