Version 3.0.3

Changes:

• fixes initiateSpataObjectVisium() for different chemistry versions of 10X
• introduces reduceResolutionVisiumHD() and individual adjustment of resolution during initiation with initiateSpataObjectVisiumHD()

Version 3.0.2

Changes:

• fixes normalizeCounts()

Version 3.0.1

Changes:

• fixes identifyTissueOutline(..., method = "image")
• updates documentation
• updates tutorials

Additions:

• reduceResolutionVisiumHD()
• ggpLayerGridVisiumHD()

Version 3.0.0

The release of SPATA2 v3.0.0, coinciding with the official publication of SPATA2:

Kueckelhaus, J., Frerich, S., Kada-Benotmane, J. et al. Inferring histology-associated gene expression gradients in spatial transcriptomic studies. Nat Commun 15, 7280 (2024). https://doi.org/10.1038/s41467-024-50904-x

Version 2.0.4

Changes:

• Fixes asSPATA2() for Giotto.
• Fixes order in which to install the packages in the article on how to install the package.
• Fixes article on image handling.
• Changes default clrp to 'sifre'. (Can always be changed with setDefault(object, pt_clrp = "...", clrp = "...") )
• Splits setTissueOutline() in identifyTissueSections() and identifyTissueOutline()

Additions:

• Uploads the tutorial on platform compatibility.

Version 2.0.3

Changes:

• Fixes crash of createSpatialSegmentation() and createImageAnnotation() when clicking on 'Zoom in'
• Fixes createSpatialTrajectories()
• Allows the option to set use_scattermore = FALSE in case of more tan 10.000 data points.
• Splits setTissueOutline() in identifyTissueSections() and identifyTissueOutline()
• Improves ggpLayerTissueOutline()

Additions:

• Adds the function mergeTissueSections() to deal with tissue sections that were mistakenly identified as non-contiguous

Version 2.0.2

Changes:

• Fixes runSeuratClustering()
• Adjusts ggpLayerScaleAxesSI() to be compatible with gradient line- and ridgeplots e.g. plotIasLineplot(), plotIasRidgeplot()

Additions:

• Adds bcsp_rm argument to ggpLayerGroupOutline()
• Adds ggpLayerHorizonIAS()

Version 2.0.1

Changes:

• Fixes initiateSpataObject_10X()

Additions:

• none

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 to spatialTrajectoryScreening(). 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 class spatial_trajectory has been supervised and is now called SpatialTrajectory.
• 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 class HistologyImaging 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 via relateToImageAnnotation().
• 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 from infercnv via ggplot2
• An inbuilt system of spatial measures for intutitive and resolution independent working with distances in SI units (mm, um etc.)

Version 1.0.0

First version release.