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DLPFC issue creating Giotto object #5

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tkcaccia opened this issue Jul 6, 2023 · 0 comments
Open

DLPFC issue creating Giotto object #5

tkcaccia opened this issue Jul 6, 2023 · 0 comments

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@tkcaccia
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tkcaccia commented Jul 6, 2023

I following the R script "DLPFC_Giotto.R"

After I run the function here below:

##### 2. Create Giotto object & process data.
visium_brain <- createGiottoObject(raw_exprs = raw_matrix, 
                                   spatial_locs = spatial_locations[,.(row_pxl,-col_pxl)], 
                                   instructions = myinst, 
                                   cell_metadata = spatial_locations[,.(in_tissue, array_row, array_col)])

I meet the following error:

Error in data.table::setnames(meta[], old = ID_col_name, new = "cell_ID") : 
  Items of 'old' not found in column names: [cell_ID]. Consider skip_absent=TRUE.
In addition: Warning messages:
1: In createGiottoObject(raw_exprs = raw_matrix, spatial_locs = spatial_locations[,  :
  raw_exprs argument is deprecated, use expression argument in the future 

2: In evaluate_cell_metadata(metadata = metadata, verbose = verbose) :
  Cell metadata input: no col named cell_ID.
 Setting temporary NA values
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