source('/scSVAtools/R/FUNCTIONS.R');
NNG_InputParameters<-jsonlite::read_json("/home/NNG_InputParameters.json",simplifyVector = T)
if(NNG_InputParameters$path==""){
file_name<-"/home/DMap_eigenvectors_output.csv"
} else {
file_name<-NNG_InputParameters$path
}
start.time <- Sys.time()
mat<-as.matrix(fread(file_name,nThread = NNG_InputParameters$nThreads))
NNs<-GetANNs(mat,
nNN = NNG_InputParameters$nNN,
nThreads = NNG_InputParameters$nThreads,
returnDistance = FALSE,
nTrees = NNG_InputParameters$nTrees,
M = NNG_InputParameters$M,
efC = NNG_InputParameters$efC,
efS = NNG_InputParameters$efS,
AnnMethod = NNG_InputParameters$AnnMethod
)
end.time <- Sys.time()
print(paste0("Total NNG Computation Time: ",as.numeric(end.time-start.time, units = "secs")," secs"))
#save adjacency table
fwrite(x = as.data.frame(cbind(1:nrow(NNs$NN.ind),NNs$NN.ind)),
file = "/home/NNG_output.csv",
nThread = NNG_InputParameters$nThreads,
quote = F,
row.names = F,
col.names = F
)
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