Version 2.0.0
Official release of SPATA2 Version 2.0.0
The website of the package has been updated with new tutorials and articles. Newly introduced concepts are explained in detail with the Code & Concept series.
Changes:
- The function
assessTrajectoryTrends()
has been renamed tospatialTrajectoryScreening()
. In combination with image annotation screening (see Additions:) the concept of spatial gradient screening has been wrapped in a set of functions with coherent nomenclature. The S4 classspatial_trajectory
has been supervised and is now calledSpatialTrajectory
. - Some functions and have been deprecated or deleted. Some arguments have been renamed or deleted. Find an overview as well as the replacement with
deprecatedInfo()
. Names of that list correspond to the deprecated functions or arguments. Values correspond to the replacement. - @slot images of the
spata2
object now contains an image container of classHistologyImaging
with a variety of new image based analysis and visualization options (see Additions: )
Additions:
- Introduction of the concept of image annotations to annotate histological microstructures and areas directly on the image
for group-independent analysis and gene screening. Spatial information regarding image annotations can be extracted with a variety ofgetImgAnn*()
functions. Observations in space (e.g. single cells) can be related to image annotations viarelateToImageAnnotation()
. - Introduction of image annotation screening as implemented in the function
imageAnnotationScreening()
and abbreviated with the acronym<fn.name>Ias<fn.name>
or<fn.name>IAS
. - Introduction of
ggpLayer*()
- functions. plotCnvHeatmap()
to visualize results frominfercnv
via ggplot2- An inbuilt system of spatial measures for intutitive and resolution independent working with distances in SI units (mm, um etc.)