Create an S4 dimObj
Usage
createDimObj(
coordinates,
name = "test",
spat_unit = "cell",
feat_type = "rna",
method = NULL,
reduction = "cells",
provenance = NULL,
misc = NULL,
my_rownames = NULL
)Arguments
- coordinates
embedding coordinates
- name
name of dimObj
- spat_unit
spatial unit of aggregated expression (e.g. 'cell')
- feat_type
feature type of aggregated expression (e.g. 'rna', 'protein')
- method
method used to generate dimension reduction
- reduction
reduction on columns (e.g. cells) or rows (e.g. features)
- provenance
origin data of aggregated expression information (if applicable)
- misc
misc
- my_rownames
(optional) if needed, set coordinates rowname values here
Examples
x <- matrix(c(2.81, 5.59, 10.54, 2.25, 5.12, 2.79), nrow = 3)
rownames(x) <- c("cell_1", "cell_2", "cell_3")
colnames(x) <- c("Dim.1", "Dim.2")
createDimObj(coordinates = x, name = "pca", method = "pca")
#> An object of class dimObj : "pca"
#> --| Contains dimension reduction generated with: pca
#> ----| for feat_type: rna
#> ----| spat_unit: cell
#>
#> 2 dimensions for 3 data points
#>