def test_load_data_xls(self):
kwargs = {"header_rows": 0, "header_cols": 0}
xls_path = os.path.join(os.path.dirname(__file__), "data/data.xlsx")
xls_loader = ExcelLoader(xls_path)
xls_attrs, xls_X, xls_M, xls_M_index = xls_loader._load_data(**kwargs)
csv_loader = Loader(
os.path.join(os.path.dirname(__file__),
"data/DATA_MATRIX_LOG_TPM.txt"))
csv_attrs, csv_X, csv_M, csv_M_index = csv_loader._load_data(**kwargs)
self.assertEqual(xls_attrs, csv_attrs)
npt.assert_array_almost_equal(xls_X, csv_X)
npt.assert_array_equal(xls_M, csv_M)
npt.assert_array_equal(xls_M_index, csv_M_index)
def test_file_summary_gz(self):
file_name = os.path.join(os.path.dirname(__file__), "data/data.txt.gz")
loader = Loader(file_name)
self.assertEqual(loader.file_size, 361)
self.assertEqual(loader.n_rows, 10)
self.assertEqual(loader.n_cols, 15)
self.assertEqual(round(loader.sparsity, 2), 0.86)
def test_file_summary_broad(self):
file_name = os.path.join(os.path.dirname(__file__),
"data/DATA_MATRIX_LOG_TPM.txt")
loader = Loader(file_name)
self.assertAlmostEqual(loader.file_size, 1084, delta=15)
self.assertEqual(loader.n_rows, 10)
self.assertEqual(loader.n_cols, 15)
self.assertEqual(round(loader.sparsity, 2), 0.86)
def __init__(self):
super().__init__()
self._current_path = ""
self._data_loader = Loader()
icon_open_dir = self.style().standardIcon(QStyle.SP_DirOpenIcon)
# Top grid with file selection combo box
self.file_layout = grid = QGridLayout()
lb = QLabel("File:")
lb.setSizePolicy(QSizePolicy.Fixed, QSizePolicy.Fixed)
self.recent_combo = cb = QComboBox(
sizeAdjustPolicy=QComboBox.AdjustToMinimumContentsLengthWithIcon,
minimumContentsLength=20,
toolTip="Select a recent file")
self.recent_model = cb.model() # type: QStandardItemModel
self.recent_combo.activated[int].connect(self._select_recent)
browse = QPushButton("...",
autoDefault=False,
icon=icon_open_dir,
clicked=self.browse)
# reload = QPushButton("Reload", autoDefault=False, icon=icon_reload)
grid.addWidget(lb, 0, 0, Qt.AlignVCenter)
grid.addWidget(cb, 0, 1)
grid.addWidget(browse, 0, 2)
# grid.addWidget(reload, 0, 3)
self.summary_label = label = QLabel("", self)
label.ensurePolished()
f = label.font()
if f.pointSizeF() != -1:
f.setPointSizeF(f.pointSizeF() * 5 / 6)
else:
f.setPixelSize(f.pixelSize() * 5 / 6)
label.setFont(f)
grid.addWidget(label, 1, 1, 1, 3)
self.controlArea.layout().addLayout(grid)
box = gui.widgetBox(self.controlArea,
"Headers and Row Labels",
spacing=-1)
hl = QHBoxLayout()
hl.setContentsMargins(0, 0, 0, 0)
self.header_rows_spin = spin = QSpinBox(box,
minimum=0,
maximum=3,
value=self._header_rows_count,
keyboardTracking=False)
spin.valueChanged.connect(self.set_header_rows_count)
hl.addWidget(QLabel("Data starts with", box))
hl.addWidget(self.header_rows_spin)
hl.addWidget(QLabel("header row(s)", box))
hl.addStretch(10)
box.layout().addLayout(hl)
hl = QHBoxLayout()
hl.setContentsMargins(0, 0, 0, 0)
self.header_cols_spin = spin = QSpinBox(box,
minimum=0,
maximum=3,
value=self._header_cols_count,
keyboardTracking=False)
spin.valueChanged.connect(self.set_header_cols_count)
hl.addWidget(QLabel("First", box))
hl.addWidget(self.header_cols_spin)
hl.addWidget(QLabel("column(s) are row labels", box))
hl.addStretch(10)
box.layout().addLayout(hl)
self.data_struct_box = box = gui.widgetBox(self.controlArea,
"Input Data Structure")
gui.radioButtons(box,
self,
"_cells_in_rows", [
"Genes in rows, cells in columns",
"Cells in rows, genes in columns"
],
callback=self._cells_in_rows_changed)
box = gui.widgetBox(self.controlArea, "Sample Data", spacing=-1)
grid = QGridLayout()
grid.setContentsMargins(0, 0, 0, 0)
box.layout().addLayout(grid)
