Skip to content

Dev #14

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
DoaneAS wants to merge 4 commits into
base: main
Choose a base branch
from
Open

Dev #14

Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
8cf0cd4
updated requirements.txt
DoaneAS Oct 16, 2023
4ae2951
Revert "updated requirements.txt"
DoaneAS Oct 18, 2023
5985073
fix for indexing error in get_inverse_phenotype
DoaneAS Oct 18, 2023
cad0f54
index on list error
DoaneAS Nov 12, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 2 additions & 2 deletions genevector/embedding.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -562,7 +562,7 @@ def get_inverse_predictive_genes(self, adata, label, n_genes=10):
vectors[x] = vector
markers = dict()
for x, mvec in vectors.items():
ct_sig = self.embed.get_similar_genes(mvec)[-1.*n_genes:]["Gene"].tolist()
ct_sig = self.embed.get_similar_genes(mvec)[int(-1.*n_genes):]["Gene"].tolist()
markers[x] = ct_sig
return markers

Expand Down Expand Up @@ -739,7 +739,7 @@ def cluster(self, adata, up_markers, down_markers=dict()):
down_markers = dict()
down_only = set(down_markers.keys()).difference(set(up_markers.keys()))
up_and_down = set(down_markers.keys()).intersection(set(up_markers.keys()))
phs = set(up_markers.keys()).union(set(down_markers.keys()))
phs = list(set(up_markers.keys()).union(set(down_markers.keys())))
for ph in up_only:
genes = up_markers[ph]
vec = self.embed.generate_vector(genes)
Expand Down