├── Examples ├── HSC.ipynb ├── MMD-MA-simulations.ipynb ├── Simulation1.ipynb ├── Simulation2.ipynb ├── readme.md ├── scGEM.ipynb └── scNMT.ipynb ├── LICENSE ├── MMD ├── s1_mapped1.txt ├── s1_mapped2.txt ├── s1_type1.txt ├── s1_type2.txt ├── s2_mapped1.txt ├── s2_mapped2.txt ├── s2_type1.txt ├── s2_type2.txt ├── s3_mapped1.txt ├── s3_mapped2.txt ├── s3_type1.txt └── s3_type2.txt ├── Model.py ├── README.md ├── UnionCom.py ├── __init__.py ├── __pycache__ ├── Match.cpython-36.pyc ├── Model.cpython-36.pyc ├── PrimeDual.cpython-36.pyc ├── Project.cpython-36.pyc ├── test.cpython-36.pyc ├── utils.cpython-36.pyc └── visualization.cpython-36.pyc ├── hsc ├── HSC_1.png ├── HSC_2.png ├── HSC_domains.png ├── HSC_types.png ├── domain1.txt ├── domain2.txt ├── logcounts_old.txt ├── logcounts_young.txt ├── old_type.txt ├── type1.txt ├── type1_predict.txt ├── type2.txt └── young_type.txt ├── scGEM ├── CellTypeEmbedding.png ├── DNAmethylation.txt ├── Embeddings.png ├── GeneExpression.txt ├── expression.png ├── methylation.png ├── new_data1.txt ├── new_data2.txt ├── readme.md ├── type1.txt └── type2.txt ├── scNMT ├── Eaccess_MOFA.txt ├── Emethy_MOFA.txt ├── Paccessibility_300.txt ├── Pmethylation_300.txt ├── README.md ├── RNA_300.txt ├── type1.txt ├── type2.txt └── type3.txt ├── simu1 ├── data1.txt ├── data2.txt ├── domain1.txt ├── domain2.txt ├── type1.txt └── type2.txt ├── simu2 ├── domain1.txt ├── domain2.txt ├── type1.txt └── type2.txt ├── test.py ├── utils.py ├── version.md └── visualization.py /Examples/readme.md: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | MIT License 2 | 3 | Copyright (c) 2020 Kai Cao 4 | 5 | Permission is hereby granted, free of charge, to any person obtaining a copy 6 | of this software and associated documentation files (the "Software"), to deal 7 | in the Software without restriction, including without limitation the rights 8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 9 | copies of the Software, and to permit persons to whom the Software is 10 | furnished to do so, subject to the following conditions: 11 | 12 | The above copyright notice and this permission notice shall be included in all 13 | copies or substantial portions of the Software. 14 | 15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 21 | SOFTWARE. 22 | -------------------------------------------------------------------------------- /MMD/s1_type1.txt: -------------------------------------------------------------------------------- 1 | 2.000000000000000000e+00 2 | 2.000000000000000000e+00 3 | 2.000000000000000000e+00 4 | 2.000000000000000000e+00 5 | 2.000000000000000000e+00 6 | 2.000000000000000000e+00 7 | 2.000000000000000000e+00 8 | 2.000000000000000000e+00 9 | 2.000000000000000000e+00 10 | 2.000000000000000000e+00 11 | 2.000000000000000000e+00 12 | 2.000000000000000000e+00 13 | 0.000000000000000000e+00 14 | 2.000000000000000000e+00 15 | 0.000000000000000000e+00 16 | 2.000000000000000000e+00 17 | 2.000000000000000000e+00 18 | 1.000000000000000000e+00 19 | 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2.000000000000000000e+00 299 | 2.000000000000000000e+00 300 | 0.000000000000000000e+00 301 | -------------------------------------------------------------------------------- /Model.py: -------------------------------------------------------------------------------- 1 | from torchvision import models 2 | import torch.nn as nn 3 | 4 | class model(nn.Module): 5 | def __init__(self, input_dim, output_dim): 6 | super(model, self).