chmAddUWOT: Add UWOT::UMAP coordinates to an NG-CHM.

In bmbroom/NGCHMR: Utilities for Creating Next Generation Clustered Heat Maps

Add UWOT::UMAP coordinates to an NG-CHM.

Description

Add UWOT::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

chmAddUWOT(hm, axis, uwot, pointIds, basename = "UMAP")

Arguments

hm	The NGCHM to add the coordinates to.
axis	The NGCHM axis ("row" or "column") to add the coordinates to.
uwot	UMAP coordinates (output of uwot::umap()) for the specified NGCHM axis.
pointIds	The NGCHM names for the data points in uwot
basename	The prefix to use for the coordinate names.

Details

pointIds is required because uwot::umap() 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 uwot::umap().

Value

The NGCHM with added coordinates.

See Also

chmAddPCA()

chmAddTSNE()

chmAddUMAP()

chmAddReducedDim()

Examples

umc <- uwot::umap(t(TCGA.GBM.EXPR));
hm <- chmNew ("gbm", TCGA.GBM.EXPR);
hm <- chmAddUWOT(hm, "column", umc, colnames(TCGA.GBM.EXPR));

bmbroom/NGCHMR documentation built on April 18, 2022, 6:52 p.m.