Add image annotations

Functions to add image annotations the SPATA2 object. For interactive drawing use createImageAnnotaions(). To set them with code use addImageAnnotation().

Not to confuse with createSegmentation().

addImageAnnotation(object, tags, area, id = NULL)

createImageAnnotations(object, ...)

Arguments

object

An object of class spata2.

tags

Character vector or NULL. If character, the tags for the image annotation selection. See section Selection of image annotation with tags for more information.

area

A named list of data.frames with the numeric variables x and y. Observations correspond to the vertices of the polygons that are needed to represent the image annotation. Must contain a slot named outer which sets the outer border of the image annotation. Can contain multiple slots named inner (suffixed) with numbers that correspond to inner polygons - holes within the annotation. If so, slot @mode should be 'Complex'.

...

Used to absorb deprecated arguments or functions.

Value

The input spata2 object containing the added or computed results.

Note

The interface allows to zoom in on the sample. This is useful if your spata object contains an HE-image as background and you want to classify barcode spots based on the histology. As these images are displayed by pixels the resolution decreases the more you zoom in. Many experiments (such as the Visium output) contain high resolution images. You can use the function exchangeImage() to read in images of higher resolution for a better histological classification.

See also

exchangeImage(), plotImageAnnotations(), getImageAnnotations()