NEWS
scider 1.10.0 (2026-04-25)
- Update help pages
- New function getHVG() to find top HVGs
- New function plotLISAscatter() to generate a LISA scatter plot
- New functions readVisium(), readVisiumHD(), readXenium(), readProseg() for reading in data of different types
- Use Matrix package for matrix operations
- Update gridDensity() to handle different types of input
- Speed up hexDensity computation
scider 1.8.0 (2025-10-30)
- Update help pages
- New function findNbrsGrid() to construct a neighbour list from grid coordinates
- New function findNbrsSNN() to construct a SNN neighbour list from assay
- New function findNbrsSpatial() to construct a distance-based neighbour list from cell coordinates
- New function getNiche() to build a niche assay based on the profile of neighbouring cells
- New function getClusters() to cluster cells in spe using graph methods
- New functions globalMoran() and localMoran() to calculate Moran's I statistics
- New function normalizeAssay() to perform spatial data normalization
- New function plotDR() for plotting reduced dimensions
- New functions plotImage() and plotLISA() for visualization
- New function realignVisium() to scale and straighten out Visium coordinates
- New functions runPCA() and runUMAP() for performing dimensionality reduction
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 spe@metadata 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 spe@metadata$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)
scider 0.99.0
- Initial submission to Bioconductor.