From 12c52a55f75f9826b9fe9960d894f4567a4f4e90 Mon Sep 17 00:00:00 2001
From: Sidney Bell <sidneymb@uw.edu>
Date: Tue, 7 Aug 2018 07:42:45 -0700
Subject: [PATCH] Very minor changes to elaborate in a few places

---
 README.md | 80 +++++++++++++++++++++++++++----------------------------
 1 file changed, 40 insertions(+), 40 deletions(-)

diff --git a/README.md b/README.md
index adb54b5a..06a58793 100644
--- a/README.md
+++ b/README.md
@@ -21,84 +21,84 @@ Started in the context of the Human Cell Atlas Consortium, cellxgene hopes to bo
 - OS: OSX, Windows, Linux
 - python 3.6
 - npm
-- Google Chrome 
+- Google Chrome
 
-**Clone project**  
-  
-    git clone https://github.com/chanzuckerberg/cellxgene.git    
+**Clone project**
+
+    git clone https://github.com/chanzuckerberg/cellxgene.git
+
+**Install client**
 
-**Install client**  
-  
     cd cellxgene
-    ./bin/build-client  
+    ./bin/build-client
 
-**To use with virtual env for python**  
-(optional, but recommended)  
-  
-    ENV_NAME=cellxgene  
-    python3 -m venv ${ENV_NAME}  
-    source ${ENV_NAME}/bin/activate  
+**To use with virtual env for python**
+(optional, but recommended)
 
-**Install server**    
-  
-    python3 setup.py install  
+    ENV_NAME=cellxgene
+    python3 -m venv ${ENV_NAME}
+    source ${ENV_NAME}/bin/activate
+
+**Install server**
+
+    python3 setup.py install
+
+**Run (with demo data)**
 
-**Run (with demo data)**  
-  
     cellxgene --title PBMC3K scanpy example-dataset/
-*In google chrome, navigate to the viewer via the web address printed in your console.  
+*In google chrome, navigate to the viewer via the web address printed in your console.
 E.g.,* `Running on http://0.0.0.0:5005/`
 
 **Help**
-  
+
     cellxgene --help
-_For help with the scanpy engine_  
-  
+_For help with the scanpy engine_
+
     cellxgene scanpy --help
 
 ## Using your own data
 
 ### Scanpy
 
-To prepare you data you will need to format your data into AnnData format using scanpy and calculate PCA and nearest neighbors and save in h5ad format.
+To prepare your data you will need to format your data into AnnData format using scanpy and calculate PCA and nearest neighbors and save in h5ad format.
 
-1. [Load data into scanpy](https://scanpy.readthedocs.io/en/latest/api/index.html#exporting)
+1. [Load data into scanpy](https://scanpy.readthedocs.io/en/latest/api/index.html#reading)
 
-	- Ensure that `obs`'s index is the cell names
+	- Ensure that `obs`'s index is the cell names: `print(data.obs_names)` should show your cell indices. If it shows gene names, you may need to just call `data.transpose()`.
 
 2. Calculate PCA
 
-    sc.pp.pca(data)
-    
-3. Calculate nearest neighbors (depending on layout algorithm)
-	
+    sc.pp.pca(data) ## sc is scanpy.api
+
+3. Calculate nearest neighbors  (depending on layout algorithm)
+
     ```
-    # For umap layout algorithm
+    # For umap layout algorithm, you need to use the "umap" method for neighbors
     sc.pp.neighbors(data, method="umap", metric="euclidean", use_rep="X_pca")
-    
-    # For tsne layout algorithm
+
+    # For tsne layout algorithm, you can use either "umap" or "gauss"; we recommend "gauss"
     sc.pp.neighbors(data, method="gauss", metric="euclidean", use_rep="X_pca")
     ```
-    
+
 4. Save file
 
     ```
     # cellxgene requires file to be named data.h5ad
     data.write("data.h5ad")
     ```
-   
+
 5. Create config file (optional)
 
 	If you do not have a config file, the schema (metadata names, types, and categorical/continuous) will be inferred from the observations in the data file. Config file is required to be named 'data_schema.json' and located in the same directory as data file.
-	- The config file is a JSON format file with information on the metadata associated with the cells. The key is the column name in obs. The value is an object 
+	- The config file is a JSON format file with information on the metadata associated with the cells. The key is the column name in obs. The value is an object
 	```
     type: string, int, or float (what type the values are),
-	variabletype: categorical or continuous (categorical values are displayed as checkboxes, continuous values are displayed as a histogram)
-	displayname: (what the heading should be displayed as)
-	include: True/False (whether to display values on web interface)
+	  variabletype: categorical or continuous (categorical values are displayed as checkboxes, continuous values are displayed as a histogram)
+	  displayname: (what the heading should be displayed as)
+	  include: True/False (whether to display values on web interface)
+	```
+
 	```
-    
-	```	
 	Example
     {
         "CellName": {