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Changelog

Source: NEWS.md

Version 1.7.2 (07/30/2024)

  • Fixed bug that caused error when computing Lee’s L on DelayedArray

Version 1.7.1 (07/16/2024)

  • Revamped user interface of plotGeometry to allow plotting multiple col, row, and annot geometries at once
  • Allow plotting transcript spots in plotGeometry, plotSpatialFeature, plotLocalResult, and spatialReducedDim

Version 1.6.0 (04/29/2024)

  • Option to plot polygon geometry without fill in plotGeometry
  • Option to show axes in both light and dark themes
  • Plot images of classes BioFormatsImage and ExtImage
  • Colorize image plot with different channels
  • Assign different grayscale images to channels
  • Added plotImage to only plot image without plotting geometry

Version 1.3.1 (05/15/2023)

  • Removed functions and arguments deprecated in 1.2.0

Version 1.2.7 (09/19/2023)

  • Polygon boundaries will show despite linewidth = 0 for Windows users. Set color = NA for polygons if linewidth = 0 so default will work for Windows.

Version 1.2.6 (09/19/2023)

  • Fixed bug in plotColGraph when one out of multiple samples is plotted.
  • Allow 16 bit images in spatial plotting functions.
  • Removed adespatial from Suggests as it’s only used as a reference in unit tests and it got removed from CRAN.

Version 1.2.5 (08/18/2023)

  • Use imgRaster getter rather than the S4 no-no of @image to get images to plot, as the latter will no longer work as of SFE 1.2.3 that wraps SpatRaster images when saving RDS. Reading RDS won’t unwrap so images need to be unwrapped when they’re needed.

Version 1.2.4 (07/04/2023)

  • Remove useNames = NA warning when calling MULTISPATI; the warning comes from generic of colVars.
  • Use algebraic eigenvalues for MULTISPATI when either nfposi or nfnega is 0
  • Added bins_contour argument to moranPlot to change the number of bins in cell density contours

Version 1.2.3 (05/04/2023)

  • Fix bug when plotting a feature with illegal name alongside another feature with legal name
  • Make sure runBivariate and calculateBivariate use gene symbols in results even if Ensembl IDs are specified when swap_rownames is set
  • Change secondary sequential palette in the light theme to YlOrRd so it’s more distinguishable from the Blues primary palette at low values

Version 1.2.2 (04/26/2023)

  • Some minor bugs: runBivariate gets correct feature names when only feature1 is specified and swap_rownames is used to show gene symbol
  • Correct output for cross variogram maps for only one pair of genes
  • Added default_attr to localmoran_bv’s SFEMethod
  • Don’t plot attribute when localResult is a vector and there’s no default attr
  • When plotting multiple features, the panels follow the same order the features are specified
  • Allow illegal characters in names of colData and reducedDims in plots
  • Plot only one component in spatialReducedDim with the components argument
  • Deprecate plotColDataBin2D and plotRowDataBin2D

Version 1.1.12 (04/22/2023)

  • Plot image behind geometries in all functions that plot geometries
  • Added dark theme support for functions that plot geometries

Version 1.1.11 (04/05/2023)

  • Added MULTISPATI PCA
  • Added multivariate local Geary’s C from Anselin 2019
  • Added calculateMultivariate as a unified user interface to multivariate spatial analyses
  • Variogram and variogram map with gstat and related plotting functions
  • Allow non-standard names for local results in plotLocalResult

Version 1.1.10 (03/07/2023)

  • Record parameters used to get spatial results
  • Force users to use a new name when running the same method with different parameters

Version 1.1.9 (02/12/2023)

  • Deprecated show_symbol argument, replacing with swap_rownames to be consistent with scater

Version 1.1.7

  • Added bbox argument to spatial plotting functions to zoom in with a bounding box

Version 1.0.10 (02/23/2023)

  • Added plotColDataFreqpoly when the y axis needs to be log transformed. That doesn’t work with stacked histograms and using position = “identity” causes some bars to be covered.

Version 1.0.9 (02/03/2023)

  • Fixed the bug of hardcoded ncol in plotDimLoadings.

Version 1.0.8 (01/26/2023)

  • Flipped the divergent palettes so the warm color means high value.

Version 1.0.7 (01/11/2023)

  • Fixed bug with assigning local results for each sample for colData, colGeometry, and annotGeometry.

Version 1.0.5 (12/02/2022)

  • Removed aes_string(), which is deprecated.
  • Fixed bug when show_symbol = TRUE and “symbol” column is absent from rowData.

Version 1.0.0 (11/02/2022)

  • First version on Bioconductor
  • Univariate local and global spatial statistics based on spdep
  • Plotting functions: gene expression and metadata in space, results of local spatial analyses, plot dimension reductions in space, and plot correlograms and Monte Carlo simulation results