Commit cdf63c25 authored by Gervaise Henry's avatar Gervaise Henry 🤠
Browse files

Revert to sparse matrix for shiny out

parent c9d38b61
......@@ -990,7 +990,7 @@ scShinyOutput <- function(sc10x,anal="raw"){
exp.extra[4,] <- as.numeric(sc10x$percent.ribo)
exp.extra[5,] <- as.numeric(sc10x$Stress1)
exp <- rbind(exp,exp.extra)
#Matrix::writeMM(as(exp,"dgCMatrix"),file=paste0("./analysis/shiny/",anal,"/outs/filtered_feature_bc_matrix/matrix.mtx.gz"))
Matrix::writeMM(as(exp,"dgCMatrix"),file=paste0("./analysis/shiny/",anal,"/outs/filtered_feature_bc_matrix/matrix.mtx.gz")
Matrix::writeMM(exp,file=paste0("./analysis/shiny/",anal,"/outs/filtered_feature_bc_matrix/matrix.mtx.gz"))
for (i in c("pca","tsne","umap")){
dr <- Embeddings(sc10x,i)
......@@ -1038,4 +1038,4 @@ scShinyOutput <- function(sc10x,anal="raw"){
colnames(dexp) <- gsub("\\."," ",colnames(dexp))
write_csv(dexp,paste0("./analysis/shiny/",anal,"/outs/analysis/diffexp/",gsub("integrated_snn_res.","res_",i),"/differential_expression.csv"),col_names=TRUE)
}
}
\ No newline at end of file
}
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