diff --git a/README.md b/README.md index 73b386b4..59559f4a 100644 --- a/README.md +++ b/README.md @@ -37,7 +37,7 @@ You should see your web browser open with the following There are several options available, such as: -- `--layout` to specify the layout as `tsne` or `umap` +- `--layout` to specify the layout as `tsne`, `umap`, `draw_graph_fa`, or `draw_graph_fr` - `--title` to show a title on the explorer - `--open` to automatically open the web browser after launching (OS X only) @@ -57,7 +57,7 @@ The `launch` command assumes that the data is stored in the `.h5ad` format from - an `obs` field has a unique identifier for every cell (you can specify which field to use with the `--obs-names` option, by default it will use the value of `data.obs_names`) - a `var` field has a unique identifier for every gene (you can specify which field to use with the `--var-names` option, by default it will use the value of `data.var_names`) -- an `obsm` field contains the two-dimensional coordinates for the layout that you want to render (e.g. `X_tsne` for the `tsne` layout or `X_umap` for the `umap` layout) +- an `obsm` field contains the two-dimensional coordinates for the layout that you want to render (e.g. `X_umap` for the `umap` layout) - any additional `obs` fields will be rendered as per-cell continuous or categorical metadata by the app (e.g. `louvain` cluster assignments) ### prepare diff --git a/example-dataset/pbmc3k.h5ad b/example-dataset/pbmc3k.h5ad index 381e211f..e529a6d8 100644 Binary files a/example-dataset/pbmc3k.h5ad and b/example-dataset/pbmc3k.h5ad differ