def __init__(self):
super().__init__()
self.feature_model = DomainModel(valid_types=DiscreteVariable)
self._init_vars()
self._set_info_string()
box = gui.vBox(self.controlArea, "Cluster Variable")
gui.comboBox(box, self, "cluster_var", sendSelectedValue=True,
model=self.feature_model, callback=self._aggregate_data)
box = gui.vBox(self.controlArea, "Aggregation")
gui.comboBox(box, self, "aggregate_ix", sendSelectedValue=False,
items=self.AGGREGATE_NAME, callback=self._aggregate_data)
box = gui.vBox(self.controlArea, "Options")
gui.checkBox(box, self, "biclustering", "Order cells and genes",
callback=self._calculate_table_values)
gui.checkBox(box, self, "transpose", "Transpose",
callback=self._calculate_table_values)
gui.checkBox(box, self, "log_scale", "Log scale",
callback=self._calculate_table_values)
gui.checkBox(box, self, "normalize", "Normalize data",
callback=self._calculate_table_values)
box = gui.vBox(self.controlArea, "Plot Size")
gui.radioButtons(box, self, "cell_size_ix", btnLabels=("S", "M", "L"),
callback=lambda: self.tableview.set_cell_size(self.CELL_SIZES[self.cell_size_ix]),
orientation=Qt.Horizontal)
gui.rubber(self.controlArea)
self.apply_button = gui.auto_commit(
self.controlArea, self, "auto_apply", "&Apply", box=False)
self.tableview = ContingencyTable(self)
self.mainArea.layout().addWidget(self.tableview)
def __init__(self):
super().__init__()
self.ca = None
self.clusters = None
self.data = None
self.feature_model = DomainModel(valid_types=DiscreteVariable)
self.gene_list = None
self.model = None
self.pvalues = None
self._executor = ThreadExecutor()
self._gene_selection_history = (self.gene_selection,
self.gene_selection)
self._task = None
box = gui.vBox(self.controlArea, "Info")
self.infobox = gui.widgetLabel(box, self._get_info_string())
box = gui.vBox(self.controlArea, "Cluster Variable")
gui.comboBox(box,
self,
"cluster_var",
sendSelectedValue=True,
model=self.feature_model,
callback=self._run_cluster_analysis)
layout = QGridLayout()
self.gene_selection_radio_group = gui.radioButtonsInBox(
self.controlArea,
self,
"gene_selection",
orientation=layout,
box="Gene Selection",
callback=self._gene_selection_changed)
def conditional_set_gene_selection(id):
def f():
if self.gene_selection == id:
return self._set_gene_selection()
return f
layout.addWidget(
gui.appendRadioButton(self.gene_selection_radio_group,
"",
addToLayout=False), 1, 1)
cb = gui.hBox(None, margin=0)
gui.widgetLabel(cb, "Top")
self.n_genes_per_cluster_spin = gui.spin(
cb,
self,
"n_genes_per_cluster",
minv=1,
maxv=self.N_GENES_PER_CLUSTER_MAX,
controlWidth=60,
alignment=Qt.AlignRight,
callback=conditional_set_gene_selection(0))
gui.widgetLabel(cb, "genes per cluster")
gui.rubber(cb)
layout.addWidget(cb, 1, 2, Qt.AlignLeft)
layout.addWidget(
gui.appendRadioButton(self.gene_selection_radio_group,
"",
addToLayout=False), 2, 1)
mb = gui.hBox(None, margin=0)
gui.widgetLabel(mb, "Top")
self.n_most_enriched_spin = gui.spin(
mb,
self,
"n_most_enriched",
minv=1,
maxv=self.N_MOST_ENRICHED_MAX,
controlWidth=60,
alignment=Qt.AlignRight,
callback=conditional_set_gene_selection(1))
gui.widgetLabel(mb, "highest enrichments")
gui.rubber(mb)
layout.addWidget(mb, 2, 2, Qt.AlignLeft)
layout.addWidget(
gui.appendRadioButton(self.gene_selection_radio_group,
"",
addToLayout=False,
disabled=True), 3, 1)
sb = gui.hBox(None, margin=0)
gui.widgetLabel(sb, "User-provided list of genes")
gui.rubber(sb)
layout.addWidget(sb, 3, 2)
layout = QGridLayout()
self.differential_expression_radio_group = gui.radioButtonsInBox(
self.controlArea,
self,
"differential_expression",
orientation=layout,
box="Differential Expression",
callback=self._set_gene_selection)
layout.addWidget(
gui.appendRadioButton(self.differential_expression_radio_group,
"Overexpressed in cluster",
addToLayout=False), 1, 1)
layout.addWidget(
gui.appendRadioButton(self.differential_expression_radio_group,
"Underexpressed in cluster",
addToLayout=False), 2, 1)
layout.addWidget(
gui.appendRadioButton(self.differential_expression_radio_group,
"Either",
addToLayout=False), 3, 1)
box = gui.vBox(self.controlArea, "Sorting and Zoom")
gui.checkBox(box,
self,
"biclustering",
"Biclustering of analysis results",
callback=self._set_gene_selection)
gui.radioButtons(box,
self,
"cell_size_ix",
btnLabels=("S", "M", "L"),
callback=lambda: self.tableview.set_cell_size(
self.CELL_SIZES[self.cell_size_ix]),
orientation=Qt.Horizontal)
gui.rubber(self.controlArea)
self.apply_button = gui.auto_commit(self.controlArea,
self,
"auto_apply",
"&Apply",
box=False)
self.tableview = ContingencyTable(self)
self.mainArea.layout().addWidget(self.tableview)
class OWClusterAnalysis(widget.OWWidget):
name = "Cluster Analysis"
description = "Perform cluster analysis."