__init__() 7 | self.restored = False 8 | self.input_dim = input_dim 9 | self.output_dim = output_dim 10 | 11 | num = len(input_dim) 12 | feature = [] 13 | 14 | for i in range(num): 15 | feature.append( 16 | nn.Sequential( 17 | nn.Linear(self.input_dim[i],2*self.input_dim[i]), 18 | nn.BatchNorm1d(2*self.input_dim[i]), 19 | nn.LeakyReLU(0.1, True), 20 | nn.Linear(2*self.input_dim[i],2*self.input_dim[i]), 21 | nn.BatchNorm1d(2*self.input_dim[i]), 22 | nn.LeakyReLU(0.1, True), 23 | nn.Linear(2*self.input_dim[i],self.input_dim[i]), 24 | nn.BatchNorm1d(self.input_dim[i]), 25 | nn.LeakyReLU(0.1, True), 26 | nn.Linear(self.input_dim[i],self.output_dim), 27 | nn.BatchNorm1d(self.output_dim), 28 | nn.LeakyReLU(0.1, True), 29 | )) 30 | 31 | self.feature = nn.ModuleList(feature) 32 | 33 | self.feature_show = nn.Sequential( 34 | nn.Linear(self.output_dim,self.output_dim), 35 | nn.BatchNorm1d(self.output_dim), 36 | nn.LeakyReLU(0.1, True), 37 | nn.Linear(self.output_dim,self.output_dim), 38 | nn.BatchNorm1d(self.output_dim), 39 | nn.LeakyReLU(0.1, True), 40 | nn.Linear(self.output_dim,self.output_dim), 41 | ) 42 | 43 | def forward(self, input_data, domain): 44 | feature = self.feature[domain](input_data) 45 | feature = self.feature_show(feature) 46 | 47 | return feature 48 | 49 | 50 | 51 | 52 | 53 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # UnionCom 2 | ### We released new version [UnionCom2](https://github.com/caokai1073/UnionCom2) with fast and efficient implementation 3 | 4 | ## Paper 5 | [Unsupervised Topological Alignment for Single-Cell Multi-Omics Integration](https://academic.oup.com/bioinformatics/article/36/Supplement_1/i48/5870490) 6 | 7 | + Corrigendum: In the above paper, $1_{n_x\times n_y}$ on Pages i50 and i51 should be corrected as $1_{n_x\times n_x}$. The authors thank Dr. Chanwoo park from Seoul National University for pointing out this typo. 8 | 9 | ## Enviroment 10 | python >= 3.6 11 | 12 | numpy 1.19.5 13 | torch 1.7.0 14 | scipy 1.4.1 15 | torchvision 0.4.1 16 | scikit-learn 0.23.2 17 | umap-learn 0.3.10 18 | 19 | ## Install 20 | UnionCom software is available on the Python package index (PyPI), latest version 0.4.0. To install it using pip, simply type: 21 | ``` 22 | pip3 install unioncom 23 | ``` 24 | 25 | ## Change Log 26 | ### v0.4.0 27 | + Add batch effect correction method by setting integration_type="BatchCorrect"; 28 | + Add more distances (e.g. cosine, cityblock, see sklearn.metrics.pairwise) to formulate distance matrices. 29 | + Fix some bugs; 30 | 31 | ## Examples (jupyter notebook) 32 | 33 | + [Integration of simulation 1 in UnionCom paper](https://github.com/caokai1073/UnionCom/blob/master/Examples/Simulation1.ipynb) 34 | 35 | + [Integration of simulation 2 in UnionCom paper](https://github.com/caokai1073/UnionCom/blob/master/Examples/Simulation2.ipynb) 36 | 37 | + [Integration of simulations in MMD-MA paper](https://github.com/caokai1073/UnionCom/blob/master/Examples/MMD-MA-simulations.ipynb) 38 | 39 | + [Batch correction of HSC data](https://github.com/caokai1073/UnionCom/blob/master/Examples/HSC.ipynb) 40 | 41 | + [Integration of scGEM data](https://github.com/caokai1073/UnionCom/blob/master/Examples/scGEM.ipynb) 42 | 43 | + [Integration of scNMT data](https://github.com/caokai1073/UnionCom/blob/master/Examples/scNMT.ipynb) 44 | 45 | Each row should contain the measured values for a single cell, and each column should contain the values of a feature across cells. 46 | 47 | ```python 48 | >>> from unioncom import UnionCom 49 | >>> import numpy as np 50 | >>> data1 = np.loadtxt("./simu1/domain1.txt") 51 | >>> data2 = np.loadtxt("./simu1/domain2.txt") 52 | >>> type1 = np.loadtxt("./simu1/type1.txt") 53 | >>> type2 = np.loadtxt("./simu1/type2.txt") 54 | >>> type1 = type1.astype(np.int) 55 | >>> type2 = type2.astype(np.int) 56 | >>> uc = UnionCom.UnionCom() 57 | >>> integrated_data = uc.fit_transform(dataset=[data1,data2]) 58 | >>> uc.test_LabelTA(integrated_data, [type1,type2]) 59 | >>> uc.Visualize([data1,data2], integrated_data, mode='PCA') # without datatype 60 | >>> uc.Visualize([data1,data2], integrated_data, [type1,type2], mode='PCA') # with datatype 61 | ``` 62 | 63 | ## Parameters of ```class UnionCom``` 64 | 65 | The list of parameters is given below: 66 | > + ```epoch_pd```: epoch of Prime-dual algorithm (default=2000). 67 | > + ```epoch_DNN```: epoch of training Deep Neural Network (default=100). 68 | > + ```epsilon```: training rate of data matching matrix F (default=0.01). 