Releases: saeyslab/nichenetr
Releases · saeyslab/nichenetr
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
: removedexpression_pct
parameter, replaced with...
where arguments can directly be provided toSeurat::FindMarkers
-get_ligand_signaling_path
: addedminmax_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 toggplot2::theme
-make_circos_lr
: addedseparate_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 toSeurat::AverageExpression
-generate_prioritization_tables
: addedscenario
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