icon = "icons/ClusterAnalysis.svg"
priority = 2010
class Inputs:
data = Input("Data", Table, default=True)
genes = Input("Genes", Table)
class Outputs:
selected_data = Output("Selected Data", Table, default=True)
annotated_data = Output(ANNOTATED_DATA_SIGNAL_NAME, Table)
contingency = Output("Contingency Table", Table)
N_GENES_PER_CLUSTER_MAX = 10
N_MOST_ENRICHED_MAX = 50
CELL_SIZES = (14, 22, 30)
settingsHandler = DomainContextHandler(metas_in_res=True)
cluster_var = ContextSetting(None)
selection = ContextSetting(set())
gene_selection = ContextSetting(0)
differential_expression = ContextSetting(0)
cell_size_ix = ContextSetting(2)
_diff_exprs = ("high", "low", "either")
n_genes_per_cluster = ContextSetting(3)
n_most_enriched = ContextSetting(20)
biclustering = ContextSetting(True)
auto_apply = Setting(True)
want_main_area = True
def __init__(self):
super().__init__()
self.ca = None
self.clusters = None
self.data = None
self.feature_model = DomainModel(valid_types=DiscreteVariable)
self.gene_list = None
self.model = None
self.pvalues = None
self._executor = ThreadExecutor()
self._gene_selection_history = (self.gene_selection,
self.gene_selection)
self._task = None
box = gui.vBox(self.controlArea, "Info")
self.infobox = gui.widgetLabel(box, self._get_info_string())
box = gui.vBox(self.controlArea, "Cluster Variable")
gui.comboBox(box,
self,
"cluster_var",
sendSelectedValue=True,
model=self.feature_model,
callback=self._run_cluster_analysis)
layout = QGridLayout()
self.gene_selection_radio_group = gui.radioButtonsInBox(
self.controlArea,
self,
"gene_selection",
orientation=layout,
box="Gene Selection",
callback=self._gene_selection_changed)
def conditional_set_gene_selection(id):
def f():
if self.gene_selection == id:
return self._set_gene_selection()
return f
layout.addWidget(
gui.appendRadioButton(self.gene_selection_radio_group,
"",
addToLayout=False), 1, 1)
cb = gui.hBox(None, margin=0)
gui.widgetLabel(cb, "Top")
self.n_genes_per_cluster_spin = gui.spin(
cb,
self,
"n_genes_per_cluster",
minv=1,
maxv=self.N_GENES_PER_CLUSTER_MAX,
controlWidth=60,
alignment=Qt.AlignRight,
callback=conditional_set_gene_selection(0))
gui.widgetLabel(cb, "genes per cluster")
gui.rubber(cb)
layout.addWidget(cb, 1, 2, Qt.AlignLeft)
layout.addWidget(
gui.appendRadioButton(self.gene_selection_radio_group,
"",
addToLayout=False), 2, 1)
mb = gui.hBox(None, margin=0)
gui.widgetLabel(mb, "Top")
self.n_most_enriched_spin = gui.spin(
mb,
self,
"n_most_enriched",
minv=1,
maxv=self.N_MOST_ENRICHED_MAX,
controlWidth=60,
alignment=Qt.AlignRight,
callback=conditional_set_gene_selection(1))
gui.widgetLabel(mb, "highest enrichments")
gui.rubber(mb)
layout.addWidget(mb, 2, 2, Qt.AlignLeft)
layout.addWidget(
gui.appendRadioButton(self.gene_selection_radio_group,
"",
addToLayout=False,
disabled=True), 3, 1)
sb = gui.hBox(None, margin=0)
gui.widgetLabel(sb, "User-provided list of genes")
gui.rubber(sb)
layout.addWidget(sb, 3, 2)
layout = QGridLayout()
self.differential_expression_radio_group = gui.radioButtonsInBox(
self.controlArea,
self,
"differential_expression",
orientation=layout,
box="Differential Expression",
callback=self._set_gene_selection)
layout.addWidget(
gui.appendRadioButton(self.differential_expression_radio_group,
"Overexpressed in cluster",
addToLayout=False), 1, 1)
layout.addWidget(
gui.appendRadioButton(self.differential_expression_radio_group,
"Underexpressed in cluster",
addToLayout=False), 2, 1)
layout.addWidget(
