Closed GCatatGC closed 1 year ago
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.
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:
Thanks @GCatatGC for letting us know. I've pushed a fix for this problem. It should work now.
Thanks @GCatatGC for letting us know. I've pushed a fix for this problem. It should work now.
Thanks a lot ! It works now.
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
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 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.
Thanks a lot for all the remarkable work!
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:
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...
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.