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Final annotations notes

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Sidney Bell
2019-11-22 14:53:35 -08:00
parent 2f99b317a2
commit 85c1b6957e
2 changed files with 8 additions and 4 deletions
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docs/posts/annotations.md
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We are _piloting_ a new feature in cellxgene that enables users to create and edit categorical annotations within the app. We'd love for you to try it out and [give us feedback](contact)!
## Quick start for annotations
## Quick start for annotations (RECOMMENDED for most users)
You can enable this experimental feature like so:
`cellxgene launch mydata.h5ad --experimental-annotations`
To preserve data provenance, **`cellxgene` does not alter the input h5ad file**.
Rather, newly-created annotations are saved in a specified CSV file:
To preserve data provenance, **`cellxgene` does not alter the input h5ad file**. Rather, newly-created annotations are saved in a specified CSV file:
- You will be prompted to enter a name for your annotations the first time you create a new category.
- We also assign a unique identifier in the form of an 8-character suffix, `########`; this helps cellxgene identify your file to avoid overwriting your work.
- Any annotations you create in the application will be autosaved in `cwd/name-########.csv`, where `cwd` is your current working directory (i.e., the directory you were in when you started cellxgene).
If you quit cellxgene and relaunch it with the same h5ad, we will check for this annotations csv and load it in editable mode alongside.
## Data management
### Loading, editing and updating existing draft annotations
@@ -74,6 +75,9 @@ anndata.obs = anndata.obs.join(new_annotations)
### How do I know my annotations are saved?
`cellxgene` autosaves any changes made to your annotations every 3 seconds.
### I think I deleted my annotations! Oh noes!
Not to worry! We save the last 10 versions of your annotations in `annotations-directory/NAME-backups/`
### What about creating continuous annotations?
Continuous metadata is important! However, these values (e.g., pseudotime) are the result of statistical analyses that are beyond cellxgene's visualization- and exploration-focused scope. We do, of course, provide visualization of continuous metadata values computed elsewhere and stored in `anndata.obs`.
docs/posts/launch.md
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`--open` automatically opens the web browser after launching (caveat: only works on some operating systems).
`--experimental-label-file` enables an experimental feature to allow users to create new categorical annotations in the application. These newly-created annotations are saved in the specified CSV file. If the specified file already exists, the previously-contained annotations will be loaded as mutable (changeable) values and the CSV will be updated (overwritten) with any edits made. If the file does not exist, it will be created. See [the annotations documentation](annotations) for more details.
`--experimental-annotations`, `--experimental-annotations-file` & `--experimental-annotations-output-dir` all have to do with an experimental feature to allow users to create new categorical annotations in the application. We have a [whole separate page](annotations) about their usage! :)
`--diffexp-lfc-cutoff` as explained [in the methods](methods), genes are only returned in differential expression if the effect size is above the specified threshold for log fold change. Defaults to 0.01.