chmAddTSNE | R Documentation |
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.
chmAddTSNE(hm, axis, tsne, pointIds, basename = "TSNE")
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. |
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().
The NGCHM with added coordinates.
chmAddPCA()
chmAddUMAP()
chmAddUWOT()
chmAddReducedDim()
# 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[1:10, 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))
## End(Not run)
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