gui.appendRadioButton(self.differential_expression_radio_group,
"Either",
addToLayout=False), 3, 1)
box = gui.vBox(self.controlArea, "Sorting and Zoom")
gui.checkBox(box,
self,
"biclustering",
"Biclustering of analysis results",
callback=self._set_gene_selection)
gui.radioButtons(box,
self,
"cell_size_ix",
btnLabels=("S", "M", "L"),
callback=lambda: self.tableview.set_cell_size(
self.CELL_SIZES[self.cell_size_ix]),
orientation=Qt.Horizontal)
gui.rubber(self.controlArea)
self.apply_button = gui.auto_commit(self.controlArea,
self,
"auto_apply",
"&Apply",
box=False)
self.tableview = ContingencyTable(self)
self.mainArea.layout().addWidget(self.tableview)
def _get_current_gene_selection(self):
return self._gene_selection_history[0]
def _get_previous_gene_selection(self):
return self._gene_selection_history[1]
def _progress_gene_selection_history(self, new_gene_selection):
self._gene_selection_history = (new_gene_selection,
self._gene_selection_history[0])
def _get_info_string(self):
formatstr = "Cells: {0}\nGenes: {1}\nClusters: {2}"
if self.data:
return formatstr.format(len(self.data),
len(self.data.domain.attributes),
len(self.cluster_var.values))
else:
return formatstr.format(*["No input data"] * 3)
@Inputs.data
@check_sql_input
def set_data(self, data):
if self.feature_model:
self.closeContext()
self.data = data
self.feature_model.set_domain(None)
self.ca = None
self.cluster_var = None
self.columns = None
self.clusters = None
self.gene_list = None
self.model = None
self.pvalues = None
self.n_genes_per_cluster_spin.setMaximum(self.N_GENES_PER_CLUSTER_MAX)
self.n_most_enriched_spin.setMaximum(self.N_MOST_ENRICHED_MAX)
if self.data:
self.feature_model.set_domain(self.data.domain)
if self.feature_model:
self.openContext(self.data)
if self.cluster_var is None:
self.cluster_var = self.feature_model[0]
self._run_cluster_analysis()
else:
self.tableview.clear()
else:
self.tableview.clear()
@Inputs.genes
def set_genes(self, data):
self.Error.clear()
gene_list_radio = self.gene_selection_radio_group.group.buttons()[2]
if (data is None or GENE_AS_ATTRIBUTE_NAME not in data.attributes
or not data.attributes[GENE_AS_ATTRIBUTE_NAME]
and GENE_ID_COLUMN not in data.attributes
or data.attributes[GENE_AS_ATTRIBUTE_NAME]
and GENE_ID_ATTRIBUTE not in data.attributes):
if data is not None:
self.error(
"Gene annotations missing in the input data. Use Gene Name Matching widget."
)
self.gene_list = None
gene_list_radio.setDisabled(True)
if self.gene_selection == 2:
self.gene_selection_radio_group.group.buttons()[
self._get_previous_gene_selection()].click()
else:
if data.attributes[GENE_AS_ATTRIBUTE_NAME]:
gene_id_attribute = data.attributes.get(
GENE_ID_ATTRIBUTE, None)
self.gene_list = tuple(
str(var.attributes[gene_id_attribute])
for var in data.domain.attributes
if gene_id_attribute in var.attributes
and var.attributes[gene_id_attribute] != "?")
else:
gene_id_column = data.attributes.get(GENE_ID_COLUMN, None)
self.gene_list = tuple(
str(v) for v in data.get_column_view(gene_id_column)[0]
if v not in ("", "?"))
gene_list_radio.setDisabled(False)
if self.gene_selection == 2:
self._set_gene_selection()
else:
gene_list_radio.click()
def _run_cluster_analysis(self):
self.infobox.setText(self._get_info_string())
gene_count = len(self.data.domain.attributes)
cluster_count = len(self.cluster_var.values)
self.n_genes_per_cluster_spin.setMaximum(
min(self.N_GENES_PER_CLUSTER_MAX, gene_count // cluster_count))
self.n_most_enriched_spin.setMaximum(
min(self.N_MOST_ENRICHED_MAX, gene_count))
