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[Merge on next release] Document how to install cellxgene prepare (#889)

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* Document how to install cellxgene prepare

after pr #887 merged

* formatting

* remove reference to cellxgene[louvain]
This commit is contained in:
Charlotte Weaver
2019-09-13 18:15:06 -07:00
committed by Bruce Martin
parent 84c815cc04
commit 0f520f2fd4
3 changed files with 26 additions and 23 deletions
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docs/faq.md
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@@ -12,11 +12,13 @@ Currently, you can go straight into `cellxgene launch` with your own analyzed da
If your data is in a different format, and/or you still need to perform dimensionality reduction and clustering, `cellxgene` can do that for you with the `prepare` command. `cellxgene prepare` runs `scanpy` under the hood and can read in any format that is currently supported by `scanpy` (including mtx, loom, and more listed [here](https://scanpy.readthedocs.io/en/latest/api/index.html#reading)).
To add `cellxgene prepare` to your cellxgene installation run `pip install cellxgene[prepare]`.
The output of `cellxgene prepare` is a h5ad file with your computed clusters and tsne/umap projections that can be used in `cellxgene launch`.
#### I have a directory of 10X-Genomics data with _mtx_ files and I've never used _scanpy_, can I use _cellxgene_?
Yep! This should only take a couple steps. We'll assume your data is in a folder called `data/` and you've successfully installed `cellxgene` with the `louvain` packages as described above. Just run
Yep! This should only take a couple steps. We'll assume your data is in a folder called `data/` and you've successfully installed `cellxgene` with the `prepare` packages as described above. Just run
```
cellxgene prepare data/ --output=data-processed.h5ad --layout=umap
@@ -75,14 +77,6 @@ source ${ENV_NAME}/bin/activate
pip install cellxgene
```
#### In my _prepare_ command I received the following error `Warning: louvain module is not installed, no clusters will be calculated. To fix this please install cellxgene with the optional feature louvain enabled`
Louvain clustering requires additional dependencies, so we don't include them by default. For now, you need to specify that you want these packages by using
```
pip install cellxgene[louvain]
```
#### I ran _prepare_ and I'm getting results that look unexpected
You might want to try running one of the preprocessing recipes included with `scanpy` (read more about them [here](https://scanpy.readthedocs.io/en/latest/api/index.html#recipes)). You can specify this with the `--recipe` option, such as