From 394da40bea8b2ceff594fee85778878f5493cc10 Mon Sep 17 00:00:00 2001 From: Charlotte Weaver Date: Thu, 10 Jan 2019 15:09:02 -0800 Subject: [PATCH] Doc formatting improvements (#549) --- README.md | 10 ++++------ docs/faq.md | 5 ++--- 2 files changed, 6 insertions(+), 9 deletions(-) diff --git a/README.md b/README.md index 2e5a212e..9c7c5853 100644 --- a/README.md +++ b/README.md @@ -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 diff --git a/docs/faq.md b/docs/faq.md index 399dc265..d1244ee5 100644 --- a/docs/faq.md +++ b/docs/faq.md @@ -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