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drieslab / Giotto

Spatial omics analysis toolbox
https://drieslab.github.io/Giotto_website/
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Error in validObject(.Object) #565

Open yunbokai opened 1 year ago

yunbokai commented 1 year ago

Hi, I get the Giotto object by giotto_st.RNA <- seuratToGiotto( st.RNA, spatial_assay = c("Spatial"), dim_reduction = c("pca", "umap","tsne"), subcellular_assay = "Vizgen" ) It seems that I already have the reduction information. However, I get ERROR : Error in validObject(.Object) : invalid class “dimObj” object: 1: invalid object for slot "spat_unit" in class "dimObj": got class "NULL", should be or extend class "character" invalid class “dimObj” object: 2: invalid object for slot "feat_type" in class "dimObj": got class "NULL", should be or extend class "character" when I run the code

plotPCA(giotto_st.RNA)

I check my object and find that the reduction information is exist. image Can you help me? Thanks a lot.

yunbokai commented 1 year ago

My pca is not a Gitto::dimObj, how to change it?