DPT-matrix-methods: DPT Matrix methods

In theislab/destiny: Creates diffusion maps

DPT Matrix methods

Description

Treat DPT object as a matrix of cell-by-cell DPT distances.

Usage

## S4 method for signature 'DPT,index,index,logicalOrMissing'
x[i, j, ..., drop = TRUE]

## S4 method for signature 'DPT,index,missing,logicalOrMissing'
x[i, j, ..., drop = TRUE]

## S4 method for signature 'DPT,missing,index,logicalOrMissing'
x[i, j, ..., drop = TRUE]

## S4 method for signature 'DPT,missing,missing,logicalOrMissing'
x[i, j, ..., drop = TRUE]

## S4 method for signature 'DPT,index,index'
x[[i, j, ...]]

## S4 method for signature 'DPT'
nrow(x)

## S4 method for signature 'DPT'
ncol(x)

## S4 method for signature 'DPT'
dim(x)

Arguments

x	DPT object.
i, j	Numeric or logical index.
...	ignored
drop	If TRUE, coerce result to a vector if it would otherwise have 1 %in% dim(result).

Value

[ returns a dense matrix or (if applicable and isTRUE(drop)) a vector.

[[ returns single distance value

nrow and ncol return the number of cells

dim returns c(n_cells, n_cells)

See Also

as.matrix.DPT

Examples

data(guo_norm)
dm <- DiffusionMap(guo_norm)
dpt <- DPT(dm)
set.seed(1)
plot(dpt[random_root(dpt), ], Biobase::exprs(guo_norm)['DppaI', ])

theislab/destiny documentation built on Jan. 27, 2024, 9:57 p.m.