Cellxgene

**Summary:** 0.14.0 adds ontology-based autosuggestions to the experimental annotation feature, category labeling in the main graph/embedding, and a number of bug fixes and incremental improvements.

Added:
* The experimental annotations feature is augmented with the ability to autosuggest labels from an ontology. Ontology is specified from an `.obo` file. See the `--experimental-annotations-ontology` command line flag.
* Main embedding (graph) display enhanced with the ability to display category names over the center of the constituent cells. Enabled/disabled by a new UI button in the button bar.
* When launched, cellxgene will inform users when a new version is available on PyPi.org. This check may be bypassed with the new `--no-upgrade-check` command line option.

Changed:
* Labels / names in the user interface will now display in a sorted order, including embedding names, annotation names, and categorical annotation values.
* Various internal build updates and improvements.
* Fonts needed by the application are now served by the internal web server, rather than relying on internet connectivity.
* Javascript and Python package dependencies updated.
* FAQ link removed from Info menu
* All large histograms will now have a consistent number of bins (PR 1086)
* User-created annotations may now contain additional characters (now allow alphanumeric, plus -_.() and single spaces. Fixes issue 1113.
* The recent `0.7.*` release of the anndata module is incompatible with cellxgene. This release pins the anndata dependency to 0.6.22post1 (the most recent compatible version).

Fixed:
* A significant number of bug fixes to experimental annotations, including 1050, 1057, 1036, 1055 and others.
* Annotation file name, specified by `--experimental-annotations-file`, will now allow file names containing a hyphen. Fixes issue 1072
* Fixed bug which would cause user-created annotations to lose the (mandatory) `unassigned` category. Fixes issue 1090
* Various layout and whitespace improvements throughout the app.
* Added missing python `requests` package to requirements.
* Fixed bug that would crash if the user created an annotation name which was the same as another existing annotation name. Fixes issue 1112
* Ensure that all user-created annotation labels are correctly saved, without transformation, to the annotations CSV file. There were several labels (eg, 'nan') which would not be saved correctly to the annotations CSV file. Fixes issue 1111.
* Some sequences of actions caused the `undo` button to behave unpredictably. This is fixed by 1099

Summary: 0.13.0 introduces a layout change, moving all continuous data histograms into a dedicated panel: the "right side bar". In addition, 0.13.0 includes significant improvements and bug fixes to the experimental "user annotation" feature.

Added:
* Introduced a "right side bar" containing all continuous metadata and gene expression histograms.
* _[Experimental feature, may be incomplete or unstable]_ Significant improvements to the user annotation functionality, allowing users to annotate groups of cells with categorical metadata:
* Command line options related to annotation renamed and reorganized -- see `cellxgene launch --help` for usage.
* Added simple multi-user support for hosted instances of cellxgene, to avoid the possibility of users over-writing each others’ metadata.
* Add a provenance header to the annotations output CSV file.
* Many bug fixes, usability and stability improvements.

Changed:
* Command line option `--skip-qc/--run-qc` (a toggle) changed to a flag named `--skip-qc`.
* Command line help (via the `--help` option) improved.
* Reorganized and improved cellxgene documentation, available at https://chanzuckerberg.github.io/cellxgene/.
* Javascript and Python package dependencies updated.
* Dockerfile now contains `python-requests` package (1019).
* Migrate from deprecated Pandas API (1021).

Fixed:
* Various layout issues resolved throughout app.

Summary: this release adds three major features, in addition to a number of bug fixes and other features:
* The location of the H5AD file may be specified as a URL, in addition to the currently supported file path
* Anndata "backed" mode is supported via `--backed` command line option
* A new experimental feature: the ability to create new categorical metadata for cells, aka cell annotations.

Added
* `cellxgene launch` command now accepts a URL as well as file paths. Example: "cellxgene launch http://…" Supports HTTP, HTTPS, and with optional package installations, S3 and GS URLs. (#920)
* New command line option, --backed, will load H5AD file in "backed" mode. This uses less memory, and loads faster. However, it will dramatically increase the time required to load expression histograms or compute differential expression. This feature is most useful to explore metadata and embeddings for very large datasets, or to load only the embedding and metadata on computers with limited memory. This mode is diabled by default.
* New command line option, `--about`, provides a means to link out to more information about the dataset. The link provided on the command line will appear in the application info menu, and as a link in the dataset title (upper left, next to logo) (907)
* New command line option, `--disable-diffexp`, will cause on-demand differential expression (top N gene finding) to be disabled in the application. This is useful when exploring very large datasets, where the differential expression calculation is likely to be extremely slow or unusable due to memory exhaustion. Differential expression is enabled by default.
* Hovering the cursor over a category name will highlight cells in the gene expression scatterplot (previously only highlighted cells in the embedding graph). (900)
* [_Experimental feature, may be incomplete or unstable_] Added capability to label cells with new metadata (categorical annotations). This feature is enabled with the "--experimental-label-file" command line option, which requires a CSV file name. User-created metadata will be saved to this file. We would love feedback on this feature - please submit via GitHub issues.

Changed
* Pip install for `prepare` sub-command is now separate from default installation. If you wish to use prepare, install via `pip install cellxgene[prepare]`. See getting started guide for more info. (887, 889)
* Improved layout when strings are long. Will now break/truncate data set title, category name, etc. (858, 909)
* Improved the formatting for histogram axis labels, better handling of large numbers (913)
* Significant improvements to the embedding and gene expression plots, including reduction in CPU usage, zoom/pan constraints, a new rendering method designed to highlight meaningful data and improve overall usability/visibility (893)
* Miscellaneous improvements to documentation and README (878, 857, 880)
* Python and Javascript package updates, for both security and performance
* Rename "layout" to "embedding" in the UI (921)

Fixed
* Category-specific mini histograms were computed incorrectly in some cases (869)
* Remove pinned matplotlib version, and resolve incompatibility by installing scanpy earlier in the dependency list (so it specifies the matplotlib dependency).
* H5py dependency pinned to 2.9.0 to temporarily work around regression reading older anndata files (scanpy issue 832). This will be removed in a future release. (916).
* Fixed several bugs in gene adding (both in bulk and autosuggest).
Improved performance for datasets with a very large number of continuous metadata fields.

Fixed
* FIx matplotlib incompatibility error(877)

Summary
This release implements a requested cellxgene feature: histograms on categorical values vis a vis continuous (see: 762, 616). Color by any continuous variable, like a gene, and see the breakdown of distributions by opening any categorical menu item. This answers questions such as “which clusters expressed which gene?” “What was the breakdown of total gene counts by tissue?” among others.

Added
Added mini histograms to categorical selection, displaying continuous metadata distribution (827)
Added prepare example, updated demo dataset (810, 803, 547, 529)
Documentation regarding hosted instances (807)
Hover on label increases point size of associated cells in graph (809 833)

Changed
Updated roadmap (825)
Menu bar code cleanup, logo (804)

Fixed
Fixed broken URL in docs (801, 802)
Fixed jest tests by removing async (805)

Changed
* Pinned python requirement 'tables==3.5.1' to work around installation failure in recently release of tables 3.5.2

Fixed
* Improved main graph scaling and centering of embedding (784)