diff --git a/README.md b/README.md index a7299ed..5a155d0 100644 --- a/README.md +++ b/README.md @@ -35,7 +35,7 @@ GeneVector makes use of Scanpy anndata objects and requires that the raw count d ``` from genevector.data import GeneVectorDataset -from genevector.model import GeneVectorTrainer +from genevector.model import GeneVectorModel, GeneVector from genevector.embedding import GeneEmbedding, CellEmbedding import scanpy as sc @@ -50,7 +50,6 @@ After loading the expression, creating a GeneVector object will compute the mutu cmps = GeneVector(dataset, output_file="genes.vec", emb_dimension=100, - threshold=1e-6, device="cuda") cmps.train(1000, threshold=1e-6) # run for 1000 iterations or loss delta below 1e-6. ``` @@ -69,7 +68,7 @@ gembed = GeneEmbedding("genes.vec", dataset, vector="average") ``` #### 1. Computing gene similarities -A pandas dataframe can be generated using ```compute_similarities``` that includes the most similar genes and their cosine similarities for a given gene query. A barplot figure with a specified number of the most similar genes can be generated using ```plots_similarities```. +A pandas dataframe can be generated using ```compute_similarities``` that includes the most similar genes and their cosine similarities for a given gene query. A barplot figure with a specified number of the most similar genes can be generated using ```plot_similarities```. ``` df = gembed.compute_similarities("CD8A") diff --git a/requirements.txt b/requirements.txt index 0c7c0e9..13b97b9 100644 --- a/requirements.txt +++ b/requirements.txt @@ -10,4 +10,4 @@ tqdm==4.64.1 seaborn==0.12.1 matplotlib==3.6.2 scikit-misc==0.1.4 -torch==">=1.8.0" +torch>=1.8.0