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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
committed by GitHub
parent 5d60505407
commit 394da40bea
2 changed files with 6 additions and 9 deletions
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README.md
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## getting started ## 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). 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 To install run
``` ```
@@ -118,12 +117,11 @@ pip install cellxgene
## docker ## 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 "$PWD/example-dataset/:/data/" -p 5005:5005 cellxgene launch --host 0.0.0.0 data/pbmc3k.h5ad` 2. Run the container and mount data `docker run -v "$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 ## FAQ
docs/faq.md
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description: Frequently Asked Questions description: Frequently Asked Questions
--- ---
# Data formatting # Data formatting
#### What file formats can I use with _cellxgene_? #### 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). 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`. 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 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` #### 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 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