Changelog

Source: NEWS.md

monarchr 2.1

New features

• Put example KG data in data(eds_marfan_kg)
• Added KGX format checks in engine instantiation
• Include available properties in engine summary()
• Added vignette for engine preferences

Bug fixes

• Remove stitch_vectors and merge_lists from public API
• Fix install instructions
• Fix timeout check for neo4j_engine() URL fallback

monarchr 2.0

Breaking changes

• This breaking release drops support for drop_unused_query_nodes in expand(), which was both brittle and violated the rule that expansion should return a supergraph of the query

Bug fixes

• Fixes a bug in expand() for neo4j_engine() causing an infinite loop.

monarchr 1.7

New features

• New transitive and related tools: roll_up(), roll_down(), transfer(), transitive_closure(), and transitive_reduction()

Minor Changes

• Added a reversed y scale to default plot() so trees and other hierarchies point upward (as Knuth intended)

monarchr 1.6.2

Minor Changes

• plot() now uses a more basic but KG-flexible ggraph, and by default shows node namespace and edge knowledge source if available
• Tooltips in Cytoscape plots show node namespace and edge primary knowledge source if available
• Updates to monarch_semsim() for including primary_knowledge_source and some computed edge column renaming

monarchr 1.6.1

Bug fixes

• Supported using non-default base URLs for cytoscape() plotting
• Fixed a bug resulting in duplicate entries when joining graphs from different data contexts

monarchr 1.6.0

New features

• New utility function:

  • graph_semsim
  • graph_centrality
  • graph_sparsity

• Updated plotting functions

  • Overhauled plot.tbl_kgx
  • New function for getting consistent Monarch palettes: monarch_palettes.
  • New function to apply monarch theme to existing ggraph plots: theme_monarch

• kg_edge_weights: New function to compute quantitative edge weights from discrete and continuous edge metadata.

• expand_n: New function to expand a graph to a specified number of nodes.

Bug fixes

• Improved the URL try order for the Monarch Neo4j API.

monarchr 1.5.0

New features

• Exporting to cytoscape() for visualization.
• Added caching for neo4j_engine queries (enabled by default, length of R session only)

Bug fixes

• Fixed a method signature inconsistency for summary().

monarchr 1.4.0

New features

• example_graph() function for engines
• Engine summary() now returns named lists of available node categories and edge predicates for convenient auto-completion

monarchr 1.3.0

New features

• summary() function for engines

Bugfixs

• fix backend bug in Neo4j table queries not handling default params properly
• add batch queries for Neo4j backend engine
• added summary() for KG engines to summarize total node and edge count information

monarchr 1.2.2

Bugfixs

• Add fallback URLs for monarch_engine()

monarchr 1.2.1

New features

• New save_kgx() and load_kgx() for saving/loading graphs.

Bugfixes

• Reduced size of package with smaller example data
• Fixed a bug in expand() where the engine was not carried through for file-engine backed graphs
• Unit tests dependent on live-hosted Monarch KG now allow for minor changes in result counts

monarchr 1.1.0

New features

• New kg_join() function

Bug fixes

• Fix expand() to include new edges when multiple nodes with the same id are part of the query.

1.0.1: Fix missing self loops in plot

monarchr 1.0.0

1.0.0 is a major update to monarchr functionality and APIs.

• Engines
  • monarchr now supports the Monarch cloud-hosted KG, other Neo4j-hosted KGs, and file-based KG access from kghub.org
  • Queries to hosted databases are now paged for efficiency
• API updates and new features
  • fetch_edges() is now expand()
  • fetch_nodes() now supports bulk fetching by provided ID list or node properties
  • limit parameter added to expand() and fetch_nodes() for exploratory queries
  • monarch_semsim() provides semantic-similarity matching via the Monarch cloud-hosted API
  • Basic plot() added based on ggraph
  • Improved display of graphs as node and edge tables in R markdown docs

monarchr 0.2.2

New features

• README:
  • Create to README.Rmd to enable autofilling.
  • Add badges
  • Add link to docs site
• DESCRIPTION:
  • Add URL/BugReports fields
• vignettes
  • Change Basics.Rmd –> monarchr.Rmd to match conventions.
  • Name chunks in vignette
  • Add session info to end of vignette

monarchr 0.2.1

• Add rworkflows GHA for automated checking, site building, and Docker container creation.
• Update .Rbuildignore.
• Add NEWS file.
• Add Title, Description, and Authors to DESCRIPTION.
  • Hope you don’t mind me adding our names here @oneilsh, I anticipate making lots of contributions!
• Add tidyr Import to DESCRIPTION.
• Add vignettes header info.
• Fix edges docs by adding title.
• Add VignetteBuilder: knitr to DESCRIPTION.
• Fix cypher_query example by adding ids
• Fix cypher_query_df example by adding ids
• Export cypher_query_df
• Get monarchR closer to passing rcmdcheck (methods for edges/nodes not yet being recognized)