v2.2.0

• Fixed make_line_plot() bugs (#273)
• Fixed get_exprs_avg() when cell types have underscores in their names (#274)
• Bug fixes for assign_ligands_to_celltype() (#275, #277)
• Fixed mistakes in generate_info_tables() (grouping metadata and filtered lr network) (#279)
• Replaced the GitHub Actions workflow file with something simpler (.github/workflows/check-standard.yaml) (#290)
• Removed limma from the list of dependencies (#290)
• Updated alias_to_symbol_seurat() (#299)
• Changed defaults of generate_prioritization_tables(): activity_scaled weight is set to 1 by default, and the cell type specificity weights are downweighted (#300)
• Modified make_mushroom_plot (see #300)

v2.1.0

• tidyverse is now a dependency
• New helper functions:
     - General: get_weighted_ligand_receptor_links, prepare_ligand_receptor_visualization, make_line_plot
     - Circos plot/chord diagram: assign_ligands_to_celltype, get_ligand_target_links_oi, prepare_circos_visualization, make_circos_plot
     - Prioritization: generate_info_tables
• Changes to existing functions:
     - get_lfc_celltype: removed expression_pct parameter, replaced with ... where arguments can directly be provided to Seurat::FindMarkers
     - get_ligand_signaling_path: added minmax_scaling parameter to scale the weights of signaling and regulatory networks
     - make*_heatmap_ggplot: returned plot no longer replaces hyphens with dots
     - make_mushroom_plot: additional ... parameter to pass arguments to ggplot2::theme
     - make_circos_lr: added separate_legend parameter to determine whether the plot and legend are returned as separate objects
     - Added nsga2R optimization functions, renamed old model evaluation functions of mlrMBO
     - calculate_de: default values changed from NA to NULL
     - get_exprs_avg: default values changed from NA to NULL; additional ... parameter to pass arguments to Seurat::AverageExpression
     - generate_prioritization_tables: added scenario parameter
• Revised vignettes for readability
• parameter_optimization vignette now contains code on how to submit the job to a computing cluster
• Added new vignette on using LIANA to construct the lignad-receptor network part of the prior model

v2.0.5

• Fixed get_expressed_genes compability issue with Seurat v5

v2.0.4

Bug fixes:

• Compatibility issue with Seurat v5
• Subsetting bug with calculate_de

v2.0.1

Minor fixes, added some documentation.

v2.0.0

All vignettes have been updated to use the new ligand-target model. We included new functions for prioritizing ligand-receptor interactions.

v1.1.1

Fix hard-coded parameter bug