Changelog

Source: NEWS.md

romic 1.3.0

Major changes

  • Removed plotly dependency due to plotly package retirement from CRAN #1
  • Removed interactive plotting functions [plot_heatmap]

New Features

  • Switched new primary repo to github.com/shackett/romic. github.com/calico/romic is now read-only
  • added calculate_sample_mahalanobis_distances to calculate the Mahalanobis distance of samples from the PC centroid Calico/#85
  • added tomi matrix export with tomic_to_matrix. Calico/#78

Minor Improvements and Fixes

  • Added invert arguments to filter_tomic Calico/#89
  • Allow for transposing axes when creating heatmaps. Calico/#81

romic 1.1.32023-09-21

New Features

  • get_tomic_table() makes it easy to pull individual tables out of tomic objects. Calico/#55

Minor Improvements and Fixes

  • Bug fix in add_pcs() Calico/#52
  • added option to not display percent variance explained on PCs to add_pcs() Calico/#53
  • Added passing of axis and colorbar labels in plot_heatmap() Calico/#60
  • Updated romic-package alias so package documentation properly displays with ?romic Calico/#63
  • Renamed tests and greatly expanded test coverage. Calico/#64

romic 1.1.12023-02-02

New Features

  • plot_bivariate() supports setting size, alpha, and shape. Calico/#48
  • add_pc_loadings() changed to add_pcs() for accuracy. Added fraction of variability explained by PCs to add_pcs(). Calico/#32
  • plot_univariate() and plot_bivariate() supporting providing a partial string match to a variable name. This helps to generate consistent plots even if names might change (like PC1 (10%)). Calico/#44
  • tidy_omics and triple_omics can now include a list with unstructured data. This puts the convention more in line with an H5AD file. #43. This is currently only used to return the fraction of variance explained by each PC as part of add_pcs(). Calico/#42

Minor Improvements and Fixes

  • plot_heatmap() rowlabels are suppressed when there are too many features rather than setting size to zero. Calico/#45
  • plot_heatmap() supports ordered objects. Calico/#37
  • coerce_to_classes() added support for glue objects. Calico/#35
  • Added additional checks to retain the class of primary keys and tests of coversions. Calico/#33