chmAddTSNE: Add TSNE coordinates to an NG-CHM.

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

Add TSNE coordinates to an NG-CHM.

Description

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.

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().

Value

The NGCHM with added coordinates.

See Also

chmAddPCA()

chmAddUMAP()

chmAddUWOT()

chmAddReducedDim()

Examples

rtc <- Rtsne::Rtsne(t(TCGA.GBM.EXPR));
hm <- chmNew ("gbm", TCGA.GBM.EXPR);
hm <- chmAddTSNE(hm, "column", rtc, colnames(TCGA.GBM.EXPR));

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