69 | > + ```lr```: training rate of DNN (default=0.001). 70 | > + ```batch_size```: training batch size of DNN (default=100). 71 | > + ```rho```: training damping term (default=10). 72 | > + ```delay```: delay steps of alpha (default=0). 73 | > + ```beta```: trade-off parameter of structure preserving and point matching (default=1). 74 | > + ```perplexity```: perplexity of tsne projection (default=30) 75 | > + ```kmax```: maximum value of knn when constructing geodesic distance matrix (default=40). 76 | > + ```output_dim```: output dimension of integrated data (default=32). 77 | 78 | The other parameters include: 79 | > + ```log_pd```: log step of Prime Dual (default=1000). 80 | > + ```log_DNN```: log step of training DNN (default=10). 81 | > + ```manual_seed```: random seed (default=666). 82 | > + ```distance_mode```: mode of distance. ['geodesic' (suggested for multimodal integration), 'euclidean'(suggested for batch correction)] (default='geodesic'). 83 | > + ```project_mode```: mode of project, ['tsne', 'barycentric'] (default='tsne'). 84 | > + ```integration_type```: "MultiOmics" or "BatchCorrect". "BatchCorrect" needs aligned features. (default='MultiOmics') 85 | 86 | ### Contact via caokai1073@gmail.com 87 | 88 | -------------------------------------------------------------------------------- /__init__.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | # encoding=utf-8 3 | 4 | 5 | -------------------------------------------------------------------------------- /__pycache__/Match.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/caokai1073/UnionCom/d848749f41b7cd06ca823a9db1c21b94d22164fb/__pycache__/Match.cpython-36.pyc -------------------------------------------------------------------------------- /__pycache__/Model.cpython-36.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/caokai1073/UnionCom/d848749f41b7cd06ca823a9db1c21b94d22164fb/__pycache__/Model.cpython-36.pyc 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8.113254547119140625e+00 177 | 7.483322143554687500e+00 3.613697767257690430e+00 178 | -------------------------------------------------------------------------------- /scGEM/readme.md: -------------------------------------------------------------------------------- 1 | We obtained **Cheow_expression.csv** and **Cheow_methylation.csv** from https://github.com/jw156605/MATCHER 2 | -------------------------------------------------------------------------------- /scGEM/type1.txt: -------------------------------------------------------------------------------- 1 | 1.000000000000000000e+00 2 | 1.000000000000000000e+00 3 | 1.000000000000000000e+00 4 | 1.000000000000000000e+00 5 | 1.000000000000000000e+00 6 | 1.000000000000000000e+00 7 | 1.000000000000000000e+00 8 | 1.000000000000000000e+00 9 | 1.000000000000000000e+00 10 | 1.000000000000000000e+00 11 | 1.000000000000000000e+00 12 | 1.000000000000000000e+00 13 | 1.000000000000000000e+00 14 | 1.000000000000000000e+00 15 | 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ftp://ftp.ebi.ac.uk/pub/databases/scnmt_gastrulation. We are grateful to Dr. Stephen Clark for providing the parsed data. But it seems that they have updated their data in this link. So I attached the origin "gastrulation_scnmt_mofa.RData" data in google drive. ("gastrulation_scnmt_mofa.RData"). 4 | 5 | Data pre-proecessing: We use the Promoter accessibility (1940 cells with 2500 features), Promoter methylation (1940 cells with 2500 features) and RNA expression (1940 cells with 5000 features) in MOFAmodel/data/ of gastrulation_scnmt_mofa.RData. (See "Promoter_accessibility.txt, Promoter_methylation.txt, RNA.txt") 6 | 7 | However, the data are too many missing values ('NA') in accessibility and methylation. We did the following three steps 8 | 1) We replaced the 'NA' values with 0. 9 | 2) We then filtered out cells with all features being denoted as 0, resulting in 1940 cells with 5000 features in RNA expression, 709 cells with 2500 features in the methylation and 612 cells with 2500 features in the accessibility. 