# TODO: what happens if error occurs? If CA fails, widget should properly handle it.
self._start_task_init(
partial(ClusterAnalysis, self.data, self.cluster_var.name))
def _start_task_init(self, f):
if self._task is not None:
self.cancel()
assert self._task is None
self._task = Task("init")
def callback(finished):
if self._task.cancelled:
raise KeyboardInterrupt()
self.progressBarSet(finished * 50)
f = partial(f, callback=callback)
self.progressBarInit()
self._task.future = self._executor.submit(f)
self._task.watcher = FutureWatcher(self._task.future)
self._task.watcher.done.connect(self._init_task_finished)
def _start_task_gene_selection(self, f):
if self._task is not None:
self.cancel()
assert self._task is None
self._task = Task("gene_selection")
def callback(finished):
if self._task.cancelled:
raise KeyboardInterrupt()
self.progressBarSet(50 + finished * 50)
f = partial(f, callback=callback)
self.progressBarInit()
self.progressBarSet(50)
self._task.future = self._executor.submit(f)
self._task.watcher = FutureWatcher(self._task.future)
self._task.watcher.done.connect(self._gene_selection_task_finished)
@Slot(concurrent.futures.Future)
def _init_task_finished(self, f):
assert self.thread() is QThread.currentThread()
assert self._task is not None
assert self._task.future is f
assert f.done()
self._task = None
self.progressBarFinished()
self.ca = f.result()
self._set_gene_selection()
@Slot(concurrent.futures.Future)
def _gene_selection_task_finished(self, f):
assert self.thread() is QThread.currentThread()
assert self._task is not None
assert self._task.future is f
assert f.done()
self._task = None
self.progressBarFinished()
self.clusters, genes, self.model, self.pvalues = f.result()
genes = [str(gene) for gene in genes]
self.columns = DiscreteVariable("Gene", genes, ordered=True)
self.tableview.set_headers(
self.clusters,
self.columns.values,
circles=True,
cell_size=self.CELL_SIZES[self.cell_size_ix],
bold_headers=False)
def tooltip(i, j):
return (
"<b>cluster</b>: {}<br /><b>gene</b>: {}<br /><b>fraction expressing</b>: {:.2f}<br />\
<b>p-value</b>: {:.2e}".format(
self.clusters[i], self.columns.values[j], self.model[i, j],
self.pvalues[i, j]))
self.tableview.update_table(self.model, tooltip=tooltip)
self._invalidate()
def cancel(self):
"""
Cancel the current task (if any).
"""
if self._task is not None:
self._task.cancel()
assert self._task.future.done()
# disconnect the `_task_finished` slot
if self._task.type == "init":
self._task.watcher.done.disconnect(self._init_task_finished)
else:
self._task.watcher.done.disconnect(
self._gene_selection_task_finished)
self._task = None
def onDeleteWidget(self):
self.cancel()
super().onDeleteWidget()
def _gene_selection_changed(self):
if self.gene_selection != self._get_current_gene_selection():
self._progress_gene_selection_history(self.gene_selection)
self.differential_expression_radio_group.setDisabled(
self.gene_selection == 2)
self._set_gene_selection()
def _set_gene_selection(self):
self.Warning.clear()
if self.ca is not None and (self._task is None
or self._task.type != "init"):
if self.gene_selection == 0:
f = partial(self.ca.enriched_genes_per_cluster,
self.n_genes_per_cluster)
elif self.gene_selection == 1:
f = partial(self.ca.enriched_genes_data, self.n_most_enriched)
else:
if self.data is not None and GENE_ID_ATTRIBUTE not in self.data.attributes:
self.error(
"Gene annotations missing in the input data. Use Gene Name Matching widget."
)
if self.gene_selection == 2:
self.gene_selection_radio_group.group.buttons()[
self._get_previous_gene_selection()].click()
return
relevant_genes = tuple(self.ca.intersection(self.gene_list))
if len(relevant_genes) > self.N_MOST_ENRICHED_MAX:
self.warning("Only first {} reference genes shown.".format(
self.N_MOST_ENRICHED_MAX))
f = partial(self.ca.enriched_genes,
relevant_genes[:self.N_MOST_ENRICHED_MAX])
f = partial(
f,
enrichment=self._diff_exprs[self.differential_expression],
biclustering=self.biclustering)
self._start_task_gene_selection(f)
else:
self._invalidate()
def handleNewSignals(self):
self._invalidate()
def commit(self):
if len(self.selection):
cluster_ids = set()
column_ids = set()
for (ir, ic) in self.selection:
cluster_ids.add(ir)
column_ids.add(ic)
new_domain = Domain([
self.data.domain[self.columns.values[col]]
for col in column_ids
], self.data.domain.class_vars, self.data.domain.metas)
selected_data = Values([
FilterDiscrete(self.cluster_var, [self.clusters[ir]])
for ir in cluster_ids
],
conjunction=False)(self.data)
selected_data = selected_data.transform(new_domain)
annotated_data = create_annotated_table(
self.data.transform(new_domain),
np.where(np.in1d(self.data.ids, selected_data.ids, True)))
else:
selected_data = None
annotated_data = create_annotated_table(self.data, [])
if self.ca is not None and self._task is None:
table = self.ca.create_contingency_table()
else:
table = None
self.Outputs.selected_data.send(selected_data)
self.Outputs.annotated_data.send(annotated_data)
self.Outputs.contingency.send(table)
def _invalidate(self):
self.selection = self.tableview.get_selection()
self.commit()
def send_report(self):
rows = None
columns = None
if self.data is not None:
rows = self.cluster_var
if rows in self.data.domain:
rows = self.data.domain[rows]
columns = self.columns
if columns in self.data.domain:
columns = self.data.domain[columns]
self.report_items((
("Rows", rows),
("Columns", columns),
))
class OWDotMatrix(widget.OWWidget):
name = "Dot Matrix"
description = "Perform cluster analysis."
