diff --git a/README.md b/README.md index d1ab89a..b993f9c 100644 --- a/README.md +++ b/README.md @@ -56,7 +56,7 @@ import matplotlib.pyplot as plt from sklearn.cluster import KMeans from sklearn.decomposition import PCA import phate -import umap +import umap.umap_ as umap data = pd.read_csv('TM_data.csv', header=None, delim_whitespace=False) @@ -93,7 +93,7 @@ import scipy.io as sio import numpy as np import genomap.genoDR as gp import matplotlib.pyplot as plt -import umap +import umap.umap_ as umap dx = sio.loadmat('reducedData_divseq.mat') data=dx['X'] @@ -127,7 +127,7 @@ import matplotlib.pyplot as plt from sklearn.cluster import KMeans from sklearn.decomposition import PCA import phate -import umap +import umap.umap_ as umap import genomap.genoTraj as gp # Load data diff --git a/genomap/genoDR/genoDimReduction.py b/genomap/genoDR/genoDimReduction.py index 1ba3e74..52b1255 100644 --- a/genomap/genoDR/genoDimReduction.py +++ b/genomap/genoDR/genoDimReduction.py @@ -9,7 +9,7 @@ import scanpy as sc from sklearn.feature_selection import VarianceThreshold from tensorflow.keras.optimizers import Adam -import umap +import umap.umap_ as umap from genomap.genomap import construct_genomap from genomap.utils.ConvIDEC import ConvIDEC diff --git a/genomap/genoMOI/genoMOI.py b/genomap/genoMOI/genoMOI.py index 691168d..31859e6 100644 --- a/genomap/genoMOI/genoMOI.py +++ b/genomap/genoMOI/genoMOI.py @@ -6,7 +6,7 @@ """ from tensorflow.keras.optimizers import Adam -import umap +import umap.umap_ as umap import numpy as np import scanorama import phate diff --git a/genomap/genoVis/genoVis.py b/genomap/genoVis/genoVis.py index f53ebf9..25278dc 100644 --- a/genomap/genoVis/genoVis.py +++ b/genomap/genoVis/genoVis.py @@ -9,7 +9,7 @@ from genomap.utils.ConvIDEC import ConvIDEC from sklearn.feature_selection import VarianceThreshold from genomap.genomap import construct_genomap -import umap +import umap.umap_ as umap from genomap.utils.gTraj_utils import nearest_divisible_by_four import scanpy as sc import numpy as np diff --git a/requirements.txt b/requirements.txt index 550191a..9bb771a 100644 --- a/requirements.txt +++ b/requirements.txt @@ -18,5 +18,5 @@ scikit-learn tensorflow torch tqdm -umap +umap-learn diff --git a/setup.py b/setup.py index ad9566b..5f65a8c 100644 --- a/setup.py +++ b/setup.py @@ -5,7 +5,7 @@ setup( name="genomap", - version="1.3.3", + version="1.3.4", author="Md Tauhidul Islam", author_email="tauhid@stanford.edu", description="Genomap converts tabular gene expression data into spatially meaningful images.",