NicheNet: predict active ligand-target links between interacting cells
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
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
parameterparameter_optimization
vignette now contains code on how to submit the job to a computing clusterget_expressed_genes
compability issue with Seurat v5Bug fixes:
calculate_de
Minor fixes, added some documentation.
All vignettes have been updated to use the new ligand-target model. We included new functions for prioritizing ligand-receptor interactions.