spata-class: spata object

In kueckelj/SPATA: A Toolbox for Spatial Gene Expression Analysis

spata object

Description

spata object

Value

S4 object

Slots

coordinates

A data.frame containing information about every barcode-spot. Must contain the variables:

barcodes

Character. The barcode-sequences (+ the sample belonging) of every barcode spot.

sample

Character. The sample belonging of every barcode-spot.

x

Numeric. The x-coordinates of every barcode.

y

Numeric. The y-coordinates of every barcode.

data

See documentation for S4-object 'data'

dim_red

See documentation for S4-object 'dim_red'

fdata

A data.frame containing the additionally computed features. Must contain the variables:

barcodes

Character. The barcode-sequences (+ the sample belonging) of every barcode spot.

sample

Character. The sample belonging of every barcode-spot.

image

A list of images named according to the samples the object contains.

samples

Character value. Contains the sample names.

scvelo

Currently not in use.

trajectories

A list named according to the samples the object contains. Each slot in that list contains another list of all 'spatial_trajectory'-objects created for that sample.

used_genesets

A data.frame containing the defined gene-sets. Must contain the variables:

ont

Character. The gene-set name.

gene

Character. The belonging genes.

version

A list of four slots denoting the version of SPATA under which the object has been created.

additional

A list of miscellaneous information that mainly ensures compatibility between different platforms.

kueckelj/SPATA documentation built on March 22, 2022, 9:59 p.m.