From c2b3f331cfc2349cf85f4f9a861eccfc8ff760db Mon Sep 17 00:00:00 2001 From: Charlotte Weaver Date: Fri, 3 Aug 2018 10:12:55 -0700 Subject: [PATCH] Add layout and diffexp calculations to cli options --- server/app/app.py | 2 +- server/app/scanpy_engine/scanpy_engine.py | 5 +++++ 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/server/app/app.py b/server/app/app.py index 30a7accc..a7191acf 100644 --- a/server/app/app.py +++ b/server/app/app.py @@ -53,7 +53,7 @@ def run_scanpy(args): ) from .scanpy_engine.scanpy_engine import ScanpyEngine - app.data = ScanpyEngine(args.data_directory, schema="data_schema.json") + data = ScanpyEngine(args.data_directory, schema="data_schema.json", graph_method=args.layout, diffexp_method=args.diffexp) app.run(host="127.0.0.1", debug=True, port=args.port) diff --git a/server/app/scanpy_engine/scanpy_engine.py b/server/app/scanpy_engine/scanpy_engine.py index c9240989..e28e1733 100644 --- a/server/app/scanpy_engine/scanpy_engine.py +++ b/server/app/scanpy_engine/scanpy_engine.py @@ -26,6 +26,11 @@ class ScanpyEngine(CXGDriver): @classmethod def add_to_parser(cls, subparsers, invocation_function): scanpy_group = subparsers.add_parser("scanpy", help="run cellxgene using the scanpy engine") + # TODO these choices should be generated from the actual available methods + scanpy_group.add_argument("-l", "--layout", choices=["umap", "tsne"], default="umap", + help="Algorithm to use for graph layout") + scanpy_group.add_argument("-d", "--diffexp", choices=["ttest"], default="ttest", + help="Algorithm to use to calculate differential expression") scanpy_group.add_argument("data_directory", metavar="dir", help="Directory containing data and schema file") scanpy_group.set_defaults(func=invocation_function) return scanpy_group