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

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

* docs changes for layout

* fix typo in data docs

* new help text, per PR review
This commit is contained in:
Bruce Martin
2019-09-16 15:34:14 -07:00
committed by GitHub
parent ec4da63408
commit 922c375333
7 changed files with 39 additions and 33 deletions
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server/cli/launch.py
+8 -8
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@@ -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: