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annotations cli updates (#1190)

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* Switch logic from `--annotations` to `--disable-annotations

* Rename `--annotations-file` --> `--annotations-input-file` and remove `experimental`

* update docs

* update makefile

* update tests

* Disable annotations on standard client smoke test

* Update docs/posts/annotations.md

Co-Authored-By: Matt Weiden <538456+mweiden@users.noreply.github.com>

* Update docs/posts/annotations.md

* Renaming

* Docs

* Update tests

* Pesky typo -_-

Co-authored-by: Matt Weiden <538456+mweiden@users.noreply.github.com>
This commit is contained in:
Sidney Bell
2020-03-11 11:57:52 -07:00
committed by GitHub
co-authored by Matt Weiden
parent 8beeb57c96
commit 9089fc98f2
7 changed files with 50 additions and 55 deletions
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docs/posts/launch.md
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@@ -46,7 +46,7 @@ cellxgene launch s3://mybucket.s3-us-west-2.amazonaws.com/mydata.h5ad
`--open` automatically opens the web browser after launching (caveat: only works on some operating systems).
`--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! :)
`--disable-annotations`, `--annotations-file` & `--annotations-dir` all have to do with creating 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.