10 | 3) Afterwards, we found the UMAP can obtain a best perservation of the global structure of cell lineage for this dataset than PCA and t-SNE. Therefore, we applied UMAP to conduct the dimensionality reduction of each of the 3 dataset to a dimensionality of 300, respectively, prior to the alignment. 11 | (See attached "proecess.py", "Paccessibility_300.txt, Pmethylation_300.txt, RNA_300.txt") 12 | 13 | After that, the input matrices become 612\times 300 for accessibility, 709\times 300 for methylation and 1940\times 300 for RNA expression. The alignment of accessibility and methylation is relatively easy because they share most of the cells (See scNMT/process.pu and scNMT/match.txt). However, because RNA expression has 1940 cells, much more than the other two sets, the alignmnet of 3 datasets indeed needs some tricks 14 | 1) We chose the maximum connected subgraph of RNA expression data. (line173-178 in "UnionCom.py") 15 | 2) We used a MinMaxScaler normalization for RNA expression data. (line 179-180 in attached "UnionCom.py") 16 | The result of alignment are shown in "result/". 17 | 18 | In the original version, we did not use MOFA's built-in methods for preprocessing data, but we found it is a more efficient way. The "Eaccess_MOFA.txt" and "Emethy_MOFA.txt" in Github were preprocessed by MOFA built-in methods. The numbers in "type1.txt" and "type2.txt" mean different cell stages. ''0" represents "E5.5", '1" represents "E6.5".'2" represents "E7.5" (See "proecess.py" for the generation of "type1.txt" and "type2.txt"). 19 | 20 | In the scNMT-seq data we obtained, the authors of scNMT-seq paper did not provide the "E4.5" data. But they have already updated new data. According to my observation, the RNA expression is the most difficult to match. 21 | -------------------------------------------------------------------------------- /simu1/data1.txt: -------------------------------------------------------------------------------- 1 | -2.952967089462332329e+00 -1.243192229209767186e-01 2 | -2.888994763825714518e+00 1.420938704237206286e-02 3 | -2.856364661156406193e+00 1.399926450283258544e-02 4 | -2.801517788729420033e+00 -3.426015597227628079e-02 5 | -2.770418714602120858e+00 2.387817606711337137e-02 6 | -2.774062982759772922e+00 4.501145261611865650e-02 7 | -2.679917197263484319e+00 -1.069716669940298098e-02 8 | -2.599032959748796223e+00 2.380169244290751551e-02 9 | -2.554118846459177306e+00 -3.944222991952699153e-02 10 | -2.507205503435970595e+00 -4.912332887322817809e-02 11 | -2.498701562633141471e+00 1.967090847458874414e-02 12 | -2.477674409145111056e+00 6.323809599206510479e-03 13 | -2.441326814078627727e+00 3.884819304982563976e-02 14 | 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0.000000000000000000e+00 233 | 0.000000000000000000e+00 234 | 0.000000000000000000e+00 235 | 0.000000000000000000e+00 236 | 0.000000000000000000e+00 237 | 0.000000000000000000e+00 238 | 0.000000000000000000e+00 239 | 0.000000000000000000e+00 240 | 0.000000000000000000e+00 241 | 0.000000000000000000e+00 242 | 0.000000000000000000e+00 243 | 0.000000000000000000e+00 244 | 0.000000000000000000e+00 245 | 0.000000000000000000e+00 246 | 0.000000000000000000e+00 247 | 0.000000000000000000e+00 248 | 0.000000000000000000e+00 249 | 0.000000000000000000e+00 250 | 0.000000000000000000e+00 251 | -------------------------------------------------------------------------------- /test.py: -------------------------------------------------------------------------------- 1 | import os 2 | import random 3 | import numpy as np 4 | import scipy.sparse as sp 5 | from sklearn.neighbors import NearestNeighbors, KNeighborsClassifier 6 | 7 | def align_fraction(data1, data2): 8 | row1, col1 = np.shape(data1) 9 | row2, col2 = np.shape(data2) 10 | fraction = 0 11 | for i in range(row1): 12 | count = 0 13 | diffMat = np.tile(data1[i], (row2,1)) - data2 