Nothing
knitr::opts_chunk$set( fig.width = 6, fig.align = "center", collapse = TRUE, comment = "#>" )
library(Canek) library(Seurat)
x <- lapply(names(SimBatches$batches), function(batch) { CreateSeuratObject(SimBatches$batches[[batch]], project = batch) }) x <- merge(x[[1]], x[[2]]) x[["cell_type"]] <- SimBatches$cell_types x
table(x$orig.ident)
x <- NormalizeData(x) x <- FindVariableFeatures(x, nfeatures=100) VariableFeaturePlot(x)
x <- ScaleData(x)
x <- RunPCA(x)
DimPlot(x, group.by = "orig.ident") DimPlot(x, group.by = "cell_type")
We pass the column containing the batch information.
x <- RunCanek(x, "orig.ident")
The features selected during integration are assigned as variable features.
head(VariableFeatures(x, assay="Canek"))
We scale features and run PCA.
x <- ScaleData(x) x <- RunPCA(x)
DimPlot(x, group.by = "orig.ident") DimPlot(x, group.by = "cell_type")
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