How to run TransferData from single cell RNA from seurat object？

[mengchengyao]

Hi, thanks for your great tools. I have a problem to use it, How to run TransferData from single cell RNA from seurat object( with SCT method or normal method )？

[ludvigla]

You should be able to follow the Seurat spatial vignette to obtain cell type prediction scores.

[library](https://rdrr.io/r/base/library.html)([dplyr](https://dplyr.tidyverse.org/))
singlecell_reference <- [SCTransform](https://satijalab.org/seurat/reference/SCTransform.html)(singlecell_reference , ncells = 3000, verbose = FALSE) %>%
    [RunPCA](https://satijalab.org/seurat/reference/RunPCA.html)(verbose = FALSE) %>%
    [RunUMAP](https://satijalab.org/seurat/reference/RunUMAP.html)(dims = 1:30)

Prepare Visium data set

# Normalize Visium data
visium.se <- [SCTransform](https://satijalab.org/seurat/reference/SCTransform.html)(visium.se, verbose = FALSE) %>%
    [RunPCA](https://satijalab.org/seurat/reference/RunPCA.html)(verbose = FALSE)

Predict cell types in the Visium dataset

anchors <- [FindTransferAnchors](https://satijalab.org/seurat/reference/FindTransferAnchors.html)(reference = singlecell_reference, query = visium.se, normalization.method = "SCT")
predictions.assay <- [TransferData](https://satijalab.org/seurat/reference/TransferData.html)(anchorset = anchors, refdata = singlecell_reference$celltype, prediction.assay = TRUE,
    weight.reduction = cortex[["pca"]], dims = 1:30)
visium.se[["predictions"]] <- predictions.assay

Now you should be ab le to visualize cell type predictions scores with the STUtility visualization functions

ST.FeaturePlot(visium.se, features = "celltype1")