14 | sqDiffMat = diffMat**2 15 | sqDistances = sqDiffMat.sum(axis=1) 16 | for j in range(row2): 17 | if sqDistances[j] < sqDistances[i]: 18 | count += 1 19 | fraction += count / row2 20 | 21 | return fraction / row1 22 | 23 | def transfer_accuracy(domain1, domain2, type1, type2): 24 | knn = KNeighborsClassifier() 25 | knn.fit(domain2, type2) 26 | type1_predict = knn.predict(domain1) 27 | np.savetxt("type1_predict.txt", type1_predict) 28 | count = 0 29 | for label1, label2 in zip(type1_predict, type1): 30 | if label1 == label2: 31 | count += 1 32 | return count / len(type1) 33 | 34 | def test_UnionCom(integrated_data, datatype): 35 | 36 | for i in range(len(integrated_data)-1): 37 | # fraction = align_fraction(data[i], data[-1]) 38 | # print("average fraction:") 39 | # print(fraction) 40 | 41 | acc = transfer_accuracy(integrated_data[i], integrated_data[-1], datatype[i], datatype[-1]) 42 | print("label transfer accuracy of data{:d}:".format(i+1)) 43 | print(acc) 44 | -------------------------------------------------------------------------------- /utils.py: -------------------------------------------------------------------------------- 1 | import os 2 | import random 3 | import torch 4 | import torch.backends.cudnn as cudnn 5 | import numpy as np 6 | import scipy.sparse as sp 7 | from itertools import chain 8 | from sklearn.manifold import _utils 9 | from scipy.spatial.distance import squareform 10 | from scipy.sparse import csr_matrix, issparse 11 | from sklearn.neighbors import NearestNeighbors, KNeighborsClassifier 12 | from sklearn.metrics.pairwise import pairwise_distances 13 | 14 | MACHINE_EPSILON = np.finfo(np.double).eps 15 | 16 | def init_random_seed(manual_seed): 17 | seed = None 18 | if manual_seed is None: 19 | seed = random.randint(1,10000) 20 | else: 21 | seed = manual_seed 22 | print("use random seed: {}".format(seed)) 23 | random.seed(seed) 24 | np.random.seed(seed) 25 | torch.manual_seed(seed) 26 | if torch.cuda.is_available(): 27 | torch.cuda.manual_seed_all(seed) 28 | 29 | 30 | def init_model(net, device, restore): 31 | if restore is not None and os.path.exits(restore): 32 | net.load_state_dict(torch.load(restore)) 33 | net.restored = True 34 | print("Restore model from: {}".format(os.path.abspath(restore))) 35 | else: 36 | pass 37 | 38 | if torch.cuda.is_available(): 39 | cudnn.benchmark =True 40 | net.to(device) 41 | 42 | return net 43 | 44 | def save_model(net, model_root, filename): 45 | 46 | if not os.path.exists(model_root): 47 | os.makedirs(model_root) 48 | torch.save(net.state_dict(), os.path.join(model_root, filename)) 49 | print("save pretrained model to: {}".format(os.path.join(model_root, filename))) 50 | 51 | #input -||x_i-x_j||^2/2*sigma^2, compute softmax 52 | def softmax(D, diag_zero=True): 53 | # e_x = np.exp(D) 54 | e_x = np.exp(D - np.max(D, axis=1).reshape([-1, 1])) 55 | if diag_zero: 56 | np.fill_diagonal(e_x, 0) 57 | e_x = e_x + 1e-15 58 | return e_x / e_x.sum(axis=1).reshape([-1,1]) 59 | 60 | 61 | #input -||x_i-x_j||^2, compute P_ji = exp(-||x_i-x_j||^2/2*sigma^2)/sum(exp(-||x_i-x_j||^2/2*sigma^2)) 62 | def calc_P(distances, sigmas=None): 63 | if sigmas is not None: 64 | two_sig_sq = 2. * np.square(sigmas.reshape((-1, 1))) 65 | return softmax(distances / two_sig_sq) 66 | else: 67 | return softmax(distances) 68 | 69 | #a binary search algorithm for target 70 | def binary_search(eval_fn, target ,tol=1e-10, max_iter=10000, lower=1e-20, upper=1000.): 71 | for i in range(max_iter): 72 | guess = (lower + upper) /2. 