Rename "layout" to "embedding" in the UI (#921)

* rename "layout" to "embedding" in the UI

* docs changes for layout

* fix typo in data docs

* new help text, per PR review

server/cli/launch.py

@@ -25,12 +25,12 @@ def common_args(func):
     """
     @click.option("--title", "-t", help="Title to display (if omitted will use file name).")
     @click.option(
-        "--layout",
-        "-l",
+        "--embedding",
+        "-e",
         default=[],
         multiple=True,
-        show_default=True,
-        help="Layout name, eg, 'umap'."
+        show_default=False,
+        help="Embedding name, eg, 'umap'. Repeat option for multiple embeddings. Defaults to all."
     )
     @click.option("--obs-names", default=None, metavar="", help="Name of annotation field to use for observations.")
     @click.option("--var-names", default=None, metavar="", help="Name of annotation to use for variables.")
@@ -53,9 +53,9 @@ def common_args(func):
     return wrapper
 
 
-def parse_engine_args(layout, obs_names, var_names, max_category_items, diffexp_lfc_cutoff):
+def parse_engine_args(embedding, obs_names, var_names, max_category_items, diffexp_lfc_cutoff):
     return {
-        "layout": layout,
+        "layout": embedding,
         "max_category_items": max_category_items,
         "diffexp_lfc_cutoff": diffexp_lfc_cutoff,
         "obs_names": obs_names,
@@ -101,7 +101,7 @@ def launch(
         open_browser,
         port,
         host,
-        layout,
+        embedding,
         obs_names,
         var_names,
         max_category_items,
@@ -122,7 +122,7 @@ def launch(
 
     > cellxgene launch <url>"""
 
-    e_args = parse_engine_args(layout, obs_names, var_names, max_category_items, diffexp_lfc_cutoff)
+    e_args = parse_engine_args(embedding, obs_names, var_names, max_category_items, diffexp_lfc_cutoff)
     try:
         data_locator = DataLocator(data)
     except RuntimeError as re:

server/cli/prepare.py

@@ -8,12 +8,12 @@ from scipy.sparse.csc import csc_matrix
 @click.command()
 @click.argument("data", nargs=1, metavar="<dataset: file or path to data>", required=True)
 @click.option(
-    "--layout",
-    "-l",
+    "--embedding",
+    "-e",
     default=["umap", "tsne"],
     multiple=True,
     type=click.Choice(["umap", "tsne"]),
-    help="Layout algorithm",
+    help="Embedding algorithm",
     show_default=True,
 )
 @click.option(
@@ -42,7 +42,7 @@ from scipy.sparse.csc import csc_matrix
 )
 def prepare(
         data,
-        layout,
+        embedding,
         recipe,
         output,
         plotting,
@@ -59,7 +59,7 @@ def prepare(
     This tool runs a series of scanpy routines for preparing a dataset
     for use with cellxgene. It loads data from different formats
     (h5ad, loom, or a 10x directory), runs dimensionality reduction,
-    computes nearest neighbors, computes a layout, performs clustering,
+    computes nearest neighbors, computes an embedding, performs clustering,
     and saves the results. Includes additional options for naming
     annotations, ensuring sparsity, and plotting results."""
 
@@ -162,18 +162,18 @@ def prepare(
     def run_louvain(adata):
         sc.tl.louvain(adata)
 
-    def run_layout(adata):
+    def run_embedding(adata):
         if len(unique(adata.obs["louvain"].values)) < 10:
             palette = "tab10"
         else:
             palette = "tab20"
 
-        if "umap" in layout:
+        if "umap" in embedding:
             sc.tl.umap(adata)
             if plotting:
                 sc.pl.umap(adata, color="louvain", palette=palette, save="_louvain")
 
-        if "tsne" in layout:
+        if "tsne" in embedding:
             sc.tl.tsne(adata)
             if plotting:
                 sc.pl.tsne(adata, color="louvain", palette=palette, save="_louvain")
@@ -190,12 +190,12 @@ def prepare(
             "run_pca": "Running PCA",
             "run_neighbors": "Calculating neighbors",
             "run_louvain": "Calculating clusters",
-            "run_layout": "Computing layout",
+            "run_embedding": "Computing embedding",
         }
         if item is not None:
             return names[item.__name__]
 
-    steps = [calculate_qc_metrics, make_sparse, run_recipe, run_pca, run_neighbors, run_louvain, run_layout]
+    steps = [calculate_qc_metrics, make_sparse, run_recipe, run_pca, run_neighbors, run_louvain, run_embedding]
 
     click.echo(f"[cellxgene] Loading data from {data}, please wait...")
     adata = load_data(data)