self.sample_rows_cb = cb = QCheckBox(checked=self._sample_rows_enabled)
self.sample_rows_p_spin = spin = QSpinBox(minimum=0,
maximum=100,
value=self._sample_rows_p)
spin.valueChanged.connect(self.set_sample_rows_p)
suffix = QLabel("% of cells")
cb.toggled.connect(self.set_sample_rows_enabled)
grid.addWidget(cb, 0, 0)
grid.addWidget(spin, 0, 1)
grid.addWidget(suffix, 0, 2)
self.sample_cols_cb = cb = QCheckBox(checked=self._sample_cols_enabled)
self.sample_cols_p_spin = spin = QSpinBox(minimum=0,
maximum=100,
value=self._sample_cols_p)
spin.valueChanged.connect(self.set_sample_cols_p)
suffix = QLabel("% of genes")
cb.toggled.connect(self.set_sample_cols_enabled)
grid.addWidget(cb, 1, 0)
grid.addWidget(spin, 1, 1)
grid.addWidget(suffix, 1, 2)
grid.setColumnStretch(3, 10)
self.annotation_files_box = box = gui.widgetBox(
self.controlArea, "Cell && Gene Annotation Files")
form = QFormLayout(
formAlignment=Qt.AlignLeft,
rowWrapPolicy=QFormLayout.WrapAllRows,
)
box.layout().addLayout(form)
self.row_annotations_cb = cb = QCheckBox(
"Cell annotations", checked=self._row_annotations_enabled)
self._row_annotations_w = w = QWidget(
enabled=self._row_annotations_enabled)
cb.toggled.connect(self.set_row_annotations_enabled)
cb.toggled.connect(w.setEnabled)
hl = QHBoxLayout()
hl.setContentsMargins(0, 0, 0, 0)
w.setLayout(hl)
self.row_annotations_combo = QComboBox(
sizeAdjustPolicy=QComboBox.AdjustToMinimumContentsLengthWithIcon,
minimumContentsLength=18)
self.row_annotations_combo.activated.connect(
self._row_annotations_combo_changed)
hl.addWidget(self.row_annotations_combo)
hl.addWidget(
QPushButton("...",
box,
autoDefault=False,
icon=icon_open_dir,
clicked=self.browse_row_annotations))
# hl.addWidget(QPushButton("Reload", box, autoDefault=False,
# icon=icon_reload))
form.addRow(cb, w)
self.col_annotations_cb = cb = QCheckBox(
"Gene annotations", checked=self._col_annotations_enabled)
self._col_annotations_w = w = QWidget(
enabled=self._col_annotations_enabled)
cb.toggled.connect(self.set_col_annotations_enabled)
cb.toggled.connect(w.setEnabled)
hl = QHBoxLayout()
hl.setContentsMargins(0, 0, 0, 0)
w.setLayout(hl)
self.col_annotations_combo = QComboBox(
sizeAdjustPolicy=QComboBox.AdjustToMinimumContentsLengthWithIcon,
minimumContentsLength=18)
self.col_annotations_combo.activated.connect(
self._col_annotations_combo_changed)
hl.addWidget(self.col_annotations_combo)
hl.addWidget(
QPushButton("...",
box,
autoDefault=False,
icon=icon_open_dir,
clicked=self.browse_col_annotations))
# hl.addWidget(QPushButton("Reload", box, autoDefault=False,
# icon=icon_reload))
form.addRow(cb, w)
self.controlArea.layout().addStretch(10)
self.load_data_button = button = VariableTextPushButton(
"Load data",
autoDefault=True,
textChoiceList=["Load data", "Reload"])
self.load_data_button.setAutoDefault(True)
button.clicked.connect(self.commit, Qt.QueuedConnection)
self.controlArea.layout().addWidget(button, alignment=Qt.AlignRight)
init_recent_paths_model(
self.recent_model,
[self.resolve_path(p) for p in self._recent],
)
init_recent_paths_model(
self.row_annotations_combo.model(),
[self.resolve_path(p) for p in self._recent_row_annotations])
init_recent_paths_model(
self.col_annotations_combo.model(),
[self.resolve_path(p) for p in self._recent_col_annotations])
self._update_summary()
self._update_warning()
if self._last_path != "" and os.path.exists(self._last_path):
QTimer.singleShot(0,
lambda: self.set_current_path(self._last_path))
else:
self.recent_combo.setCurrentIndex(-1)
def remove_item(self, index):
self.view.model().removeRows(index.row(), 1)
self.commit()
if not self.view.model().rowCount():
self.set_current_loader(Loader(), "")