Changes in version 1.0.5
- circos_ligand_receptor will not fail in cases where the rl_map of a
domino objects includes ligands for a receptor where the ligands are
not present in the expression matrix. A message is returned if
ligands from the rl_map had to be excluded from the plot
Changes in version 1.0.4
- refactorization of circos_ligand_receptor function to remove use of
grepl-based regular expressions to reformat cell and molecule names
from a domino object into a data frame for plotting a receptor
circos plot. Component functions for creating the data frame of
ligand expression centered on a single receptor and to render this
data frame as a circos plot are now included in the package as
"obtain_circos_expression" and "render_circos_ligand_receptor",
respectively.
Changes in version 1.0.3
- Added functions for calculation of mean gene expression among
components of a complex using purrr functions
Changes in version 1.0.2
Pkgdown Site Customization Scripts
- Restored _pkgdown.yml and index scripts that specify site building
parameters for https://FertigLab.github.io/dominoSignal to improve
formatting.
Changes in version 1.0.1
Receptor Complex Bugfix
- Resolved issue where if create_domino was run with complexes=TRUE
and no complexes were found to have active signaling, the full
signaling matrix would be replaced by a NULL value.
GitHub Actions
- Restoration of .github/workflows scripts for automatic build checks.
Changes in version 1.0.0
- Version number update to signify acceptance to bioconductor in
release 3.20
Changes in version 0.99.4
Vignettes
- Updated download instructions to use the bioconductor URL
Changes in version 0.99.3
create_domino Function Warnings
- Disabled exact p-value computation for the correlation test between
receptor expression and features to prevent repeated warning
messages due to tied ranks during Spearman correlation calculation
Vignettes
- Updated non-functional links to functional URLs
- All vignettes explicitly state the seed used when executing their
code
- The dominoSignal Object vignette states the purpose of the code used
to download and import data from a BioFileCache to demonstrate
applications of the domino objects on a real data object that is too
large to include inside the package
Testing Data
- Data used for examples and unit tests is now stored in the package's
data/ directory.
- All usage of the triple colon operator to access internal data from
sysdata have been replaced with usage of data()
- Linkage summaries for demonstrating differential linkage testing and
plotting are generated within unit test scripts rather than being
stored within the package.
- Examples are run with echo = FALSE to cut down on lines of code
printed in example pages.
- Examples for create_domino are run with verbose = FALSE
- Fixed example of changing colors for circos_ligand_receptor
- Fixed example of boolean representation of cor_heatmap
Changes in version 0.99.2
Package Name
- Update of package name from "domino2" to "dominoSignal"
Bioconductor Standards
- Update to vignettes presenting application of the DominoSignal
pipeline on data formatted as a SingleCellExperiment object
- Implemented caching of example data by BiocCache to meet package
size limits
- Removal of deprecated scripts for running SCENIC. Tutorials for
running SCENIC are still present in vignettes
- Corrected BiocCheck notes pertaining to coding practices including
paste in conditional statements, functions with dontrun examples,
usage of seq_len or seq_along in place of seq, and usage of vapply
in place of sapply
Changes in version 0.99.1
- Update to Bioconductor version numbering conventions for package
submission
Changes in version 0.2.2
Linkage functions
- Addition of new class to summarize linkages in objects
- Addition of helper functions to count linkages and compare between
objects
- Plotting function for differential linkages
Package structure
- Adjustments made to meet Bioconductor standards
Changes in version 0.2.1
Updates to domino object construction
- Uniform formats for inputs of receptor - ligand interaction
databases, transcription factor activity features, and regulon gene
lists for operability with alternative databases and transcription
factor activation inference methods
- Helper functions for reformatting pySCENIC outputs and CellPhoneDB
database files to domino-readable uniform formats
- Assessment of transcription factor linkage with receptors that
function as a heteromeric complex based on correlation between
transcription factor activity and all receptor component genes
- Assessment of complex ligand expression as the mean of component
gene expression for plotting functions
- Minimum threshold for the percentage of cells in a cluster
expressing a receptor gene for the receptor to be called active
within the cluster
- Additional linkage slots for active receptors in each cluster,
transcription factor - receptor linkages for each cluster, and
incoming ligands for active receptors on each cluster
Plotting functions
- Chord plot of ligand expression targeting a specified receptor where
chord widths correspond to the quantity of ligand expression by each
cell cluster
- Signaling networks showing only outgoing signaling from specified
cell clusters
- Gene networks between two cell clusters
Bugfixes
- Added host option for gene ortholog conversions using {biomaRt} for
access to maintained mirrors
- Transcription factor - target linkages are now properly stored so
that receptors in a transcription factor's regulon are excluded from
linkage
- Ligand nodes sizes in gene networks correspond to quantity of ligand
expression
- create_domino() can be run without providing a regulon list
- References to the host GitHub repository have been updated to
Elisseeff-Lab