byarielm.fyi
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-1
R/seurat_maps.R
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R/seurat_maps.R
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seurat_Heatmap <- function(count,genematrix,ssGSEA_result,filename){
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count <- count[, !duplicated(colnames(count))]
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celltype <- intersect(colnames(count),ssGSEA_result[,1])
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labels <- ssGSEA_result[which(ssGSEA_result[,1]%in%celltype),]
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count <- count[,labels[,1]]
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seurat.data <- CreateSeuratObject(counts = count, project = filename)#, min.cells = 3, min.features = 200)
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seurat.data
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seurat.data[["percent.mt"]] <- PercentageFeatureSet(seurat.data, pattern = "^MT-")
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head(seurat.data@reductions$tsne@cell.embeddings)
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#Add annotation information to Seurat object
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seurat.data@meta.data$cell_type_pred <- ssGSEA_result[,2]
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seurat.data@meta.data$cell_type_pred <-labels[,2]
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pdf(paste(filename, "_tSNE", ".pdf", sep=""), width=12, height=10)
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p1 <- DimPlot(seurat.data, reduction = "tsne", group.by = "cell_type_pred",label = TRUE, pt.size=1)