SpatialSegment-class: The 'SpatialSegment' - Class

In kueckelj/SPATA2: A Toolbox for Spatial Gene Expression Analysis

The SpatialSegment - Class

Description

Abstracts the concept of an annotated segment within a spatial segmentation.

Slots

info

list. Stores meta data and miscellaneous information regarding the spatial segment. Slots that should always exist:

• image_origin: Character string. Content of slot @info$origin of the HistologyImaging at the time the segment was drawn.

• parent_id: Character string. The ID of the spatial segmentation this segment is part of.

• pot: POSIXct. The point of time when the segment was drawn. Used to handle overlapping segments.

• sample: Character string. The name of the sample (slot @sample of the SPATA2 object.)

label

character. Character string. The label that was given to the segment. Corresponds to the group name of the barcode-spots that fall into the segment.

polygons

list. List of data.frames with x and y variables that contain the vertices of the polygon. The first polygon (should be named outer) defines the outer ring of the segment. Further polygons (should be named inner suffixed with a number) define holes within the segment.

kueckelj/SPATA2 documentation built on March 16, 2024, 10:25 a.m.