icon = "icons/DotMatrix.svg"
priority = 410
class Inputs:
data = Input("Data", Table, default=True)
class Outputs:
selected_data = Output("Selected Data", Table, default=True)
annotated_data = Output(ANNOTATED_DATA_SIGNAL_NAME, Table)
contingency = Output("Contingency Table", Table)
GENE_MAXIMUM = 100
CELL_SIZES = (14, 22, 30)
AGGREGATE_F = [
lambda x: np.mean(x, axis=0),
lambda x: np.median(x, axis=0),
lambda x: np.min(x, axis=0),
lambda x: np.max(x, axis=0),
lambda x: np.mean(x > 0, axis=0),
]
AGGREGATE_NAME = [
"Mean expression", "Median expression", "Min expression",
"Max expression", "Fraction expressing"
]
settingsHandler = DomainContextHandler(metas_in_res=True)
cluster_var = ContextSetting(None)
aggregate_ix = ContextSetting(0) # type: int
biclustering = ContextSetting(True)
transpose = ContextSetting(False)
log_scale = ContextSetting(False)
normalize = ContextSetting(True)
cell_size_ix = ContextSetting(2) # type: int
selection = ContextSetting(set())
auto_apply = Setting(True)
want_main_area = True
def __init__(self):
super().__init__()
self.data = None # type: Table
self.matrix = None
self.clusters = None
self.cluster_order = None
self.genes = None
self.gene_order = None
self.rows = None
self.columns = None
self.feature_model = DomainModel(valid_types=DiscreteVariable)
box = gui.vBox(self.controlArea, "Info")
self.infobox = gui.widgetLabel(box, self._get_info_string())
box = gui.vBox(self.controlArea, "Cluster Variable")
gui.comboBox(box,
self,
"cluster_var",
sendSelectedValue=True,
model=self.feature_model,
callback=self._calculate_table_values)
box = gui.vBox(self.controlArea, "Aggregation")
gui.comboBox(box,
self,
"aggregate_ix",
sendSelectedValue=False,
items=self.AGGREGATE_NAME,
callback=self._calculate_table_values)
box = gui.vBox(self.controlArea, "Options")
gui.checkBox(box,
self,
"biclustering",
"Biclustering of cells and genes",
callback=self._calculate_table_values)
gui.checkBox(box,
self,
"transpose",
"Transpose",
callback=self._refresh_table)
gui.checkBox(box,
self,
"log_scale",
"Log scale",
callback=self._refresh_table)
gui.checkBox(box,
self,
"normalize",
"Normalize data",
callback=self._refresh_table)
box = gui.vBox(self.controlArea, "Plot Size")
gui.radioButtons(box,
self,
"cell_size_ix",
btnLabels=("S", "M", "L"),
callback=lambda: self.tableview.set_cell_size(
self.CELL_SIZES[self.cell_size_ix]),
orientation=Qt.Horizontal)
gui.rubber(self.controlArea)
self.apply_button = gui.auto_commit(self.controlArea,
self,
"auto_apply",
"&Apply",
box=False)
self.tableview = ContingencyTable(self)
self.mainArea.layout().addWidget(self.tableview)
def _get_info_string(self):
formatstr = "{} genes, {} cells\n{} clusters"
if self.data:
return formatstr.format(len(self.data.domain.attributes),
len(self.data), len(self.clusters))
else:
return formatstr.format(*([0] * 3))
@Inputs.data
@check_sql_input
def set_data(self, data):
if self.feature_model:
self.closeContext()
self.data = data
self.matrix = None
self.feature_model.set_domain(None)
self.cluster_var = None
self.clusters = None
self.cluster_order = None
self.genes = None
self.gene_order = None
self.rows = None
self.columns = None
if self.data:
self.feature_model.set_domain(self.data.domain)
if self.feature_model:
self.Error.clear()
self.openContext(self.data)
if self.cluster_var is None:
self.cluster_var = self.feature_model[0]
self._calculate_table_values()
else:
self.tableview.clear()
self.error("No discrete variables in data.")
self.data = None
else:
self.tableview.clear()
self.Error.clear()
@staticmethod
def _group_by(table: Table, var: DiscreteVariable):
column = table.get_column_view(var)[0]
return (table[column == value] for value in np.unique(column))
def _calculate_table_values(self):
if self.data is None:
self.Warning.clear()
else:
self.clusters = [
self.cluster_var.values[int(ix)] for ix in np.unique(
self.data.get_column_view(self.cluster_var)[0])
]
self.genes = [var.name for var in self.data.domain.attributes]
self.infobox.setText(self._get_info_string())
if len(self.genes) > 100:
self.warning(
"Too many genes on input, first {} genes displayed.".
