From a83ec603085310acfa1c9804f7f87f2de6a0be49 Mon Sep 17 00:00:00 2001
From: fionagriffin <41973921+fionagriffin@users.noreply.github.com>
Date: Thu, 29 Nov 2018 13:59:10 -0800
Subject: [PATCH] add FAQs to readme (#482)

Added question and answer to FAQ; added link to scanpy documentation on scientific recipes.
---
 README.md | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index fe645069..f56356d3 100644
--- a/README.md
+++ b/README.md
@@ -68,7 +68,7 @@ To prepare from an existing `.h5ad` file use
 cellxgene prepare dataset.h5ad --output=dataset-processed.h5ad
 ```
 
-This will load the input data, perform PCA and nearest neighbor calculations, compute `umap` and `tsne` layouts and `louvain` cluster assignments, and save the results in a new file called `dataset-processed.h5ad` that can be loaded using `cellxgene launch`. Data can be loaded from several formats, including `.h5ad` `.loom` and a `10-Genomics-formatted` `mtx` directory. Several options are available, including running one of the preprocessing `recipes` included with `scanpy`, which include steps like cell filtering and gene selection. 
+This will load the input data, perform PCA and nearest neighbor calculations, compute `umap` and `tsne` layouts and `louvain` cluster assignments, and save the results in a new file called `dataset-processed.h5ad` that can be loaded using `cellxgene launch`. Data can be loaded from several formats, including `.h5ad` `.loom` and a `10-Genomics-formatted` `mtx` directory. Several options are available, including running one of the preprocessing `recipes` included with `scanpy`, which include steps like cell filtering and gene selection. To learn more about the `recipes` please see the `scanpy` [documentation](https://github.com/theislab/scanpy/blob/master/scanpy/preprocessing/recipes.py).
 
 Depending on the options chosen, `prepare` can take a long time to run (a few minutes for datasets with 10-100k cells, up to an hour or more for datasets with >100k cells). If you want `prepare` to run faster we recommend using the `sparse` option and only computing the layout for `umap`, using a call like this
 
@@ -159,6 +159,12 @@ Currently we use a [Welch's *t*-test](https://en.wikipedia.org/wiki/Welch%27s_t-
 
 This is likely because you do not have node and npm installed, we recommend using [nvm](https://github.com/creationix/nvm) if you're new to using these tools.
 
+> What part of the anndata objects does cellxgene pull in for visualization?
+
+- `.obs` and `.var` annotations are use to extract metadata for filtering
+- `.X` is used to display expression (histograms, scatterplot & colorscale) and to compute differential expression
+- `.obsm` is used for layout
+
 ## developer guide
 
 This project has made a few key design choices