> For the complete documentation index, see [llms.txt](https://jieandze1314.osca.top/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://jieandze1314.osca.top/03/03-15.md). # 3.15 不同R包数据的相互转换 ## 1 前言 > 这部分内容是来自Seurat： 单细胞数据格式目前有这么几大派： * Bioconductor主导的SingleCellExperiment数据格式：例如scran、scater、monocle（尽管它的对象不直接使用SingleCellExperiment，但灵感来源于SingleCellExperiment，并且操作也是类似的） * Seurat：SeuratObject格式 * scanpy：AnnData格式 这么一来，很多分析流程就被固定在某个包中了，比如使用Seurat会一用到底，也不会去学习scater或其他R包了，但也许就错过了其他R包好用的一些功能（比如我感觉`scater`的`uniquifyFeatureNames`就很好用） 既然有需求，就有开发者添加功能 ，这里Davis McCarthy 和Alex Wolf就为Seurat添加了和其他数据类型转换的函数 ## 2 Seurat与SingleCellExperiment的相互转换 ```r library(scater) # devtools::install_github(repo = "satijalab/seurat", ref = "loom") library(loomR) library(Seurat) library(patchwork) ``` ### **2.1 Seurat转SingleCellExperiment** ```r # 使用Seurat内置数据 data("pbmc_small") > pbmc_small An object of class Seurat 230 features across 80 samples within 1 assay Active assay: RNA (230 features) 2 dimensional reductions calculated: pca, tsne # 一个函数即可 pbmc.sce <- as.SingleCellExperiment(pbmc_small) > pbmc.sce class: SingleCellExperiment dim: 230 80 metadata(0): assays(2): counts logcounts rownames(230): MS4A1 CD79B ... SPON2 S100B rowData names(5): vst.mean vst.variance vst.variance.expected vst.variance.standardized vst.variable colnames(80): ATGCCAGAACGACT CATGGCCTGTGCAT ... GGAACACTTCAGAC CTTGATTGATCTTC colData names(8): orig.ident nCount_RNA ... RNA_snn_res.1 ident reducedDimNames(2): PCA TSNE spikeNames(0): altExpNames(0): # 接下来就是scater的操作了 p1 <- plotExpression(pbmc.sce, features = "MS4A1", x = "ident") + theme(axis.text.x = element_text(angle = 45, hjust = 1)) p2 <- plotPCA(pbmc.sce, colour_by = "ident") p1 + p2 ``` ![](https://jieandze1314-1255603621.cos.ap-guangzhou.myqcloud.com/blog/2020-07-18-121906.png) ### **2.2 SingleCellExperiment转Seurat** ```r # 导入sce对象（https://scrnaseq-public-datasets.s3.amazonaws.com/scater-objects/manno_human.rds） manno <- readRDS(file = "manno_human.rds") > manno class: SingleCellExperiment dim: 20560 4029 metadata(0): assays(2): counts logcounts rownames(20560): 'MARC1' 'MARC2' ... ZZEF1 ZZZ3 rowData names(10): feature_symbol is_feature_control ... total_counts log10_total_counts colnames(4029): 1772122_301_C02 1772122_180_E05 ... 1772116-063_G02 1772099-259_H03 colData names(34): Species cell_type1 ... pct_counts_ERCC is_cell_control reducedDimNames(0): altExpNames(0): manno <- runPCA(manno) # 转为seurat对象 manno.seurat <- as.Seurat(manno, counts = "counts", data = "logcounts") # 看下这个函数 # as.Seurat( # x, # counts = "counts", # data = "logcounts", # assay = "RNA", # project = "SingleCellExperiment", # ... # ) # 既然有默认参数，因此直接按下面这么写就可以： manno.seurat <- as.Seurat(manno) > manno.seurat An object of class Seurat 20560 features across 4029 samples within 1 assay Active assay: RNA (20560 features) 1 dimensional reduction calculated: PCA