format(self.GENE_MAXIMUM))
else:
self.Warning.clear()
self.matrix = np.stack(
(self.AGGREGATE_F[self.aggregate_ix](
cluster.X[:self.GENE_MAXIMUM])
for cluster in self._group_by(self.data, self.cluster_var)),
axis=0)
if self.biclustering:
self.cluster_order, self.gene_order = ClusterAnalysis.biclustering(
self.matrix, ClusterAnalysis.neighbor_distance)
else:
self.cluster_order, self.gene_order = np.arange(
len(self.clusters)), np.arange(len(self.genes))
self.matrix = self.matrix[self.cluster_order][:, self.gene_order]
self._refresh_table()
self._invalidate()
def _refresh_table(self):
if self.matrix is not None:
if not self.transpose:
self.rows, self.columns = self.clusters, self.genes
row_order, column_order = self.cluster_order, self.gene_order
else:
self.rows, self.columns = self.genes, self.clusters
row_order, column_order = self.gene_order, self.cluster_order
self.tableview.set_headers(
np.array(self.rows)[row_order],
np.array(self.columns)[column_order],
circles=True,
cell_size=self.CELL_SIZES[self.cell_size_ix],
bold_headers=False)
if self.matrix.size > 0:
matrix = self.matrix
if self.log_scale:
matrix = np.log(matrix + 1)
if self.normalize:
matrix = (matrix - np.mean(matrix, axis=0, keepdims=True)
) / np.std(matrix, axis=0, keepdims=True)
matrix[matrix < -3] = -3
matrix[matrix > 3] = 3
matrix = matrix - matrix.min(axis=0, keepdims=True)
matrix = matrix / matrix.max(axis=0, keepdims=True)
else:
matrix = matrix - matrix.min()
matrix = matrix / matrix.max()
if self.transpose:
matrix = matrix.T
def tooltip(i, j):
if not self.transpose:
cluster, gene, value = self.clusters[i], self.genes[
j], self.matrix[i, j]
else:
cluster, gene, value = self.clusters[j], self.genes[
i], self.matrix[j, i]
return "Cluster: {}\nGene: {}\n{}: {:.1f}".format(
cluster, gene, self.AGGREGATE_NAME[self.aggregate_ix],
value)
self.tableview.update_table(matrix, tooltip=tooltip)
def commit(self):
if len(self.selection):
cluster_ids = set()
gene_ids = set()
for (ir, ic) in self.selection:
if not self.transpose:
cluster_ids.add(ir)
gene_ids.add(ic)
else:
cluster_ids.add(ic)
gene_ids.add(ir)
new_domain = Domain(
[self.data.domain[self.genes[i]] for i in gene_ids],
self.data.domain.class_vars, self.data.domain.metas)
selected_data = Values([
FilterDiscrete(self.cluster_var, [self.clusters[i]])
for i in cluster_ids
],
conjunction=False)(self.data)
selected_data = selected_data.transform(new_domain)
annotated_data = create_annotated_table(
self.data.transform(new_domain),
np.where(np.in1d(self.data.ids, selected_data.ids, True)))
else:
selected_data = None
annotated_data = create_annotated_table(self.data, [])
if self.matrix is not None:
table = ClusterAnalysis.contingency_table(
self.matrix,
DiscreteVariable(self.cluster_var.name,
np.array(self.clusters)),
np.array(self.genes)[self.gene_order],
self.cluster_order[..., np.newaxis])
else:
table = None
self.Outputs.selected_data.send(selected_data)
self.Outputs.annotated_data.send(annotated_data)
self.Outputs.contingency.send(table)
def _invalidate(self):
self.selection = self.tableview.get_selection()
self.commit()
class OWDotMatrix(widget.OWWidget):
name = "Dot Matrix"
description = "Perform cluster analysis."
icon = "icons/DotMatrix.svg"
priority = 410
class Inputs:
data = Input("Data", Table, default=True)
class Outputs:
selected_data = Output("Selected Data", Table, default=True)
annotated_data = Output(ANNOTATED_DATA_SIGNAL_NAME, Table)
contingency = Output("Contingency Table", Table)
class Error(OWWidget.Error):
no_discrete_variable = Msg("No discrete variables in data.")
class Warning(OWWidget.Warning):
to_many_attributes = Msg("Too many genes on input, first {} genes displayed.")
