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@csangara csangara released this 03 May 12:45
· 18 commits to master since this release
dd7a859
  • 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_oiprepare_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