Add TSNE coordinates to an NG-CHM.

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

Usage

chmAddTSNE(hm, axis, tsne, pointIds, basename = "TSNE")

Arguments

hm

The NGCHM to add the coordinates to

axis

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

tsne

TSNE coordinates (output of Rtsne::Rtsne()) for the specified NGCHM axis

pointIds

The NGCHM names for the data points in tsne

basename

The prefix to use for the coordinate names.

Value

The NGCHM with added coordinates.

Details

pointIds is required because Rtsne::Rtsne() does not preserve the rownames of the data matrix it was applied to. Their values must match those on that axis of the NGCHM, but their order must match those in the data matrix passed to Rtsne::Rtsne().

See also

chmAddPCA()

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")
    mat <- TCGA.GBM.EXPR[1:10, 1:10]
    rtc <- Rtsne::Rtsne(t(mat), check_duplicates = FALSE, perplexity = 3)
    hm <- chmNew("gbm", mat)
    hm <- chmAddTSNE(hm, "column", rtc, colnames(mat))
  }
  # Small example not requiring NGCHMDemoData
  matrix <- matrix(rnorm(100),
    nrow = 10, ncol = 10,
    dimnames = list(paste0("r", 1:10), paste0("c", 1:10))
  )
  rtc <- Rtsne::Rtsne(t(matrix), check_duplicates = FALSE, perplexity = 3)
  hm <- chmNew("Demo TSNE", matrix)
  hm <- chmAddTSNE(hm, "column", rtc, colnames(matrix))
} # }