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Changelog

Source: NEWS.md

scider 1.4.0 (2024-10-30)

  • gridDensity() now supports hexagonal grids.
  • Make ‘grid.length.x’ = 100 by default in gridDensity() and remove the default value for ‘ngrid.x’.
  • New functions plotGrid() and gridSPE()
  • gridSPE() has an option to calculate grid-level count matrix for each cell type
  • Remove redundant argument ‘n’ in plotSpatial()
  • Rename ‘coi’ to ‘contour’, ‘all’ to ‘self.included’ in plotCellCompo()
  • Fixed a bug in plotContour() where ‘overlay’ is not working properly
  • Fixed a bug in corDensity() that produced NaN values
  • New argument ‘contour’ in allocateCells() allowing user to specify the contour levels for cell allocation. Default to all detected contours.
  • corDensity() can be run without running findROI(), and it returns a DataFrame instead of a list of DataFrames if no ROI detected.
  • New argument ‘probs’ added to plotDensity() for grid filtering when ROIs are not identified previously.
  • ‘equal.cell’ is set to TRUE by default in getContour().
  • plotContour() now plots contour for all the cells when ‘coi’ is NULL (by default).
  • When ‘coi’ contains multiple cell types, plotContour() looks for the corresponding contour in for plotting.
  • Added another option ‘none’ for ‘overlay’ in plotContour().
  • For multiple ‘coi’, getContour() now includes all coi in the contour labelling.
  • gridDensity() returns an extra column ‘density_overall’ in $grid_density.
  • plotDensity() plots overall cell density by default.
  • The default value of ‘probs’ in plotDensity() is now 0.5.
  • For multiple ‘coi’, plotDensity() now plots the total instead of average.
  • Fixed a ggtitle() bug in plotDensity() when ‘coi’ contains more than one cell type.
  • findROI() now use all cells (overall) by default.
  • coord_fixed for both plotDensity() and plotROI().
  • plotROI() now plots all the cells in the background when ‘roi’ is ‘overall’.
  • In corDensity(), ‘trace’ is now set to FALSE by default.
  • Fixed a bug in cellsInRegion() when there is only one ROI.
  • Fixed bugs in contour2sf() when no ‘areas_up’.
  • Converted cell numbers as a vector in spe2PB().
  • Fixed a bug in spe2PB() when the count table from spe is not matrix.
  • Fixed a bug in plotContour() to ensure exact match for cell types to avoid similar cell type names.

scider 1.2.0 (2023-10-30)

  • Bioconductor release.

scider 0.99.0

  • Initial submission to Bioconductor.