73 | val = eval_fn(guess) 74 | if val > target: 75 | upper = guess 76 | else: 77 | lower = guess 78 | if np.abs(val - target) <= tol: 79 | break 80 | return guess 81 | 82 | #input matrix P, compute perp(P_i)=2^H(P_i), where H(P_i)=-sum(p_ij * log2 P_ij) 83 | def calc_perplexity(prob_matrix): 84 | entropy = -np.sum(prob_matrix * np.log2(prob_matrix), 1) 85 | perplexity = 2 ** entropy 86 | return perplexity 87 | 88 | #input -||x_i-x_j||^2 and sigma, out put perplexity 89 | def perplexity(distances, sigmas): 90 | return calc_perplexity(calc_P(distances, sigmas)) 91 | 92 | def find_optimal_sigmas(distances, target_perplexity): 93 | sigmas = [] 94 | for i in range(distances.shape[0]): 95 | eval_fn = lambda sigma: perplexity(distances[i:i+1, :], np.array(sigma)) 96 | correct_sigma = binary_search(eval_fn, target_perplexity) 97 | sigmas.append(correct_sigma) 98 | return np.array(sigmas) 99 | 100 | def p_conditional_to_joint(P): 101 | return (P + P.T) / (2. * P.shape[0]) 102 | 103 | def p_joint(X, target_perplexity): 104 | # distances = neg_squared_euc_dists(X) 105 | distances = -X 106 | sigmas = find_optimal_sigmas(distances, target_perplexity) 107 | p_conditional = calc_P(distances, sigmas) 108 | P = p_conditional_to_joint(p_conditional) 109 | return P 110 | 111 | def neg_square_dists(X): 112 | sum_X = torch.sum(X*X, 1) 113 | tmp = torch.add(-2 * X.mm(torch.transpose(X,1,0)), sum_X) 114 | D = torch.add(torch.transpose(tmp,1,0), sum_X) 115 | return -D 116 | 117 | def Q_tsne(Y): 118 | distances = neg_square_dists(Y) 119 | inv_distances = torch.pow(1. - distances, -1) 120 | inv_distances = inv_distances - torch.diag(inv_distances.diag(0)) 121 | inv_distances = inv_distances + 1e-15 122 | return inv_distances / torch.sum(inv_distances) 123 | 124 | 125 | def joint_probabilities(distances, desired_perplexity, verbose=0): 126 | """Compute joint probabilities p_ij from distances. 127 | 128 | Parameters 129 | ---------- 130 | distances : array, shape (n_samples * (n_samples-1) / 2,) 131 | Distances of samples are stored as condensed matrices, i.e. 132 | we omit the diagonal and duplicate entries and store everything 133 | in a one-dimensional array. 134 | 135 | desired_perplexity : float 136 | Desired perplexity of the joint probability distributions. 137 | 138 | verbose : int 139 | Verbosity level. 140 | 141 | Returns 142 | ------- 143 | P : array, shape (n_samples * (n_samples-1) / 2,) 144 | Condensed joint probability matrix. 145 | """ 146 | # Compute conditional probabilities such that they approximately match 147 | # the desired perplexity 148 | distances = distances.astype(np.float32, copy=False) 149 | 150 | conditional_P = _utils._binary_search_perplexity( 151 | distances, desired_perplexity, verbose) 152 | 153 | P = conditional_P + conditional_P.T 154 | 155 | 156 | sum_P = np.maximum(np.sum(P), MACHINE_EPSILON) 157 | 158 | # P = np.maximum(squareform(P) / sum_P, MACHINE_EPSILON) 159 | P = np.maximum(P / sum_P, MACHINE_EPSILON) 160 | 161 | return P 162 | 163 | def geodesic_distances(X, kmax): 164 | kmin = 5 165 | nbrs = NearestNeighbors(n_neighbors=kmin, metric='euclidean', n_jobs=-1).fit(X) 166 | knn = nbrs.kneighbors_graph(X, mode='distance') 167 | connected_components = sp.csgraph.connected_components(knn, directed=False)[0] 168 | while connected_components is not 1: 169 | if kmin > np.max((kmax, 0.01*len(X))): 170 | break 171 | kmin += 2 172 | nbrs = NearestNeighbors(n_neighbors=kmin, metric='euclidean', n_jobs=-1).fit(X) 173 | knn = nbrs.kneighbors_graph(X, mode='distance') 174 | connected_components = sp.csgraph.connected_components(knn, directed=False)[0] 175 | 176 | dist = sp.csgraph.floyd_warshall(knn, directed=False) 177 | 178 | dist_max = np.nanmax(dist[dist != np.inf]) 179 | dist[dist > dist_max] = 2*dist_max 180 | 181 | return dist 182 | 183 | def Maximum_connected_subgraph(X, kmax): 184 | kmin = 5 185 | 186 | nbrs = NearestNeighbors(n_neighbors=kmin, metric='euclidean', n_jobs=-1).fit(X) 187 | knn = nbrs.kneighbors_graph(X, mode='distance') 188 | connected_components = sp.csgraph.connected_components(knn, directed=False)[0] 189 | not_connected = False 190 | index = 0 191 | 192 | while connected_components is not 1: 193 | if kmin > np.max((kmax, 0.01*len(X))): 194 | not_connected = True 195 | break 196 | kmin += 2 197 | nbrs = NearestNeighbors(n_neighbors=kmin, metric='euclidean', n_jobs=-1).fit(X) 198 | knn = nbrs.kneighbors_graph(X, mode='distance') 