Idents(manno.seurat) <- "cell_type1" p1 <- DimPlot(manno.seurat, reduction = "PCA", group.by = "Source") + NoLegend() p2 <- RidgePlot(manno.seurat, features = "ACTB", group.by = "Source") p1 + p2 ``` ![](https://jieandze1314-1255603621.cos.ap-guangzhou.myqcloud.com/blog/2020-07-18-115930.png) ## 3 Seurat与loom的相互转换 还记得上次在[单细胞交响乐16-处理大型数据](https://www.jianshu.com/p/786752478e08)中说到：处理大型数据遇到内存不足时，可以使用这个`HDF5Array`R包（类似的还有 `bigmemory`, `matter`），它会将底层数据做成HDF5格式，用硬盘空间来存储数据，必要时再调用一部分数据到内存。loom格式就是处理HDF5使用的 ### **3.1 Seurat转为loom** ```r pbmc.loom <- as.loom(pbmc, filename = "pbmc3k.loom", verbose = FALSE) pbmc.loom ## Class: loom ## Filename: /__w/1/s/output/pbmc3k.loom ## Access type: H5F_ACC_RDWR ## Attributes: version, chunks, LOOM_SPEC_VERSION, assay, last_modified ## Listing: ## name obj_type dataset.dims dataset.type_class ## col_attrs H5I_GROUP ## col_graphs H5I_GROUP ## layers H5I_GROUP ## matrix H5I_DATASET 2638 x 13714 H5T_FLOAT ## row_attrs H5I_GROUP ## row_graphs H5I_GROUP # 最后使用完要记得关上loom对象 pbmc.loom$close_all() ``` ### **3.2 loom转为Seurat** **首先读取：用 loomR 的connect** ```r l6.immune <- connect(filename = "../data/l6_r1_immune_cells.loom", mode = "r") l6.immune ## Class: loom ## Filename: /__w/1/s/data/l6_r1_immune_cells.loom ## Access type: H5F_ACC_RDONLY ## Attributes: CreationDate, last_modified ## Listing: ## name obj_type dataset.dims dataset.type_class ## col_attrs H5I_GROUP ## col_graphs H5I_GROUP ## layers H5I_GROUP ## matrix H5I_DATASET 14908 x 27998 H5T_FLOAT ## row_attrs H5I_GROUP ## row_graphs H5I_GROUP ``` **然后转换** ```r l6.seurat <- as.Seurat(l6.immune) VlnPlot(l6.seurat, features = c("Sparc", "Ftl1", "Junb", "Ccl4"), ncol = 2, pt.size = 0.1) ``` ![](https://jieandze1314-1255603621.cos.ap-guangzhou.myqcloud.com/blog/2020-07-18-120927.png) **最后处理完，记得关闭loom文件** ```r l6.immune$close_all() ``` ### **3.3 补充** **如果使用Seurat V2**，还有一个自带的函数`Convert` ```r data("pbmc_small") pbmc_small pfile <- Convert(from = pbmc_small, to = "loom", filename = "pbmc_small.loom", display.progress = FALSE) pfile ## Class: loom ## Filename: /home/paul/Documents/Satija/pbmc_small.loom ## Access type: H5F_ACC_RDWR ## Attributes: version, chunks ## Listing: ## name obj_type dataset.dims dataset.type_class ## col_attrs H5I_GROUP ## col_graphs H5I_GROUP ## layers H5I_GROUP ## matrix H5I_DATASET 80 x 230 H5T_FLOAT ## row_attrs H5I_GROUP ## row_graphs H5I_GROUP ``` ## 4 Scanpy转Seurat Seurat有一个函数`ReadH5AD`可以读取AnnData的H5AD文件 ```r pbmc3k <- ReadH5AD(file = "pbmc3k.h5ad") # 利用Seurat操作 Idents(pbmc3k) <- "louvain" p1 <- DimPlot(pbmc3k, label = TRUE) p2 <- VlnPlot(pbmc3k, features = c("CST3", "NKG7", "PPBP"), combine = FALSE) wrap_plots(c(list(p1), p2), ncol = 2) & NoLegend() ``` ![](https://jieandze1314-1255603621.cos.ap-guangzhou.myqcloud.com/blog/2020-07-18-121342.png) 目前还不能直接将Seurat写成H5AD文件，因此不能之间将Seurat转为Scanpy；但是可以将loom文件作为桥梁实现Seurat转Scanpy，例如`Scanpy` 有一个函数`scanpy.read_loom()` > 参考：