chmAddReducedDim: Add Single Cell reduced dimension coordinates to an NG-CHM.

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

Add Single Cell reduced dimension coordinates to an NG-CHM.

Description

Add SingleCellExperiment::reducedDim or Seurat reduced dimension coordinates from a single cell object sce as hidden covariate bars to an axis of an NG-CHM. dimName specifies the name of the reduced dimension of interest in sce. One hidden covariate bar is added for each coordinate. If specified, maxDim limits the maximum number of covariate bars added to the chm. Coordinates have names 'BASENAME.coordinate.N', where BASENAME is specified by the parameter basename (defaults to dimName if omitted) and N ranges from 1 to the number of added covariate bars.

Usage

chmAddReducedDim(hm, axis, sce, dimName, maxDim, basename, dimAxis)

Arguments

hm	The NGCHM to add the coordinates to.
axis	The NGCHM axis ("row" or "column") to add the coordinates to.
sce	An object containing the reduced dimension.
dimName	The name of the reduced dimension to create covariate bars for.
maxDim	The maximum number of coordinates to add (default all).
basename	The prefix to use for the coordinate names (defaults to dimName).
dimAxis	The axis on the sce object containing the named dimension.

Value

The NGCHM with added coordinates.

See Also

chmAddPCA()

chmAddTSNE()

chmAddUMAP()

chmAddUWOT()

Examples

hm <- chmAddReducedDim(hm, "column", sce, "PCA", 3, "PC");
hm <- chmAddReducedDim(hm, "column", sce, "TSNE");

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