针对您提出的“error: cannot find 'umap' in this seurat object”问题,这里有几个可能的解决方案和检查步骤,帮助您解决这个问题: 确认'umap'是否已正确安装在环境中: 虽然UMAP通常作为Seurat包的一部分自动安装,但确保您的R环境中已安装并加载了Seurat包。您可以通过以下代码来安装和加载Seurat包: R if (!requi...
已知单细胞常见的可视化方式有DimPlot,FeaturePlot ,DotPlot ,VlnPlot 和 DoHeatmap集中 ,在Seurat中均可以实现,本次再介绍一种更惊艳的umap图。 2022年发表于Cell Metabolism 的Mapping the single-cell transcriptomic response of murine diabetic kidney disease to therapies 文献中有一张主图中绘制的细胞大群及亚群...
Hi, I'm excited to use the new integration with UMAP but I can't get it to work. Below is the R code and verification that it is installed. > scRNAseq.integrated <- RunUMAP(object = scRNAseq.integrated, reduction = "pca", dims = 1:30) Er...
Thank you in advance for any great help! Best, Yue > pbmc_batch <- RunPCA(object = pbmc_batch, seed.use=123, npcs=50, features = VariableFeatures(object = pbmc_batch), ndims.print=1,nfeatures.print=1) PC_ 1 Positive: C1QC Negative: GPM6A > pbmc_batch <- RunUMAP(pbmc_batch, ...
test<- system.file("extdata","seuratTest.RDS", package ="scRNAtoolVis") tmp <- readRDS(test) 具体见最开始参考教程。自己使用的一个示例: library(scRNAtoolVis) png(paste0("featureplot-main_marker.png"), width =18, height =6, res =400, units ="in") ...
锁定版本: seurat-4.1.0, seurat-object-4.0.4 截止 2022.1.31 1.调包侠出场 单细胞转录组典型分析代码:Seurat 4 单细胞转录组分析核心代码 # step 11 Run non-linear dimensional reduction (UMAP/tSNE) # If you haven't installed UMAP, you can do so via reticulate::py_install(packages = 'umap-le...
error in evaluating the argument 'x' in selecting a method for function 't': object 'R_empty_factors' not found my sessionInfo: > sessionInfo() R version 4.0.5 (2021-03-31) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 18362) ...
First I want to thank you for sharing this great work. It is very useful for me. The first time I execute UMAP fit and transform I get some numba warnings. They do not seem to be critical, but they are somewhat disturbing. numba.__versio...