NEWS

dominoSignal 1.6.0

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

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.

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.

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.

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().

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.

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

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.

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.

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.

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.