Definition of the linkage summary class added to facilitate comparisons of linkages established in domino objects across sample covariates.

updating readme with archived versions of domino from publication.

also includes a bug fix where lists of linkage counts were being saved into the resulting data frame instead of a numeric vector.

Changed base from master to alt_gene_conversions_&_class_checks to integrate with compare_linkages changes intended for v0.2.2

Changed base from master to alt_gene_conversions_&_class_checks to integrate with compare_linkages changes intended for v0.2.2

…heck

Changed base from master to alt_gene_conversions_&_class_checks to integrate with compare_linkages changes intended for v0.2.2

Removed deleted function get_regulon_info

Krishnan pkgdown_initial

…checks

…hecks

Alt gene conversion and class checks

Compare domino linkages

formatR::tidy_dir("R/", arrow = TRUE, blank = FALSE)

formatR::tidy_dir("R/", arrow = TRUE, blank = FALSE, indent = 2)

Meeting R package standards for calling functions and classes from exterior packages. Recompiled documentation with roxygen2. Also corrects documentation of function descriptions.

Adds .Rbuildignore as a tracked file. Ignores directories associated with R projects, pkgdwn, and git for R BUILD.

Jtm/v0.2.2/r check errors

Reduced file sizes for testing functions

All imported packages are included in whole except for those that matching object names such as NMF, igraph, and ggpubr

Adjusted documentation of the domino class to reflect current usage. This branch is being merged back to development despite not correcting the NAMESPACE error because I have yet to find a solution. I want to give time to hear back from BiocCheck's developers while addressing other tasks at hand.

35 error. Error message in BiocCheck is not resolved, but dev_tools::check finds no issues with NAMESPACE

Initial addition of BiocViews. Uses Views "SystemsBiology, SingleCell, Transcriptomics, Network". BiocCheck recommends including "Transcription, Sequencing, DataImport"

Tabs had been used in a code block for the bash script used to run pySCENIC.

Most functions in the plotting_fxns script did not have \@return fields filled out. Also added these descriptions for the print functions for the domino S4 class.

…ting_functions

value added for docs on plotting functions

…ino2 into krishnan_pkgdown

Replaces instances of using NMF::aheatmap to render heatmaps with ComplexHeatmap functions. Existing purposes of the plots and capabilities to pass arguments to the domino plotting function to the Heatmap() function are maintained.

R CMD CHECK failed when rebuilding vignettes because of issues parsing lines in function arguments that included comments. the comments have been moved to separate lines.

Rerun construction of pkgdown files to account for changes to plotting functions used in the vignettes.

Function definition appeared a second time. Likely arose from merging branches earlier.

Update pkgdown files, reorganize data files

aheatmap is no longer used in the package, so NMF no longer needs to be imported

Resolve devtools::check() for usage of Seurat, loomR, and patchwork in the vignette markdown scripts.