199 | connected_components = sp.csgraph.connected_components(knn, directed=False)[0] 200 | 201 | dist = sp.csgraph.floyd_warshall(knn, directed=False) 202 | 203 | connected_element = [] 204 | if not_connected: 205 | inf_matrix = [] 206 | 207 | for i in range(len(X)): 208 | inf_matrix.append(list(chain.from_iterable(np.argwhere(np.isinf(dist[i]))))) 209 | 210 | for i in range(len(X)): 211 | if i==0: 212 | connected_element.append([]) 213 | connected_element[0].append(i) 214 | else: 215 | for j in range(len(connected_element)+1): 216 | if j == len(connected_element): 217 | connected_element.append([]) 218 | connected_element[j].append(i) 219 | break 220 | if inf_matrix[i] == inf_matrix[connected_element[j][0]]: 221 | connected_element[j].append(i) 222 | break 223 | for i in range(len(connected_element)): 224 | if i==0: 225 | mx = len(connected_element[0]) 226 | index = 0 227 | if len(connected_element[i])>mx: 228 | mx = len(connected_element[0]) 229 | index = i 230 | 231 | X = X[connected_element[index]] 232 | kmin = 5 233 | nbrs = NearestNeighbors(n_neighbors=kmin, metric='euclidean', n_jobs=-1).fit(X) 234 | knn = nbrs.kneighbors_graph(X, mode='distance') 235 | connected_components = sp.csgraph.connected_components(knn, directed=False)[0] 236 | while connected_components is not 1: 237 | kmin += 2 238 | nbrs = NearestNeighbors(n_neighbors=kmin, metric='euclidean', n_jobs=-1).fit(X) 239 | knn = nbrs.kneighbors_graph(X, mode='distance') 240 | connected_components = sp.csgraph.connected_components(knn, directed=False)[0] 241 | 242 | dist = sp.csgraph.floyd_warshall(knn, directed=False) 243 | 244 | return not_connected, connected_element, index 245 | 246 | def euclidean_distances(data): 247 | row, col = np.shape(data) 248 | dist = np.zeros((row, row)) 249 | for i in range(row): 250 | diffMat = np.tile(data[i], (row,1)) - data 251 | sqDiffMat = diffMat**2 252 | sqDistances = sqDiffMat.sum(axis=1) 253 | dist[i]=sqDistances 254 | return dist, 5 255 | 256 | 257 | 258 | 259 | 260 | 261 | 262 | 263 | -------------------------------------------------------------------------------- /version.md: -------------------------------------------------------------------------------- 1 | ## v0.1.6 2 | + Software optimization. 3 | + Change Euclidean distance to geodesic distance in KL divergence. 4 | 5 | ## v0.2.0 6 | + Software optimization. 7 | + Split function train into functions Match and Project. 8 | + Use Kuhn-Munkres to find optimal pairs between datasets instead of parbabilistic matrix matching. 9 | + Add a new parameter "project" to provide options for barycentric projection. 10 | 11 | ### v0.2.1 12 | + Software optimization 13 | + Split function "train" into functions "Match" and "Project" 14 | + Use Kuhn-Munkres algorithm to find optimal pairs between datasets instead of parbabilistic matrix matching 15 | + Add a new parameter "project" to provide options for barycentric projection 16 | + Separate "test_label_transfer_accuracy" function from "fit_transform" function 17 | + fix some bugs 18 | 19 | ## v0.2.2 20 | + Fix some bugs; 21 | + Change function "PCA_visualize" to "Visualize", and provide PCA, TSNE and UMAP for visulalization; 22 | + Add a function to find maximum connected subgraph; 23 | 24 | ## v0.3.0 25 | + Add more comments and make the software easier to understand; 26 | + Fix some bugs; -------------------------------------------------------------------------------- /visualization.py: -------------------------------------------------------------------------------- 1 | import numpy as np 2 | from matplotlib import pyplot as plt 3 | from sklearn.decomposition import PCA 4 | from sklearn.manifold import TSNE 5 | import umap 6 | 7 | def visualize(data, data_integrated, datatype=None, mode='PCA'): 8 | 9 | assert (mode in ["PCA", "UMAP", 'TSNE']), "mode has to be either one of 'PCA', 'UMAP', or 'TSNE'." 