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Code Issues Packages Projects Releases Wiki Activity

Doc formatting improvements (#549)

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This commit is contained in:
Charlotte Weaver
2019-01-10 15:09:02 -08:00
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parent 5d60505407
commit 394da40bea
2 changed files with 6 additions and 9 deletions
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10
README.md
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@@ -8,10 +8,9 @@
## getting started
You'll need **python 3.6** and **Google Chrome**. (*Warning*: Python 3.7 is **not** supported at this time)
You'll need **python 3.6** and **Google Chrome**. (_Warning_: Python 3.7 is **not** supported at this time)
The web UI is tested on OSX and Windows using Chrome, and the python CLI is tested on OSX and Ubuntu (via WSL/Windows). It should work on other platforms, but if you run into trouble let us know (see [help](#help-and-contact) below).
To install run
```
@@ -118,12 +117,11 @@ pip install cellxgene
## docker
We have included a dockerfile to conveniently run cellxgene from docker.
We have included a dockerfile to conveniently run cellxgene from docker.
1. Build the image `docker build . -t cellxgene`
1. Build the image `docker build . -t cellxgene`
2. Run the container and mount data `docker run -v "$PWD/example-dataset/:/data/" -p 5005:5005 cellxgene launch --host 0.0.0.0 data/pbmc3k.h5ad`
* You will need to use --host 0.0.0.0 to have the container listen to incoming requests from the browser
- You will need to use --host 0.0.0.0 to have the container listen to incoming requests from the browser
## FAQ

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docs/faq.md
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@@ -4,13 +4,13 @@ title: FAQ
description: Frequently Asked Questions
---
# Data formatting
#### What file formats can I use with _cellxgene_?
Currently, you can go straight into `cellxgene launch` with your own analyzed data in h5ad format, after you have performed dimenstionality reduction (tsne, umap) and clustering (louvain).
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)).
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)).
The output of `cellxgene prepare` is a h5ad file with your computed clusters and tsne/umap projections that can be used in `cellxgene launch`.
@@ -67,7 +67,6 @@ 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