WhichCells(object = object, downsample = 500): https://satijalab.org/seurat/reference/WhichCells.html [12] WhichCells(object = object, expression = name > low & name < high): https://satijalab.org/seurat/reference/WhichCells.html [13] subset(x = object, subset = name > low & name...
DimPlot(pbmc) pbmc.no.umap <- pbmc pbmc.no.umap[["umap"]] <- NULL DimPlot(pbmc.no.umap) + RotatedAxis() # DoHeatmap now shows a grouping bar, splitting the heatmap into groups or clusters. This can be changed with the `group.by` parameter DoHeatmap(pbmc, features = VariableFeatu...
final, downsample = 100), features = features, size = 3) FeaturePlot新增功能 代码语言:javascript 复制 # Plot a legend to map colors to expression levels FeaturePlot(pbmc3k.final, features = "MS4A1") 代码语言:javascript 复制 # Adjust the contrast in the plot FeaturePlot(pbmc3k.final, ...
这里注意Idents的应用,可以直接指定meta.data某一列作为pbmc@active.ident.演示完了,我们再把标签换回来。 # alternately : DimPlot(pbmc, reduction = 'umap', group.by = 'replicate') you can pass the # shape.by to label points by both replicate and cell type # Switch back to cell type labels ...
DoHeatmap(subset(pbmc, downsample = 100), features = features, size = 3) 接下来我们一起看看基于R编程语言的Seurat包的5个基础函数的可视化,如何使用Python编程语言进行“平替”: 基于R编程语言的Seurat包 library(Seurat) library(ggplot2) library(gridExtra) ...
subset(x = pbmc, downsample = 100) 多个Seurat对象的合并 # Merge两个Seurat对象 merge(x = pbmc1, y = pbmc2) # Merge多个Seurat对象 merge(x = pbmc1, y = list(pbmc2, pbmc3)) 3. 数据访问 #查看metadata数据库框, metadata存储在object@meta.data ...
DoHeatmap(subset(pbmc, downsample = 100), features = features, size = 3) new-additions-to-featureplot # Plot a legend to map colors to expression levels FeaturePlot(pbmc, features = "MS4A1") # Adjust the contrast in the plot FeaturePlot(pbmc, features = "MS4A1", min.cutoff = 1, max...
"CD8A",'FOXP3', 'FCGR3A', 'MS4A7', 'GNLY', 'NKG7', 'FCER1A', 'CST3','PPBP') ##气泡图 DotPlot(pbmc, features = unique(features)) + RotatedAxis() #downsample 在每个细胞亚群中均抽样100个细胞做热图 DoHeatmap(subset(pbmc, downsample = 100), features = features, size = 3) ...
[--downsample downsample] [--legend.position legend.position [legend.position ...]] [--group.by group.by] [-H height] [-W width] [-o outdir] [-p prefix] Seurat single cell qc analysis : https://nbisweden.github.io/workshop- ...
0.1, slot = "counts")3.4 DotPlot DotPlot(object = object, features = genes)3.5 DoHeatmap DoHeatmap(object = object, features = genes)由于不同cluster细胞数目不同，建议抽样之后再画 DoHeatmap(object = object, features = genes, cells = downsampledCells)...