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[FIX] LoadData - Manually add gene and cell annotations, correct Source name #401

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merged 3 commits into from
May 29, 2024
Merged

[FIX] LoadData - Manually add gene and cell annotations, correct Source name #401

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b8d96a3
Fix for gene annotation
lenatr99 May 15, 2024
e0663da
Check different file names for gene cell annotations.
lenatr99 May 22, 2024
3d7c04c
Fix for inheriting source names
lenatr99 May 22, 2024
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30 changes: 23 additions & 7 deletions orangecontrib/single_cell/widgets/load_data.py
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Original file line number Diff line number Diff line change
Expand Up @@ -488,10 +488,18 @@ def leading_cols(self, value):

def _set_annotation_files(self):
dir_name, _ = os.path.split(self._file_name)
genes_path = os.path.join(dir_name, "genes.tsv")
if os.path.isfile(genes_path):
self.col_annotation_file = RecentPath.create(genes_path, [])
barcodes_path = os.path.join(dir_name, "barcodes.tsv")
genes_paths = ['genes.tsv', 'features.tsv', 'genes.tsv.gz', 'features.tsv.gz']
for genes_path in genes_paths:
genes_path = os.path.join(dir_name, genes_path)
if os.path.isfile(genes_path):
self.col_annotation_file = RecentPath.create(genes_path, [])
break
barcodes_paths = ['barcodes.tsv', 'barcodes.tsv.gz']
for barcodes_path in barcodes_paths:
barcodes_path = os.path.join(dir_name, barcodes_path)
if os.path.isfile(barcodes_path):
self.row_annotation_file = RecentPath.create(barcodes_path, [])
break
if os.path.isfile(barcodes_path):
self.row_annotation_file = RecentPath.create(barcodes_path, [])

Expand Down Expand Up @@ -756,13 +764,21 @@ def key(var):
metas=sorted(metas, key=key))
concat_data_t = concat_data.transform(domain)
data_t = data.transform(domain)
source_var.values + (source_name, )

new_values = source_var.values + (source_name,)
new_source_var = DiscreteVariable(source_var.name, values=new_values)
new_metas = tuple(var if var.name != source_var.name else new_source_var for var in domain.metas)
new_domain = Domain(domain.attributes, metas=new_metas)
concat_data_t = concat_data_t.transform(new_domain)
data_t = data_t.transform(new_domain)
source_var_index = new_source_var.values.index(source_name)
# metas can be unlocked, source_var added to metas by append_source_name
with data_t.unlocked(data_t.metas):
data_t[:, source_var] = np.full(
(len(data), 1), len(source_var.values) - 1, dtype=object
data_t[:, new_source_var] = np.full(
(len(data_t), 1), source_var_index, dtype=object
)
concat_data = Table.concatenate((concat_data_t, data_t), axis=0)
source_var = new_source_var # Update source_var for the next iteration
return concat_data

@staticmethod
Expand Down
2 changes: 2 additions & 0 deletions orangecontrib/single_cell/widgets/owloaddata.py
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Original file line number Diff line number Diff line change
Expand Up @@ -613,6 +613,7 @@ def browse_row_annotations(self):
pathitem = RecentPath.create(filename, [])
index = insert_recent_path(m, pathitem)
self.row_annotations_combo.setCurrentIndex(index)
self._row_annotations_combo_changed()
self._invalidate()

@Slot()
Expand All @@ -632,6 +633,7 @@ def browse_col_annotations(self):
pathitem = RecentPath.create(filename, [])
index = insert_recent_path(m, pathitem)
self.col_annotations_combo.setCurrentIndex(index)
self._col_annotations_combo_changed()
self._invalidate()

def _invalidate(self):
Expand Down
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