GENE_MAXIMUM = 100
CELL_SIZES = (14, 22, 30)
AGGREGATE_F = [
lambda x: np.mean(x, axis=0),
lambda x: np.median(x, axis=0),
lambda x: np.min(x, axis=0),
lambda x: np.max(x, axis=0),
lambda x: np.mean(x > 0, axis=0),
]
AGGREGATE_NAME = [
"Mean expression",
"Median expression",
"Min expression",
"Max expression",
"Fraction expressing"
]
settingsHandler = DomainContextHandler()
cluster_var = ContextSetting(None)
aggregate_ix = ContextSetting(0) # type: int
biclustering = ContextSetting(True)
transpose = ContextSetting(False)
log_scale = ContextSetting(False)
normalize = ContextSetting(True)
cell_size_ix = ContextSetting(2) # type: int
selection_indices = ContextSetting(set())
auto_apply = Setting(True)
want_main_area = True
def __init__(self):
super().__init__()
self.feature_model = DomainModel(valid_types=DiscreteVariable)
self._init_vars()
self._set_info_string()
box = gui.vBox(self.controlArea, "Cluster Variable")
gui.comboBox(box, self, "cluster_var", sendSelectedValue=True,
model=self.feature_model, callback=self._aggregate_data)
box = gui.vBox(self.controlArea, "Aggregation")
gui.comboBox(box, self, "aggregate_ix", sendSelectedValue=False,
items=self.AGGREGATE_NAME, callback=self._aggregate_data)
box = gui.vBox(self.controlArea, "Options")
gui.checkBox(box, self, "biclustering", "Order cells and genes",
callback=self._calculate_table_values)
gui.checkBox(box, self, "transpose", "Transpose",
callback=self._calculate_table_values)
gui.checkBox(box, self, "log_scale", "Log scale",
callback=self._calculate_table_values)
gui.checkBox(box, self, "normalize", "Normalize data",
callback=self._calculate_table_values)
box = gui.vBox(self.controlArea, "Plot Size")
gui.radioButtons(box, self, "cell_size_ix", btnLabels=("S", "M", "L"),
callback=lambda: self.tableview.set_cell_size(self.CELL_SIZES[self.cell_size_ix]),
orientation=Qt.Horizontal)
gui.rubber(self.controlArea)
self.apply_button = gui.auto_commit(
self.controlArea, self, "auto_apply", "&Apply", box=False)
self.tableview = ContingencyTable(self)
self.mainArea.layout().addWidget(self.tableview)
def _init_vars(self):
self.data = None # type: Table
self.matrix = None
self.clusters = None
self.clusters_unordered = None
self.aggregated_data = None
self.cluster_var = None
self.selected_names = {}
def _set_info_string(self):
formatstr = "{} genes\n{} cells\n{} clusters"
if self.data:
self.info.set_input_summary(
str(len(self.data)),
formatstr.format(len(self.data.domain.attributes), len(self.data), len(self.clusters_unordered)))
else:
self.info.set_input_summary(self.info.NoInput)
@Inputs.data
@check_sql_input
def set_data(self, data):
if self.feature_model:
self.closeContext()
self._init_vars()
self.Error.no_discrete_variable.clear()
self.Warning.clear()
self.data = data
if self.data:
self.feature_model.set_domain(self.data.domain)
if self.feature_model:
self.openContext(self.data)
if self.cluster_var is None:
self.cluster_var = self.feature_model[0]
self._aggregate_data()
else:
self.tableview.clear()
self.Error.no_discrete_variable()
self.data = None
self._set_info_string()
self.commit()
else:
self.tableview.clear()
self._set_info_string()
self.commit()
@staticmethod
def _group_by(table: Table, var: DiscreteVariable):
column = table.get_column_view(var)[0]
return (table[column == value] for value in np.unique(column))
@staticmethod
def _transpose(matrix: np.ndarray, clusters, genes):
return matrix.T, np.array([str(g) for g in genes]), [ContinuousVariable(c) for c in clusters]
@staticmethod
def _normalize(matrix: np.ndarray):
matrix = (matrix - np.mean(matrix, axis=0, keepdims=True)) / (
np.std(matrix, axis=0, keepdims=True) + 1e-10)
matrix[matrix < -3] = -3
matrix[matrix > 3] = 3
return matrix
@staticmethod
def _norm_min_max(matrix: np.ndarray):
matrix = matrix - matrix.min()
return matrix / (matrix.max() + 1e-12)
def _aggregate_data(self):
self.Warning.clear()
if self.data is None:
return
self.clusters_unordered = np.array(
[self.cluster_var.values[int(ix)]
for ix in np.unique(self.data.get_column_view(self.cluster_var)[0])])
self._set_info_string()
if len(self.data.domain.attributes) > self.GENE_MAXIMUM:
self.Warning.to_many_attributes(self.GENE_MAXIMUM)
self.aggregated_data = np.stack([self.AGGREGATE_F[self.aggregate_ix](cluster.X[:, :self.GENE_MAXIMUM])
for cluster in self._group_by(self.data, self.cluster_var)],
axis=0)
self._calculate_table_values()
def _calculate_table_values(self):
genes = self.data.domain.attributes[:self.GENE_MAXIMUM]
matrix = self.aggregated_data
clusters = self.clusters_unordered
if self.transpose:
matrix, clusters, genes = self._transpose(matrix, clusters, genes)
# create data table since imputation of nan values is required
matrix = Table(Domain(genes), matrix)
matrix_before_norm = matrix.copy() # for tooltip
