Commit a0defb2a authored by Gervaise Henry's avatar Gervaise Henry 🤠
Browse files

Remove tsne plotting from ID

parent 74ac6ca5
......@@ -118,11 +118,11 @@ if (ncol(sc10x.epi) > 1000) {
} else if (ncol(sc10x.epi) > 100) {
pc.calc.epi <- ncol(sc10x.epi)-1
}
results <- scPC(sc10x.epi,pc=pc.calc.epi,hpc=0.9,file="epi",print="2")
results <- scPC(sc10x.epi,pc=pc.calc.epi,hpc=0.9,file="epi",print="umap")
sc10x.epi <- results[[1]]
pc.use.epi <- results[[2]]
rm(results)
sc10x.epi <- scCluster(sc10x.epi,res=res,red="pca",dim=pc.use.epi,print="2",folder="epi")
sc10x.epi <- scCluster(sc10x.epi,res=res,red="pca",dim=pc.use.epi,print="umap",folder="epi")
#DimPlot(sc10x.epi,group.by="integrated_snn_res.0.1",reduction="umap",label=TRUE,repel=TRUE)+theme(legend.position="none")
if (ncol(sc10x.fmst) > 1000) {
......@@ -132,11 +132,11 @@ if (ncol(sc10x.fmst) > 1000) {
} else if (ncol(sc10x.fmst) > 100) {
pc.calc.fmst <- ncol(sc10x.fmst)-1
}
results <- scPC(sc10x.fmst,pc=pc.calc.fmst,hpc=0.9,file="fmst",print="2")
results <- scPC(sc10x.fmst,pc=pc.calc.fmst,hpc=0.9,file="fmst",print="umap")
sc10x.fmst <- results[[1]]
pc.use.fmst <- results[[2]]
rm(results)
sc10x.fmst <- scCluster(sc10x.fmst,res=res,red="pca",dim=pc.use.fmst,print="2",folder="fmst")
sc10x.fmst <- scCluster(sc10x.fmst,res=res,red="pca",dim=pc.use.fmst,print="umap",folder="fmst")
#DimPlot(sc10x.fmst,group.by="integrated_snn_res.0.1",reduction="umap",label=TRUE,repel=TRUE)+theme(legend.position="none")
if (ncol(sc10x.fib) > 1000) {
......@@ -146,11 +146,11 @@ if (ncol(sc10x.fib) > 1000) {
} else if (ncol(sc10x.fib) > 100) {
pc.calc.fib <- ncol(sc10x.fib)-1
}
results <- scPC(sc10x.fib,pc=pc.calc.fib,hpc=0.9,file="all",print="2")
results <- scPC(sc10x.fib,pc=pc.calc.fib,hpc=0.9,file="all",print="umap")
sc10x.fib <- results[[1]]
pc.use.fib <- results[[2]]
rm(results)
sc10x.fib <- scCluster(sc10x.fib,res=res,red="pca",dim=pc.use.fib,print="2",folder="fib")
sc10x.fib <- scCluster(sc10x.fib,res=res,red="pca",dim=pc.use.fib,print="umap",folder="fib")
#DimPlot(sc10x.fib,group.by="integrated_snn_res.0.1",reduction="umap",label=TRUE,repel=TRUE)+theme(legend.position="none")
if (ncol(sc10x.sm) > 1000) {
......@@ -160,11 +160,11 @@ if (ncol(sc10x.sm) > 1000) {
} else if (ncol(sc10x.sm) > 100) {
pc.calc.sm <- ncol(sc10x.sm)-1
}
results <- scPC(sc10x.sm,pc=pc.calc.sm,hpc=0.9,file="sm",print="2")
results <- scPC(sc10x.sm,pc=pc.calc.sm,hpc=0.9,file="sm",print="umap")
sc10x.sm <- results[[1]]
pc.use.sm <- results[[2]]
rm(results)
sc10x.sm <- scCluster(sc10x.sm,res=res,red="pca",dim=pc.use.sm,print="2",folder="sm")
sc10x.sm <- scCluster(sc10x.sm,res=res,red="pca",dim=pc.use.sm,print="umap",folder="sm")
#DimPlot(sc10x.sm,group.by="integrated_snn_res.0.1",reduction="umap",label=TRUE,repel=TRUE)+theme(legend.position="none")
if (ncol(sc10x.leu) > 1000) {
......@@ -174,11 +174,11 @@ if (ncol(sc10x.leu) > 1000) {
} else if (ncol(sc10x.leu) > 100) {
pc.calc.leu <- ncol(sc10x.leu)-1
}
results <- scPC(sc10x.leu,pc=pc.calc.leu,hpc=0.9,file="leu",print="2")
results <- scPC(sc10x.leu,pc=pc.calc.leu,hpc=0.9,file="leu",print="umap")
sc10x.leu <- results[[1]]
pc.use.leu <- results[[2]]
rm(results)
sc10x.leu <- scCluster(sc10x.leu,res=res,red="pca",dim=pc.use.leu,print="2",folder="leu")
sc10x.leu <- scCluster(sc10x.leu,res=res,red="pca",dim=pc.use.leu,print="umap",folder="leu")
#DimPlot(sc10x.leu,group.by="integrated_snn_res.0.1",reduction="umap",label=TRUE,repel=TRUE)+theme(legend.position="none")
if (opt$o == "pr" && opt$s == "hu") {
......
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