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GiottoVisuals 0.2.14

bug fixes

  • allow coord_fix_ratio = TRUE usage again after ggplot2 changes

changes

  • change spatInSituPlotPoints() param spat_enr_names to spat_enr_name

enhancements

  • show_axes param for spatInSituPlotPoints()

GiottoVisuals 0.2.13 (2025/09/30)

bug fixes

  • update for removal of ggplot2::aes_string() in ggplot2 v4 #1192 by jdub0211

changes

  • replacement of argument radius by pie_scale in spatDeconvPlot() to modify pie size.

GiottoVisuals 0.2.12 (2025/05/06)

new

  • ridgePlot()

bug fixes

  • fix spatInSituPlotDensity() polygon_alpha default setting when polygons plotted last

enhancements

  • requested images not within the plotting window are now handled as warning instead of erroring
  • y_axis_title param added to plotMetaDataCellsHeatmap()
  • spatInSituPlotDensity() xlim/ylim now crops on polys
  • spatInSituPlotDensity() feature plotting via spatValues()retrieval

GiottoVisuals 0.2.11 (2025/01/17)

enhancements

  • improve efficiency of spatInSituPlotDensity()
  • use_overlap param for spatInSituPlotDensity() to allow the unoverlapped data to be used for density

bug fixes

  • fix color code/name checking to allow hex codes in cell_color plotting param.

GiottoVisuals 0.2.10 (2024/12/04)

bug fixes

  • fix missing e extent error during spatInSituPlotPoints() with show_image = TRUE introduced in v0.2.9 #96 by kunleng

GiottoVisuals 0.2.9 (2024/11/18)

bug fixes

  • spatInSituPlotPoints() xlim and ylim params now also affect image resampling

enhancements

  • group_by and group_by_subset for dimFeatPlot2D() #1069 by xhNorthwestern
  • image plotting will now scale values to the 99th percentile when a specific max intensity is not set.

GiottoVisuals 0.2.8 (2024/11/14)

enhancements

  • spatPlot3D() now works with non-categorical data. Uses same params as spatPlot2D() for color/gradient selection

changes

  • spatPlot3D() other_point_size default changed to 3 from 0.5 which was too hard to notice.

GiottoVisuals 0.2.7 (2024/11/08)

enhancements

  • scattermore plotting for spatPlot2D() and spatFeatPlot2D()

bug fixes

  • fix color scaling bug for spatFeatPlot2D() introduced in 0.2.6

GiottoVisuals 0.2.6 (2024/10/27)

new

  • combine_aes() for combining ggplot2 mappings in a last item wins manner. Allows more than 2 aes to be combined at the same time and provides an optional informative warning
  • gg_params() for combining and sorting ggplot2 mappings, toplevel params, and data into an arg list for plotting.

GiottoVisuals 0.2.5 (2024/09/27)

new

  • gpsparam() for generating an object containing plot saving parameters
  • cowplot::plot_grid() re-exported
  • dotPlot() visualization

bug fixes

  • fix coord_fix_ratio passing in spatFeatPlot2D() #972 by kaizen89

GiottoVisuals 0.2.4 (2024/07/26)

enhancements

  • giottoLargeImage max_window and colors slot info is now followed during ggplot plotting
  • giottoAffineImage compatibility for giotto ggplot2 plotting functions
  • gg_annotation_raster() now also performs geom_blank() with the extent provided through ext param. This can be turned off by setting geom_blank() = FALSE

new

  • geom_text_repel() and geom_label_repel() from ggplot2 are now re-exported

GiottoVisuals 0.2.3 (2024/05/28)

bug fixes

  • hotfix for sprintf numerics usage %d -> %f

GiottoVisuals 0.2.2 (2024/05/22)

breaking changes

  • option "giotto.color_c_pal" has been split into "giotto.color_cd_pal" and "giotto.color_cs_pal" for divergent and sequential continuous palettes

enhancements

  • some options are now initialized on library load to make them easier to access

GiottoVisuals 0.2.0 (2024/05/13)

changes

  • GiottoClass >= 0.3.0 is now required. (object no longer has @largeImages slot)
  • largeImage_name arg is deprecated. image_name arg should be used instead
  • spatial y dim values are not vertically plotted
  • deprecated spatDimGenePlot3D(), spatGenePlot3D(), dimGenePlot3D in favor of the 'feat' naming scheme

bug fixes

  • removed centroid point that unintentionally gets plotted in polygons

enhancements

  • theme_param arg has been added to some plotting functions that provides access to ggplot2::theme() finetuning
  • gg_annotation_raster() now performs plot extent detection and resampling of largeImages
  • resampling args are now globally settable (see ?auto_image_resample)
  • polygon_alpha default is now 1 when plotting polys without images, and 0.5 when plotting with images.

GiottoVisuals 0.1.7 (2024/03/11)

Changes

  • Change default values show_plot = NA, return_plot = NA, save_plot = NA -> show_plot = NULL, return_plot = NULL, save_plot = NULL.
  • Add examples to exported functions
  • Update License

GiottoVisuals 0.1.6 (2024/03/07)

bug fixes

  • fix spatPlot2D() and spatFeatPlot2D() largeImage plotting when using group_by
  • fix edge_alpha arg in spatFeatPlot2D()

new

  • mixRGB() vectorized additive mixing in RGB space
  • mixHSV() vectorized color mixing in HSV space

GiottoVisuals 0.1.4 (2024/01/25)

bug fixes

  • fix plotting color gradient when using arg point_shape = "no_border"
  • fix image NA value #865 by rbutleriii

new

  • gg_annotation_raster() internal generic for adding a giottoImage, giottoLargeImage, or list thereof to a ggplot object

GiottoVisuals 0.1.2 (2023/01/12)

bug fixes

  • fix ComplexHeatmap saving size issue #861 by rbutleriii

GiottoVisuals 0.1.1 (2023/12/16)

Breaking Changes

  • Removed: getDistinctColors() to GiottoUtils

Added

  • Add: getDistinctColors() and getRainbowColors() as re-exports from GiottoUtils

Changes

  • Changed: Package internal functions now have . prefix
  • Changed: GiottoUtils and GiottoClass moved to Imports
  • Changed: Other internal function naming changes to bring in line with updates to GiottoUtils

GiottoVisuals 0.1.0 (23/11/29)

Initial release