NEWS
dominoSignal 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.
dominoSignal 1.4.1
- Updated maintainer information.
dominoSignal 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.
dominoSignal 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.
dominoSignal 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
dominoSignal 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.
dominoSignal 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.