chmAddUMAP: Add UMAP coordinates to an NG-CHM.

In bmbroom/NGCHMR: Utilities for Creating 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

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

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