differential expression improvements (#452)

* add cutoff for low expression genes in topN selection

* remove debugging printfs

* change cli param name for diffexp cutoff

* change CLI param name

* second try at diffexp - using lfc sort with pval cutoff

* use lfc cutoff

* update comments to match code; cap p-value adjustment to max of 1

* lint

* explain diffexp in readme

* add link

* add diffexp-lfc-cutoff to test config

* update test to match revised diffexp spec

* fix latent bug in GET arg handling that was breaking tests

* lint

* comment cleanup

* fix variance overestimation so it is symmetric

* lint

server/cli/launch.py

@@ -27,8 +27,10 @@ from server.app.util.errors import ScanpyFileError
               help="Bind to all interfaces (this makes the server accessible beyond this computer).")
 @click.option("--max-category-items", default=100, metavar="", show_default=True,
               help="Limits the number of categorical annotation items displayed.")
+@click.option("--diffexp-lfc-cutoff", default=0.01, show_default=True,
+              help="Relative expression cutoff used when selecting top N differentially expressed genes")
 def launch(data, layout, diffexp, title, verbose, debug, obs_names, var_names,
-           open_browser, port, listen_all, max_category_items):
+           open_browser, port, listen_all, max_category_items, diffexp_lfc_cutoff):
     """Launch the cellxgene data viewer.
     This web app lets you explore single-cell expression data.
     Data must be in a format that cellxgene expects, read the
@@ -92,6 +94,7 @@ def launch(data, layout, diffexp, title, verbose, debug, obs_names, var_names,
         "layout": layout,
         "diffexp": diffexp,
         "max_category_items": max_category_items,
+        "diffexp_lfc_cutoff": diffexp_lfc_cutoff,
         "obs_names": obs_names,
         "var_names": var_names
     }