Error in trainNMF(x = x, y = y, groups = groups, mgs = mgs, n_top = n_top, : ids %in% names(mgs) are not TRUE

[BenjaminDEMAILLE]

Hi I wanted to use SPLOTlight on spatial data but I'm facing some issue. can you help me ?

I run like this :

load("/Users/benjamin/Dropbox (U932)/Salmon team/Data_storage/Seq_data/scRNASeq/public_data/Lung/Grout_Leader_data_dn1000_SCT.RData")
genes <- !grepl(pattern = "^RP[L|S]|MT", x = rownames(Grout_Leader_data))
Grout_Leader_data <- subset(x = Grout_Leader_data, Cell_subtype %in% unique(mgs_df$cluster))
Grout_Leader_data <- subset(x = Grout_Leader_data, Cell_subtype %in% c("Mitocondrials", "Junk"), invert = T)

mgs <- scoreMarkers(as.SingleCellExperiment(Grout_Leader_data), 
                    groups = Grout_Leader_data$Cell_subtype, 
                    BPPARAM=MulticoreParam(parallel::detectCores()))

mgs_fil <- lapply(names(mgs), function(i) {
    x <- mgs[[i]]
    # Filter and keep relevant marker genes, those with AUC > 0.8
    x <- x[x$mean.AUC > 0.8, ]
    if (dim(x)[1]>0) {
      # Sort the genes from highest to lowest weight
      x <- x[order(x$mean.AUC, decreasing = TRUE), ]
      # Add gene and cluster id to the dataframe
      x$gene <- rownames(x)
      x$cluster <- i
      data.frame(x)
    }
})

mgs_df <- do.call(rbind, mgs_fil)

Grout_Leader_data <- subset(x = Grout_Leader_data, Cell_subtype %in% names(mgs))

Grout_Leader_data$Cell_subtype <- as.character(Grout_Leader_data$Cell_subtype)

Idents(Grout_Leader_data) <- as.character(Grout_Leader_data$Cell_subtype)

DefaultAssay(Grout_Leader_data) <- "RNA"
res <- SPOTlight(
    x = Grout_Leader_data,
    y = Plasticity_spatial.integrated,
    groups = as.character(Grout_Leader_data$Cell_subtype),
    mgs = mgs,
    weight_id = "median.AUC",
    group_id = "cluster",
    gene_id = "gene")

When I did :

names(mgs) %in% unique(Grout_Leader_data$Cell_subtype)

I got

 [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[33] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE

How can I do ?

thanks for your help

Both are Seurat object

[feasiblee]

Hello, how did you solve it, thank you.

[MarcElosua]

Hi apologies for the late response here, would it be possible to get a more extended error message to help me debug this?