10 | 11 | dataset_num = len(data) 12 | 13 | # styles = ['g', 'r', 'b', 'y', 'k', 'm', 'c', 'greenyellow', 'lightcoral', 'teal'] 14 | # data_map = ['Chromatin accessibility', 'DNA methylation', 'Gene expression'] 15 | # color_map = ['E5.5','E6.5','E7.5'] 16 | embedding = [] 17 | dataset_xyz = [] 18 | for i in range(dataset_num): 19 | dataset_xyz.append("data{:d}".format(i+1)) 20 | if mode=='PCA': 21 | embedding.append(PCA(n_components=2).fit_transform(data[i])) 22 | elif mode=='TSNE': 23 | embedding.append(TSNE(n_components=2).fit_transform(data[i])) 24 | else: 25 | embedding.append(umap.UMAP(n_components=2).fit_transform(data[i])) 26 | 27 | fig = plt.figure() 28 | if datatype is not None: 29 | for i in range(dataset_num): 30 | plt.subplot(1,dataset_num,i+1) 31 | for j in set(datatype[i]): 32 | index = np.where(datatype[i]==j) 33 | plt.scatter(embedding[i][index,0], embedding[i][index,1], s=5.) 34 | plt.title(dataset_xyz[i]) 35 | if mode=='PCA': 36 | plt.xlabel('PCA-1') 37 | plt.ylabel('PCA-2') 38 | elif mode=='TSNE': 39 | plt.xlabel('TSNE-1') 40 | plt.ylabel('TSNE-2') 41 | else: 42 | plt.xlabel('UMAP-1') 43 | plt.ylabel('UMAP-2') 44 | # plt.title(data_map[i]) 45 | else: 46 | for i in range(dataset_num): 47 | plt.subplot(1,dataset_num,i+1) 48 | plt.scatter(embedding[i][:,0], embedding[i][:,1], s=5.) 49 | plt.title(dataset_xyz[i]) 50 | if mode=='PCA': 51 | plt.xlabel('PCA-1') 52 | plt.ylabel('PCA-2') 53 | elif mode=='TSNE': 54 | plt.xlabel('TSNE-1') 55 | plt.ylabel('TSNE-2') 56 | else: 57 | plt.xlabel('UMAP-1') 58 | plt.ylabel('UMAP-2') 59 | plt.title(dataset_xyz[i]) 60 | 61 | plt.tight_layout() 62 | 63 | data_all = np.vstack((data_integrated[0], data_integrated[1])) 64 | for i in range(2, dataset_num): 65 | data_all = np.vstack((data_all, data_integrated[i])) 66 | if mode=='PCA': 67 | embedding_all = PCA(n_components=2).fit_transform(data_all) 68 | elif mode=='TSNE': 69 | embedding_all = TSNE(n_components=2).fit_transform(data_all) 70 | else: 71 | embedding_all = umap.UMAP(n_components=2).fit_transform(data_all) 72 | 73 | tmp = 0 74 | num = [0] 75 | for i in range(dataset_num): 76 | num.append(tmp+np.shape(data_integrated[i])[0]) 77 | tmp += np.shape(data_integrated[i])[0] 78 | 79 | embedding = [] 80 | for i in range(dataset_num): 81 | embedding.append(embedding_all[num[i]:num[i+1]]) 82 | 83 | 84 | color = [[1,0.5,0], [0.2,0.4,0.1], [0.1,0.2,0.8], [0.5, 1, 0.5], [0.1, 0.8, 0.2]] 85 | # marker=['x','^','o','*','v'] 86 | 87 | fig = plt.figure() 88 | if datatype is not None: 89 | 90 | datatype_all = np.hstack((datatype[0], datatype[1])) 91 | for i in range(2, dataset_num): 92 | datatype_all = np.hstack((datatype_all, datatype[i])) 93 | 94 | plt.subplot(1,2,1) 95 | for i in range(dataset_num): 96 | plt.scatter(embedding[i][:,0], embedding[i][:,1], c=color[i], s=5., alpha=0.8) 97 | plt.title('Integrated Embeddings') 98 | if mode=='PCA': 99 | plt.xlabel('PCA-1') 100 | plt.ylabel('PCA-2') 101 | elif mode=='TSNE': 102 | plt.xlabel('TSNE-1') 103 | plt.ylabel('TSNE-2') 104 | else: 105 | plt.xlabel('UMAP-1') 106 | plt.ylabel('UMAP-2') 107 | 108 | plt.subplot(1,2,2) 109 | for j in set(datatype_all): 110 | index = np.where(datatype_all==j) 111 | plt.scatter(embedding_all[index,0], embedding_all[index,1], s=5., alpha=0.8) 112 | 113 | plt.title('Integrated Cell Types') 114 | if mode=='PCA': 115 | plt.xlabel('PCA-1') 116 | plt.ylabel('PCA-2') 117 | elif mode=='TSNE': 118 | plt.xlabel('TSNE-1') 119 | plt.ylabel('TSNE-2') 120 | else: 121 | plt.xlabel('UMAP-1') 122 | plt.ylabel('UMAP-2') 123 | 124 | else: 125 | 126 | for i in range(dataset_num): 127 | plt.scatter(embedding[i][:,0], embedding[i][:,1], c=color[i], s=5., alpha=0.8) 128 | plt.title('Integrated Embeddings') 129 | if mode=='PCA': 130 | plt.xlabel('PCA-1') 131 | plt.ylabel('PCA-2') 132 | elif mode=='TSNE': 133 | plt.xlabel('TSNE-1') 134 | plt.ylabel('TSNE-2') 135 | else: 136 | plt.xlabel('UMAP-1') 137 | plt.ylabel('UMAP-2') 138 | 139 | plt.tight_layout() 140 | plt.show() 141 | --------------------------------------------------------------------------------