Releases: theMILOlab/SPATA2
Releases · theMILOlab/SPATA2
Version 3.1.0
Changes:
- Fixes spatialTrajectoryScreening() in case of missing capture areas.
- Improved precision in computing the capture area of Visium Experiments.
- Fixes bad polygon display in case of ggpLayerSpatAnnOutline() with
expand_outline = 0
. - Improved options and comfort in createSpatialSegmentation().
Additions:
- reduceResolutionVisiumHD() to create SPATA2 objects with individual VisiumHD resolution beyond the standard (16um, 8um and 2um).
- resizeImage() for memory friendly handling of large images.
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()
inidentifyTissueSections()
andidentifyTissueOutline()
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()
inidentifyTissueSections()
andidentifyTissueOutline()
- 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 toggpLayerGroupOutline()
- 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 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.)