search

satijalab / seurat

R toolkit for single cell genomics
http://www.satijalab.org/seurat
Other
2.26k stars 908 forks source link

featureplot #2061

Closed BenxiaHu closed 5 years ago

BenxiaHu commented 5 years ago

I have downloaded a scRNA-seq matrix which has been clustered or named the cell types. Now I do not want to reanalyze this data, I just want to make the featureplot for several genes with seurat. I am not sure whether it is possible to do this one. https://github.com/satijalab/seurat/issues/2030 scRNAseq<-read.table("singlecellexpression.txt",sep="\t",header=T) rownames(scRNAseq)<-scRNAseq[,1] scRNAseq<-scRNAseq[,-1] sc<-CreateSeuratObject(counts=scRNAseq,project="scRNAseq") head(sc) An object of class Seurat 1 features across 3462 samples within 1 assay Active assay: RNA (1 features) FeaturePlot(sc, features = 'GRIN2B',combine=FALSE,cols = c("lightgrey", "red")) which produced this error: Error in [[.Seurat(object, reduction) : Cannot find 'NA' in this Seurat object Do you know how to deal with it?

thanks in advance, best,

yuhanH commented 5 years ago

HI, The seurat object you generate doesn't have any reduction graph, so you cannot visualize it. When you create the seurat object, you still need to Normalize data, FindVariableFeatures ,Scale data, RunPCA, ect. You need to run the whole process in the pbmc tutorial. https://satijalab.org/seurat/v3.1/pbmc3k_tutorial.html Then, you can do the FeaturePlot.