Changelog

Source: NEWS.md

coconatfly 0.2.4

What’s Changed

• Handle missing partners in cf_cosine_plot() by @jefferis in https://github.com/natverse/coconatfly/pull/36
• Fill in instance column across datasets by @jefferis in https://github.com/natverse/coconatfly/pull/39
• warn but still complete without errors when there are no partners at all for inputs or ouptuts in cf_partners(). An example of when this happens is when running cf_cosine_plot() for sensory neurons where all the inputs are below threshold. #36
• suggest malecns >= 0.3.3 (https://github.com/flyconnectome/malecns/releases/tag/v0.3.3) to prefer manc types for ANs + SAs (see https://github.com/flyconnectome/malecns/pull/28)

Full Changelog: https://github.com/natverse/coconatfly/compare/v0.2.3…v0.2.4

coconatfly 0.2.3

• empty query fixes for all keys and banc metadata by @jefferis in https://github.com/natverse/coconatfly/pull/34
• Fix malecns class in cf_partners() by @jefferis in https://github.com/natverse/coconatfly/pull/35
• also support for rootSide in malecns in #35

Full Changelog: https://github.com/natverse/coconatfly/compare/v0.2.2…v0.2.3

coconatfly 0.2.2

• support malecns superclass/class/subclass change. To stay backward compatible for the time being the class hierarchy is mapped onto
  • class
  • subclass
  • subsubclass but the intent is to switch to superclass/class/subclass in the next version by @jefferis in https://github.com/natverse/coconatfly/pull/32
• Correct handling of malecns lineage information by @jefferis in https://github.com/natverse/coconatfly/pull/33
• cf_cosine_plot() now fetches all metadata cols by default (f1667a3c8318120626ae95c2116f73576fd2dfb4)
• fix: pass on keep.all when cf_meta() receives keys
• cf_cosine_plot(): Now reports % of partner connections kept across datasets.

Full Changelog: https://github.com/natverse/coconatfly/compare/v0.2.1…v0.2.2

coconatfly 0.2.1

• cf_meta() gets a MoreArgs argument to pass on to subsidiary functions for each dataset
• Using this cf_cosine_plot() and friends now prefer malecns foreign types (flywireType, mancType) when available and co-clustering with another dataset by @jefferis in https://github.com/natverse/coconatfly/pull/27
• cf_meta(): new keep.all argument keep all columns, not just shared columns by @jefferis in https://github.com/natverse/coconatfly/pull/30
• support for min_datasets in cosine clustering by @jefferis in https://github.com/natverse/coconatfly/pull/31

Full Changelog: https://github.com/natverse/coconatfly/compare/v0.2.0…v0.2.1

coconatfly 0.2.0

Although coconatfly has been in use for some time, this is the first stable release. It corresponds to what was used in the recent publication:

Schlegel, P., Yin, Y., Bates, A.S. et al.  Whole-brain annotation and multi-connectome cell typing of Drosophila. Nature 634, 139–152 (2024). https://doi.org/10.1038/s41586-024-07686-5

The release is motivated in part because of some forthcoming changes that will slightly alter some core functionality of the package.

What’s Changed

• Minimal support for FANC clustering by @jefferis in https://github.com/natverse/coconatfly/pull/1
• Feature/flywire examples by @jefferis in https://github.com/natverse/coconatfly/pull/5
• First version cf_partner_summary by @jefferis in https://github.com/natverse/coconatfly/pull/7
• malevnc_meta -> manc_meta by @jefferis in https://github.com/natverse/coconatfly/pull/10
• fix handling of manc partners by @jefferis in https://github.com/natverse/coconatfly/pull/11
• Update test-triple.R by @jefferis in https://github.com/natverse/coconatfly/pull/12
• Support for the upcoming optic lobe release by @jefferis in https://github.com/natverse/coconatfly/pull/14
• Allow messier input keys by @jefferis in https://github.com/natverse/coconatfly/pull/15
• cf_partner summary enh by @jefferis in https://github.com/natverse/coconatfly/pull/16
• flywire/fanc use different threshold definition by @jefferis in https://github.com/natverse/coconatfly/pull/17
• Add connectivity and basic metadata support for banc by @jefferis in https://github.com/natverse/coconatfly/pull/19
• Feature/fanc meta by @jefferis in https://github.com/natverse/coconatfly/pull/21
• Fix/banc optic meta by @jefferis in https://github.com/natverse/coconatfly/pull/25
• Feature/cosine plot warn on drop by @jefferis in https://github.com/natverse/coconatfly/pull/26

Full Changelog: https://github.com/natverse/coconatfly/commits/v0.2.0