Nothing
knitr::opts_chunk$set( collapse = TRUE, comment = "#>" )
library(bbknnR) library(Seurat) library(dplyr) library(patchwork) data("panc8_small")
Note that RunBBKNN()
also compute t-SNE and UMAP by default.
panc8_small <- RunBBKNN(panc8_small, batch_key = "tech")
panc8_small <- FindClusters(panc8_small, graph.name = "bbknn")
p1 <- DimPlot(panc8_small, reduction = "umap", group.by = "celltype", label = TRUE, label.size = 3 , repel = TRUE) + NoLegend() p2 <- DimPlot(panc8_small, reduction = "umap", group.by = "tech") p3 <- DimPlot(panc8_small, reduction = "umap") wrap_plots(list(p1, p2, p3), ncol = 1)
p1 <- DimPlot(panc8_small, reduction = "tsne", group.by = "celltype", label = TRUE, label.size = 3 , repel = TRUE) + NoLegend() p2 <- DimPlot(panc8_small, reduction = "tsne", group.by = "tech") p3 <- DimPlot(panc8_small, reduction = "tsne") wrap_plots(list(p1, p2, p3), ncol = 1)
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