From 8cf0cd4698d402b95f8273e279061052e290a126 Mon Sep 17 00:00:00 2001 From: DoaneAS Date: Mon, 16 Oct 2023 18:21:26 -0400 Subject: [PATCH 1/4] updated requirements.txt --- requirements.txt | 18 ++++++++++-------- 1 file changed, 10 insertions(+), 8 deletions(-) diff --git a/requirements.txt b/requirements.txt index e8a2490..038df59 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,13 +1,15 @@ -scipy==1.11.2 -leidenalg==0.8.10 -numpy==1.25.2 +scipy==1.11.3 +leidenalg==0.10.0 +numpy==1.24.4 scikit-learn==1.3.1 -pandas==1.5.3 -scanpy==1.9.1 -umap-learn==0.5.3 +pandas==1.5.1 +scanpy==1.9.5 +umap-learn==0.5.4 tqdm==4.64.1 seaborn==0.12.1 matplotlib==3.6.2 -scikit-misc==0.1.4 +scikit-misc==0.3 +torchaudio==2.1.0 +torchvision==0.16.0 torch==2.0.1 -PyYAML==6.0.1 \ No newline at end of file +PyYAML==6.0.1 From 4ae29516c2211e31e5c5ab7da48b0968406cb0e2 Mon Sep 17 00:00:00 2001 From: DoaneAS Date: Wed, 18 Oct 2023 14:37:27 -0400 Subject: [PATCH 2/4] Revert "updated requirements.txt" This reverts commit 8cf0cd4698d402b95f8273e279061052e290a126. --- requirements.txt | 18 ++++++++---------- 1 file changed, 8 insertions(+), 10 deletions(-) diff --git a/requirements.txt b/requirements.txt index 038df59..e8a2490 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,15 +1,13 @@ -scipy==1.11.3 -leidenalg==0.10.0 -numpy==1.24.4 +scipy==1.11.2 +leidenalg==0.8.10 +numpy==1.25.2 scikit-learn==1.3.1 -pandas==1.5.1 -scanpy==1.9.5 -umap-learn==0.5.4 +pandas==1.5.3 +scanpy==1.9.1 +umap-learn==0.5.3 tqdm==4.64.1 seaborn==0.12.1 matplotlib==3.6.2 -scikit-misc==0.3 -torchaudio==2.1.0 -torchvision==0.16.0 +scikit-misc==0.1.4 torch==2.0.1 -PyYAML==6.0.1 +PyYAML==6.0.1 \ No newline at end of file From 598507332a2e2b5973bd1ed1953709d730da9539 Mon Sep 17 00:00:00 2001 From: DoaneAS Date: Wed, 18 Oct 2023 14:43:12 -0400 Subject: [PATCH 3/4] fix for indexing error in get_inverse_phenotype --- genevector/embedding.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/genevector/embedding.py b/genevector/embedding.py index 9a19e44..77f4e20 100644 --- a/genevector/embedding.py +++ b/genevector/embedding.py @@ -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 From cad0f54d3b0e40d37119383c6b7ba2c46516138f Mon Sep 17 00:00:00 2001 From: DoaneAS Date: Sun, 12 Nov 2023 17:35:38 -0500 Subject: [PATCH 4/4] index on list error --- genevector/embedding.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/genevector/embedding.py b/genevector/embedding.py index 77f4e20..fef5c71 100644 --- a/genevector/embedding.py +++ b/genevector/embedding.py @@ -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)