An error from createGiottoCosMxObject() with the Giotto 3.0

[GCatatGC]

Hi.
I am excited for the saveGiotto() function in new version 3.0, so I installed it today (3pm, 11/19/2022).
And I was following the tutorial of Cosmx (https://giottosuite.readthedocs.io/en/latest/subsections/datasets/Nanostring_Lung12_jan26_21.html).
On CosMx Project loading function chapter, I got an error:

fov_join = createGiottoCosMxObject(cosmx_dir = data_path,
                                    data_to_use = 'subcellular',
                                    FOVs = c(2,3,4),
                                    instructions = instrs)

A structured CosMx directory will be used

Checking directory contents...
--| CellLabels folder found
--| CompartmentLabels folder found
--| CellComposite folder found
--| CellOverlay folder found
--| transcript locations file found
--| fov positions file found
--| expression matrix file found
--| metadata file found
Directory check done
Loading subcellular information...
Subcellular load done
Starting FOV 002
Loading image information...
Image load done
Building subcellular giotto object...

1. Start extracting polygon information
   polygonlist is a list with names
   [ cell ] Process polygon info...
   Error in match.arg(mask_method, choices = c("guess", "single", "multiple")) :
   'arg' must be NULL or a character vector

Unfortunately, I did not save the previous version (Giotto 2.0).

Can we fix this error in Giotto3.0? Because I really want to use the saveGiotto() function.

[RubD]

The createGiottoCosMxObject is probably not yet updated, but the step-by-step workflow might work. This would mean starting from #2 and not use the convenience function.

[GCatatGC]

The createGiottoCosMxObject is probably not yet updated, but the step-by-step workflow might work. This would mean starting from #2 and not use the convenience function.

Hi RubD,
Thanks for your reply.
I ran step-by-step workflow and it resulted into similar error.

fovsubset = createGiottoObjectSubcellular(gpoints = list('rna' = tx_coord), gpolygons = list('cell' = segmentation_mask), polygon_mask_list_params = list(mask_method = 'guess', flip_vertical = TRUE, flip_horizontal = FALSE, shift_horizontal_step = FALSE), instructions = instrs)
and got:

1. Start extracting polygon information
   polygonlist is a list with names
   [ cell ] Process polygon info...
   Error in match.arg(mask_method, choices = c("guess", "single", "multiple")) :
   'arg' must be NULL or a character vector

[RubD]

Thanks @GCatatGC for letting us know. I've pushed a fix for this problem. It should work now.

[GCatatGC]

Thanks @GCatatGC for letting us know. I've pushed a fix for this problem. It should work now.

Thanks a lot ! It works now.

[GCatatGC]

Thanks @GCatatGC for letting us know. I've pushed a fix for this problem. It should work now.

Hi RubD,
I got a new error when I ran "Annotate Giotto object" part, in the tutorial of Nanostring_Lung1

#add cell types

clusters_cell_types_lung = c('Normal Epithelial', 'Cancer', 'Stromal', 'Plasma Cells',
                             'Cytotoxic T Cells', 'Cancer Stem Cells',
                             'Macrophage', 'Memory B Cell', 'Memory B Cell')

names(clusters_cell_types_lung) = as.character(sort(cluster_order))

fov_join = annotateGiotto(gobject = fov_join,
                          annotation_vector = clusters_cell_types_lung,
                          cluster_column = 'leiden_clus')

plotUMAP(fov_join,
         cell_color = 'cell_types',
         point_size = 1.5)

The Error is:
Error in get_cell_metadata(gobject, spat_unit = spat_unit, feat_type = feat_type, :
metadata referenced is not cellMetaObj

[jiajic]

Hi RubD, I got a new error when I ran "Annotate Giotto object" part, in the tutorial of Nanostring_Lung1

#add cell types

clusters_cell_types_lung = c('Normal Epithelial', 'Cancer', 'Stromal', 'Plasma Cells',
                             'Cytotoxic T Cells', 'Cancer Stem Cells',
                             'Macrophage', 'Memory B Cell', 'Memory B Cell')

names(clusters_cell_types_lung) = as.character(sort(cluster_order))

fov_join = annotateGiotto(gobject = fov_join,
                          annotation_vector = clusters_cell_types_lung,
                          cluster_column = 'leiden_clus')

plotUMAP(fov_join,
         cell_color = 'cell_types',
         point_size = 1.5)

The Error is: Error in get_cell_metadata(gobject, spat_unit = spat_unit, feat_type = feat_type, : metadata referenced is not cellMetaObj

Hi @GCatatGC, thank you for letting us know about this error.
createGiottoCosMxObject() has been partially updated for the 'subcellular' workflow in the 3.1 update (#458). The issue with annotateGiotto() was also addressed.

The CosMx tutorial has also been updated.

[GCatatGC]

Thanks a lot for all the remarkable work!