romic 1.3.3

Minor Improvements and Fixes

• Docstring cleanup and wrapping imputation function in dontrun since impute may not be installed from Bioconductor.

romic 1.3.2

Minor Improvements and Fixes

• upgraded defunction mutate_ call #7
• upgraded mutate_at, mutate_if, select_if, etc to use mutate/select and across
• improved warnings and errors by switching to cli

romic 1.3.1

Minor Improvements and Fixes

• updated pkgdown site deployment and link urls.

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 1.1.3

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 1.1.1

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