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NEWS
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Changes in version 0.1.0 (2019-09-17):
+ initial commit
Changes in version 0.2.0 (2019-11-28):
+ The functions calculateSummary, plotCellCounts, and plotDist have been added
Changes in version 0.3.0 (2021-05-07):
+ Added helper functions for spillover correction
+ Removed redundant functions
Changes in version 0.3.1 (2021-05-15):
+ readSCEfromTXT accepts list and path
Changes in version 0.3.2 (2021-05-16):
+ adjusted plotSpotHeatmap function and unit test
Changes in version 0.3.3 (2021-05-17):
+ unit tests for binAcrossPixels
Changes in version 0.3.4 (2021-05-18):
+ added readImagefromTXT function and tests
Changes in version 0.3.5 (2021-05-20):
+ unit tests and docs for filterPixels
Changes in version 0.3.6 (2021-06-04):
+ added read_steinbock function, docs and tests
Changes in version 0.3.7 (2021-06-14):
+ added read_cpout function, docs and tests
Changes in version 0.3.8 (2021-06-30):
+ Adjusted default parameters for read_steinbock function
+ Added updated test data
Changes in version 0.3.9 (2021-07-29):
+ Added buildSpatialGraph function
+ Added plotSpatial function
+ Added aggregateNeighbors function
Changes in version 0.3.10 (2021-08-18):
+ Added countInteractions function
+ Added testInteractions function
Changes in version 0.3.11 (2021-08-19):
+ Added flip_x, flip_y argument for plotSpatial function
+ readSCEfromTXT does not require spot names anymore
+ knn graph construction can be pruned by distance
+ added
Changes in version 0.3.12 (2021-09-01):
+ clean up for Bioconductor submission
Changes in version 0.99.0 (2021-09-14):
+ Bioconductor submission
Changes in version 0.99.7 (2021-10-10):
+ Added all unit tests
+ Fixed read_steinbock x/y axis defaults
Changes in version 0.99.8 (2021-10-11):
+ Added patch detection method
Changes in version 0.99.9 (2021-10-22):
+ Removed certain unit tests for 64-bit windows
Changes in version 1.1.1 (2021-11-16):
+ Bug fix in testInteractions: consider now all possible combinations of cell types
Changes in version 1.1.2 (2021-11-28):
+ Moved all helper functions to single script
Changes in version 1.1.3 (2021-12-15):
+ Bug fix: divide number of interactions by total number of cells for classic and patch interaction counting
Changes in version 1.1.4 (2021-12-23):
+ Added option to restrict the maximum distance between neighbors in delaunay triangulation
Changes in version 1.1.5 (2022-01-07):
+ More specific access of metal tags
Changes in version 1.1.6 (2022-01-12):
+ Bug fix: correctly index graphs when reading in steinbock data
Changes in version 1.1.7 (2022-03-30):
+ readSCEfromTXT: only read in last metal occurrence in .txt file name
Changes in version 1.1.8 (2022-04-03):
+ Adjusted read_cpout function to newest pipeline
Changes in version 1.1.9 (2022-04-19):
+ Bug fix: patchDetection now works on SpatialExperiment object
+ Fix for release
Changes in version 1.3.1 (2022-04-28):
+ Bug fix: avoid using factors in testInteraction function for group_by
Changes in version 1.3.2 (2022-05-30):
+ Bug fix: avoid duplication of metadata entries
Changes in version 1.3.3 (2022-06-03):
+ Bug fix: specify the number of nodes in patchDetection function
Changes in version 1.3.4 (2022-06-14):
+ Avoid duplicated columns when generating nodes for plotSpatial
Changes in version 1.3.5 (2022-06-15):
+ Added three spatial context functions
Changes in version 1.3.6 (2022-07-28):
+ new function to measure size of patch
Changes in version 1.3.7 (2022-08-11)
+ new function to measure minimal distances to cells of interest
Changes in version 1.3.8 (2022-10-13)
+ exclude a single validity check to to class changes in the ggraph package
Changes in version 1.3.9 (2022-10-14)
+ new function for spatial community detection
Changes in version 1.3.10 (2022-10-22)
+ fix axis.ratio to 1 in plotSpatial function and set scales = "fixed"
Changes in version 1.5.1 (2022-11-22)
+ fix axis.ratio to 1 in plotSpatial function and set scales = "fixed"
Changes in version 1.5.2 (2022-11-23)
+ Bug fix minDistToCells: return NA when all cells of an image belong to a patch
Changes in version 1.5.3 (2023-03-23)
+ Replaced merge function by left_join as safety measure
Changes in version 1.5.4 (2023-04-04)
+ Added option to get permutation counts returned from testInteractions
Changes in version 1.5.5 (2023-04-20)
+ Bug fix: in corner cases, levels of the permuted factors in the testInteractions function do not match the baseline.
+ Bug fix: testInteractions now works for cells that are not ordered by grouping level
+ Added explicitly message for some functions that the output is ordered by image
Changes in version 1.7.1 (2023-06-07)
+ More info on reproducibility using detectCommunity
Changes in version 1.7.3 (2023-06-20)
+ More info on reproducibility using testInteractions
Changes in version 1.7.4 (2023-08-09)
+ Bug fix: correctly setting the "aspect.ratio" argument in plotSpatial to fix the physical units of the x- and y-axis
Changes in version 1.7.5 (2023-09-14)
+ Added more internal validity checks for 'read_steinbock'
+ Changed the way messages in vroom are silenced
+ Stop allowing Object numbers to be different between intensities and regionprops
+ Stop allowing missing files in regionprops and neighbors
Changes in version 1.7.6 (2023-09-26)
+ Updated example data in "inst" to newest version
Changes in version 1.7.7 (2023-10-02)
+ Bug fix: in rare cases the testInteractions p-values were not correctly computed due to machine precision issues
Changes in version 1.7.8 (2023-10-19)
+ spatialCoords are not initialised with rownames anymore
Changes in version 1.9.1 (2023-11-20)
+ Switched from aes_ to .data
+ Initialise SPE and SCE objects with colnames
+ Additional test within binAcrossPixels
Changes in version 1.9.2 (2023-12-14)
+ maintainer change
Changes in version 1.11.1 (2024-10-03)
+ fixed BiocNeighbors error for DFrame type data
Changes in version 1.11.2 (2024-10-08)
+ fixed testInteraction and countInteraction tests due to machine precision issues
Changes in version 1.11.3 (2024-10-25)
+ fixed testdetectCommunity function
Changes in version 1.11.4 (2024-10-28)
+ changed testdetectCommunity function for group_by parameter