matrix = SklImpute()(matrix)
if self.log_scale:
matrix.X = np.log(matrix.X + 1)
if self.normalize:
matrix.X = self._normalize(matrix.X)
# values must be in range [0, 1] for visualisation
matrix.X = self._norm_min_max(matrix.X)
if self.biclustering:
cluster_order, gene_order = self.cluster_data(matrix)
else:
cluster_order, gene_order = np.arange(matrix.X.shape[0]), np.arange(matrix.X.shape[1])
# reorder
self.matrix = matrix[cluster_order][:, gene_order]
self.matrix_before_norm = matrix_before_norm[cluster_order][:, gene_order]
self.clusters = clusters[cluster_order]
self._refresh_table()
self._update_selection()
self._invalidate()
def cluster_data(self, matrix):
with self.progressBar():
# cluster rows
if len(matrix) > 1:
rows_distances = Euclidean(matrix)
cluster = hierarchical.dist_matrix_clustering(rows_distances)
row_order = hierarchical.optimal_leaf_ordering(
cluster, rows_distances, progress_callback=self.progressBarSet)
row_order = np.array([x.value.index for x in leaves(row_order)])
else:
row_order = np.array([0])
# cluster columns
if matrix.X.shape[1] > 1:
columns_distances = Euclidean(matrix, axis=0)
cluster = hierarchical.dist_matrix_clustering(columns_distances)
columns_order = hierarchical.optimal_leaf_ordering(
cluster, columns_distances,
progress_callback=self.progressBarSet)
columns_order = np.array([x.value.index for x in leaves(columns_order)])
else:
columns_order = np.array([0])
return row_order, columns_order
def _refresh_table(self):
if self.matrix is None:
return
columns = np.array([str(x) for x in self.matrix.domain.attributes])
rows = self.clusters
# row_order, column_order = self.gene_order, self.cluster_order
self.tableview.set_headers(rows, columns, circles=True,
cell_size=self.CELL_SIZES[self.cell_size_ix], bold_headers=False)
if self.matrix.X.size > 0:
matrix = self.matrix.X
def tooltip(i, j):
cluster, gene, value = rows[i], columns[j], self.matrix_before_norm[i, j]
return "Cluster: {}\nGene: {}\n{}: {:.1f}".format(
cluster, gene, self.AGGREGATE_NAME[self.aggregate_ix], value)
self.tableview.update_table(matrix, tooltip=tooltip)
def commit(self):
if self.data is None:
self.Outputs.selected_data.send(None)
self.Outputs.annotated_data.send(None)
self.Outputs.contingency.send(None)
return
if len(self.selection_indices):
cluster_ids = set()
gene_ids = set()
for (ir, ic) in self.selection_indices:
if not self.transpose:
cluster_ids.add(ir)
gene_ids.add(ic)
else:
cluster_ids.add(ic)
gene_ids.add(ir)
columns = self.clusters if self.transpose else [str(x) for x in self.matrix.domain.attributes]
rows = self.clusters if not self.transpose else [str(x) for x in self.matrix.domain.attributes]
new_domain = Domain([self.data.domain[columns[i]] for i in gene_ids],
self.data.domain.class_vars,
self.data.domain.metas)
selected_data = Values([FilterDiscrete(self.cluster_var, [rows[i]])
for i in cluster_ids],
conjunction=False)(self.data)
selected_data = selected_data.transform(new_domain)
annotated_data = create_annotated_table(self.data,
np.where(np.in1d(self.data.ids, selected_data.ids, True)))
else:
selected_data = None
annotated_data = create_annotated_table(self.data, [])
clusters_values = list(set(self.clusters))
table = ClusterAnalysis.contingency_table(
self.matrix,
DiscreteVariable("Gene" if self.transpose else self.cluster_var.name, clusters_values),
[str(x) for x in self.matrix.domain.attributes],
[[clusters_values.index(c)] for c in self.clusters]
)
self.Outputs.selected_data.send(selected_data)
self.Outputs.annotated_data.send(annotated_data)
self.Outputs.contingency.send(table)
def _update_selection(self):
"""
This function updates widget selection in case when any item is selected.
It updates selection when order has changed
"""
rows = self.clusters.tolist()
columns = [str(x) for x in self.matrix.domain.attributes]
if self.transpose:
new_selection = {(rows.index(g), columns.index(c)) for g, c in self.selected_names}
else:
new_selection = {(rows.index(c), columns.index(g)) for g, c in self.selected_names}
self.tableview.set_selection(new_selection)
def _invalidate(self):
self.save_selection_names()
self.commit()
def save_selection_names(self):
"""
With this method we save the names of selected genes-clusters pairs, since options changes
the columns, rows orders and we want to keep the selection.
"""
self.selection_indices = self.tableview.get_selection()
genes = self.clusters if self.transpose else [str(x) for x in self.matrix.domain.attributes]
clusters = self.clusters if not self.transpose else [str(x) for x in self.matrix.domain.attributes]
if self.transpose:
self.selected_names = {(genes[g], clusters[c]) for g, c in self.selection_indices}
else:
self.selected_names = {(genes[g], clusters[c]) for c, g in self.selection_indices}