NEWS

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imcRtools 1.9.2 (2023-12-14)

• maintainer change

imcRtools 1.9.1 (2023-11-20)

• Switched from aes_ to .data
• Initialise SPE and SCE objects with colnames
• Additional test within binAcrossPixels

imcRtools 1.7.8 (2023-10-19)

• spatialCoords are not initialised with rownames anymore

imcRtools 1.7.7 (2023-10-02)

• Bug fix: in rare cases the testInteractions p-values were not correctly computed due to machine precision issues

imcRtools 1.7.6 (2023-09-26)

• Updated example data in "inst" to newest version

imcRtools 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

imcRtools 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

imcRtools 1.7.3 (2023-06-20)

• More info on reproducibility using testInteractions

imcRtools 1.7.1 (2023-06-07)

• More info on reproducibility using detectCommunity

imcRtools 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

imcRtools 1.5.4 (2023-04-04)

• Added option to get permutation counts returned from testInteractions

imcRtools 1.5.3 (2023-03-23)

• Replaced merge function by left_join as safety measure

imcRtools 1.5.2 (2022-11-23)

• Bug fix minDistToCells: return NA when all cells of an image belong to a patch

imcRtools 1.5.1 (2022-11-22)

• fix axis.ratio to 1 in plotSpatial function and set scales = "fixed"

imcRtools 1.3.10 (2022-10-22)

• fix axis.ratio to 1 in plotSpatial function and set scales = "fixed"

imcRtools 1.3.9 (2022-10-14)

• new function for spatial community detection

imcRtools 1.3.8 (2022-10-13)

• exclude a single validity check to to class changes in the ggraph package

imcRtools 1.3.7 (2022-08-11)

• new function to measure minimal distances to cells of interest

imcRtools 1.3.6 (2022-07-28)

• new function to measure size of patch

imcRtools 1.3.5 (2022-06-15)

• Added three spatial context functions

imcRtools 1.3.4 (2022-06-14)

• Avoid duplicated columns when generating nodes for plotSpatial

imcRtools 1.3.3 (2022-06-03)

• Bug fix: specify the number of nodes in patchDetection function

imcRtools 1.3.2 (2022-05-30)

• Bug fix: avoid duplication of metadata entries

imcRtools 1.3.1 (2022-04-28)

• Bug fix: avoid using factors in testInteraction function for group_by

imcRtools 1.1.9 (2022-04-19)

• Bug fix: patchDetection now works on SpatialExperiment object
• Fix for release

imcRtools 1.1.8 (2022-04-03)

• Adjusted read_cpout function to newest pipeline

imcRtools 1.1.7 (2022-03-30)

• readSCEfromTXT: only read in last metal occurrence in .txt file name

imcRtools 1.1.6 (2022-01-12)

• Bug fix: correctly index graphs when reading in steinbock data

imcRtools 1.1.5 (2022-01-07)

• More specific access of metal tags

imcRtools 1.1.4 (2021-12-23)

• Added option to restrict the maximum distance between neighbors in delaunay triangulation

imcRtools 1.1.3 (2021-12-15)

• Bug fix: divide number of interactions by total number of cells for classic and patch interaction counting

imcRtools 1.1.2 (2021-11-28)

• Moved all helper functions to single script

imcRtools 1.1.1 (2021-11-16)

• Bug fix in testInteractions: consider now all possible combinations of cell types

imcRtools 0.99.9 (2021-10-22)

• Removed certain unit tests for 64-bit windows

imcRtools 0.99.8 (2021-10-11)

• Added patch detection method

imcRtools 0.99.7 (2021-10-10)

• Added all unit tests
• Fixed read_steinbock x/y axis defaults

imcRtools 0.99.0 (2021-09-14)

• Bioconductor submission

imcRtools 0.3.12 (2021-09-01)

• clean up for Bioconductor submission

imcRtools 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

imcRtools 0.3.10 (2021-08-18)

• Added countInteractions function
• Added testInteractions function

imcRtools 0.3.9 (2021-07-29)

• Added buildSpatialGraph function
• Added plotSpatial function
• Added aggregateNeighbors function

imcRtools 0.3.8 (2021-06-30)

• Adjusted default parameters for read_steinbock function
• Added updated test data

imcRtools 0.3.7 (2021-06-14)

• added read_cpout function, docs and tests

imcRtools 0.3.6 (2021-06-04)

• added read_steinbock function, docs and tests

imcRtools 0.3.5 (2021-05-20)

• unit tests and docs for filterPixels

imcRtools 0.3.4 (2021-05-18)

• added readImagefromTXT function and tests

imcRtools 0.3.3 (2021-05-17)

• unit tests for binAcrossPixels

imcRtools 0.3.2 (2021-05-16)

• adjusted plotSpotHeatmap function and unit test

imcRtools 0.3.1 (2021-05-15)

• readSCEfromTXT accepts list and path

imcRtools 0.3.0 (2021-05-07)

• Added helper functions for spillover correction
• Removed redundant functions

imcRtools 0.2.0 (2019-11-28)

• The functions calculateSummary, plotCellCounts, and plotDist have been added

imcRtools 0.1.0 (2019-09-17)

• initial commit