Changes in version 1.6.0                        

New Features

  - Added print() and show() methods for linkage_summary objects to
    provide concise summary output.

Bug Fixes

  - Fixed create_rl_map_cellphonedb() handling of partner B complex
    mappings and gene assignment.
  - Fixed gene_network() to avoid repeated prefixing of outgoing cluster
    names and to correctly subset outgoing signaling matrices.
  - Fixed gene_network() to only include receptor and TF nodes that are
    associated with a ligand if OutgoingSignalingClust is used.
  - Fixed gene_network() to accumulate ligand expression across clusters
    for ligand node scaling.
  - Fixed signaling_network() to assign undefined (NA) vertex sizes to 0
    when scaling by signaling.
  - Fixed dom_linkages() with by_cluster = TRUE and link_type =
    "tf-receptor" to return clust_tf_rec.
  - Fixed dom_signaling(cluster = ...) to return the selected cluster
    matrix via list indexing.

Documentation

  - Added figure alt text to images in vignettes for accessibility.
  - Updated pkgdown and vignette links to use working URLs.
  - Updated README/index documentation links and citation text to
    current release metadata.

                        Changes in version 1.4.1                        

  - Updated maintainer information.

                        Changes in version 1.2.0                        

Bug Fixes

  - Fixed circos_ligand_receptor() to not fail when rl_map includes
    ligands not present in the expression matrix. Missing ligands are
    excluded with informative message.
  - Fixed create_domino() to prevent overwriting signaling matrix with
    NULL when complexes = TRUE but no complexes are found to have active
    signaling.

                        Changes in version 1.0.0                        

  - Accepted to Bioconductor in release 3.20.

Bug Fixes

  - Disabled exact p-value computation for correlation test between
    receptor expression and features to prevent repeated warning
    messages due to inevitable tied ranks during Spearman correlation
    calculation in create_domino().

Documentation

  - Updated vignette download instructions to use the Bioconductor URL
  - All vignettes explicitly state seed used when executing code if
    applicable.
  - Example code runs with echo = FALSE to reduce output verbosity in
    documentation
  - create_domino() examples run with verbose = FALSE to reduce
    extensive output in documentation.
  - Vignette regarding dominoSignal object structure explains the
    purpose of downloading and importing data with BiocFileCache to
    demonstrate applications on large real data objects.
  - Fixed example code for circos_ligand_receptor() color customization
    and cor_heatmap() boolean representation.
  - Updated non-functional links to correct URLs.

                       Changes in version 0.99.2                        

  - Package renamed from "domino2" to "dominoSignal".

Documentation

  - Updated vignettes to demonstrate pipeline on data formatted as
    SingleCellExperiment objects.
  - Added SCENIC tutorial vignette in place of deprecated example
    scripts

                        Changes in version 0.2.2                        

New Features

  - Added new linkage_summary class to summarize linkages in domino
    objects.
  - Added helper functions to count linkages and compare between domino
    objects.
  - Added plotting function for differential linkages.

                        Changes in version 0.2.1                        

New Features

Function Inputs

  - Standardized input formats for receptor-ligand databases,
    transcription factor activity scores, and regulon gene lists to
    support alternative databases and transcription factor activation
    inference methods.
  - Added helper functions to reformat pySCENIC outputs and CellPhoneDB
    database files to standardized input formats.
  - Added host option for gene ortholog conversions using biomaRt for
    access to maintained mirrors.

Improved Linkages

  - Implemented assessment of transcription factor linkages with
    heteromeric receptor complexes based on correlation between
    transcription factor activity and all receptor component genes
  - Implemented assessment of complex ligand expression as the mean of
    component gene expression for plotting functions.
  - Added minimum threshold parameter for the percentage of cells in a
    cluster expressing a receptor gene.
  - Added linkage slots for active receptors per cluster, transcription
    factor-receptor linkages per cluster, and incoming ligands for
    active receptors within each cluster.

Plotting Functions

  - Added chord plot of ligand expression targeting a specified
    receptor, with chord widths proportional to ligand expression per
    cell cluster.
  - Added arguments to gene network plots to show communication between
    two clusters.
  - Added filtering to signaling network plots to show outgoing
    signaling from specified clusters.

Bug Fixes

  - Fixed transcription factor-target linkages to exclude receptors
    within transcription factor regulon.
  - Enabled create_domino() to run without providing a regulon list.
  - Fixed ligand node sizing in gene network plots to correspond to the
    level of ligand expression.