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