liana
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Error in `*tmp*`@metadata : no applicable method for `@` applied to an object of class "NULL"
I would appreciate it if you can help me. Not sure how to fix it.
> tensor <- liana_tensor_c2c(context_df_dict = context_df_dict,
+ sender_col = "source", # Column name of the sender cells
+ receiver_col = "target", # Column name of the receiver cells
+ ligand_col = "ligand.complex", # Column name of the ligands
+ receptor_col = "receptor.complex", # Column name of the receptors
+ score_col = 'magnitude_rank', # Column name of the communication scores to use
+ how='outer', # What to include across all samples
+ lr_fill = NaN, # What to fill missing LRs with
+ cell_fill = NaN, # What to fill missing cell types with
+ lr_sep='^', # How to separate ligand and receptor names to name LR pair
+ sort_elements = FALSE, # Whether sorting alphabetically element names of each tensor dim. Does not apply for context order if context_order is passed.
+ use_available = TRUE,
+ build_only = FALSE, # set this to FALSE to combine the downstream rank selection and decomposition steps all here
+ )
Building the tensor using magnitude_rank...
100%|██████████| 1/1 [00:03<00:00, 3.65s/it]Estimating ranks...
100%|██████████| 25/25 [09:01<00:00, 21.65s/it]Decomposing the tensor...
The rank at the elbow is: 6
Error in `*tmp*`@metadata :
no applicable method for `@` applied to an object of class "NULL"
> context_df_dict
$`4`
# A tibble: 18,919 × 6
source target ligand.complex receptor.complex magnitude_rank dataset
<chr> <chr> <chr> <chr> <dbl> <chr>
1 Oligodendrocytes Immature neurons IL1RAPL1 PTPRD 4.43e-13 4
2 Oligodendrocyte precursor cells GABAergic neurons NLGN1 NRXN3 6.92e-12 4
3 GABAergic neurons Oligodendrocyte precursor cells NRXN3 NLGN1 6.92e-12 4
4 Oligodendrocytes Unknown IL1RAPL1 PTPRD 2.84e-11 4
5 Oligodendrocytes Mature neurons IL1RAPL1 PTPRD 5.54e-11 4
6 Oligodendrocyte precursor cells Mature neurons NLGN1 NRXN3 1.22e-10 4
7 Mature neurons Oligodendrocyte precursor cells NRXN3 NLGN1 1.22e-10 4
8 Oligodendrocyte precursor cells Unknown NLGN1 NRXN3 2.72e-10 4
9 Unknown Oligodendrocyte precursor cells NRXN3 NLGN1 2.72e-10 4
10 Oligodendrocyte precursor cells Oligodendrocyte precursor cells NRXN1 NLGN1 5.13e-10 4
# ℹ 18,909 more rows
# ℹ Use `print(n = ...)` to see more rows