search

satijalab / seurat-data

Dataset distribution for Seurat
GNU General Public License v3.0
122 stars 45 forks source link

Help to understand spatial transcriptomic data #67

Open Lkz30 opened 1 year ago

Lkz30 commented 1 year ago

Hi everyone

I'm new in the part of spatial transcriptomic analysis from 10x Visium. I was checking Seurat and this tutorail (https://satijalab.org/seurat/articles/seurat5_spatial_vignette.html). I succeded to import my data from 10x, as a result I got a Seurat object called ava139

An object of class Seurat 18085 features across 638 samples within 1 assay Active assay: Spatial (18085 features, 0 variable features) 1 image present: slice1

I understood that all the information relevant to gene expression by spot is stored in this element: ava139@assays$Spatial@data where rownames are genes and column names are the spot which names started with AACACTTGGCAAGGAA-1 , with 638 columns (spots) and 18085 genes, but my question is... which type of information is in: ava139@assays$Spatial@data@p and ava139@assays$Spatial@data@i both of them are vectors the first one with 1845348 elements and the second one with 638 elements but with values from 0 to 1845348. I don't know is both of them are useful or not. I would like to use ggplot do the graphs but I don't know is these files are importat for the matrix construction or not.

Thanks for your help