View source: R/manifoldAlignment.R
manifoldAlignment | R Documentation |
Build comparable low-dimensional features for two weight-averaged denoised single-cell gene regulatory networks. Using a non-linear network embedding method manifoldAlignment
aligns two gene regulatory networks and finds the structural similarities between them. This function is a wrapper of the Python
code provided by Vu et al., (2012) at https://github.com/all-umass/ManifoldWarping.
manifoldAlignment(X, Y, d = 30, nCores = parallel::detectCores())
X |
A gene regulatory network. |
Y |
A gene regulatory network. |
d |
The dimension of the low-dimensional feature space. |
nCores |
An integer value. Defines the number of cores to be used. |
Manifold alignment builds connections between two or more disparate data sets by aligning their underlying manifolds and provides knowledge transfer across the data sets. For further information please see: Wang et al., (2009)
A low-dimensional projection for two the two gene regulatory networks used as input. The output is a labeled matrix with two times the number of shared genes as rows ( X_ genes followed by Y_ genes in the same order) and d
number of columns.
Vu, Hoa Trong, Clifton Carey, and Sridhar Mahadevan. "Manifold warping: Manifold alignment over time." Twenty-Sixth AAAI Conference on Artificial Intelligence. 2012.
Wang, Chang, and Sridhar Mahadevan. "A general framework for manifold alignment." 2009 AAAI Fall Symposium Series. 2009.
library(scTenifoldNet) # Simulating of a dataset following a negative binomial distribution with high sparcity (~67%) nCells = 2000 nGenes = 100 set.seed(1) X <- rnbinom(n = nGenes * nCells, size = 20, prob = 0.98) X <- round(X) X <- matrix(X, ncol = nCells) rownames(X) <- c(paste0('ng', 1:90), paste0('mt-', 1:10)) # Performing Single cell quality control qcOutput <- scQC( X = X, minLibSize = 30, removeOutlierCells = TRUE, minPCT = 0.05, maxMTratio = 0.1 ) # Computing 3 single-cell gene regulatory networks each one from a subsample of 500 cells xNetworks <- makeNetworks(X = X, nNet = 3, nCells = 500, nComp = 3, scaleScores = TRUE, symmetric = FALSE, q = 0.95 ) # Computing a K = 3 CANDECOMP/PARAFAC (CP) Tensor Decomposition tdOutput <- tensorDecomposition(xNetworks, K = 3, maxError = 1e5, maxIter = 1e3) ## Not run: # Computing the alignment # For this example, we are using the same input, the match should be perfect. maOutput <- manifoldAlignment(tdOutput$X, tdOutput$X) # Separating the coordinates for each gene X <- maOutput[grepl('X_', rownames(maOutput)),] Y <- maOutput[grepl('Y_', rownames(maOutput)),] # Plotting # X Points plot(X, pch = 16) # Y Points points(Y, col = 'red') # Legend legend('topright', legend = c('X', 'Y'), col = c('black', 'red'), bty = 'n', pch = c(16,1), cex = 0.7) ## End(Not run)
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