diff --git a/Docs/ChangeLog.md b/Docs/ChangeLog.md index 6416b49..4bef56c 100644 --- a/Docs/ChangeLog.md +++ b/Docs/ChangeLog.md @@ -1,3 +1,9 @@ +# Version: 1.107.5 +## Date: 2024-06-18 +### Changes: +- Fix: Fixed the bug of when plot the Taxa-Functions Network, the fcous list items which are not linked to any other items were not removed. +- Change: Changed the default label width of the Taxa-Functions Network plot to 300 characters, then the label will be broken into multiple lines if the label is too long. + # Version: 1.107.4 ## Date: 2024-06-17 ### Changes: diff --git a/utils/GUI.py b/utils/GUI.py index a1a4e7a..e7dfee7 100644 --- a/utils/GUI.py +++ b/utils/GUI.py @@ -167,7 +167,8 @@ def __init__(self, MainWindow): 'taxa_color': '#374E55','taxa_focus_color': '#6A6599', 'func_color': '#DF8F44', 'func_focus_color': '#B24745', 'line_opacity': 0.5, 'line_width': 3, 'line_curve': 0, - 'line_color': '#9aa7b1', 'repulsion': 500, 'font_weight': 'bold' + 'line_color': '#9aa7b1', 'repulsion': 500, 'font_weight': 'bold', + 'label_position':"bottom", 'text_width' : 300, 'gravity' : 0.2 } @@ -516,7 +517,7 @@ def get_table_by_df_type(self, df_type:str | None = None, dft = self.tfa.replace_if_two_index(dft) return dft - def get_list_by_df_type(self, df_type:str) -> list: + def get_list_by_df_type(self, df_type:str, remove_no_linked:bool=False, silent:bool=False) -> list|None: ''' return the list of df_type, ignore capital case df_type: str, one of ['taxa', 'functions', 'taxa-functions', 'peptides', 'proteins', 'custom'] @@ -532,6 +533,10 @@ def get_list_by_df_type(self, df_type:str) -> list: res_list = list_dict.get(df_type, None) if res_list is None: raise ValueError(f"Invalid df_type: {df_type}") + + if remove_no_linked and df_type in ['taxa', 'functions', 'taxa-functions']: + res_list = self.remove_no_linked_taxa_and_func_after_filter_tflink(res_list, type=df_type, silent=silent) + return res_list def change_event_checkBox_basic_plot_table(self): @@ -2718,30 +2723,6 @@ def update_func_taxa_group_to_combobox(self): - - #! This function seems not used - # def show_others_linked(self): - # func = self.comboBox_others_func.currentText().strip() - # taxa = self.comboBox_others_taxa.currentText().strip() - # self.logger.write_log(f'show_others_linked: func: {func}, taxa: {taxa}') - # try: - # if not func and not taxa: - # QMessageBox.warning(self.MainWindow, 'Warning', 'Please select function or taxa!') - # elif func and taxa: - # QMessageBox.warning(self.MainWindow, 'Warning', 'Please select only one of function or taxa!') - # elif not func: - # df = self.tfa.taxa_func_df.loc[taxa, :] - # func = df.index.tolist() - # self.comboBox_others_func.clear() - # self.comboBox_others_func.addItems(func) - # else: - # df = self.tfa.func_taxa_df.loc[func, :] - # taxa = df.index.tolist() - # self.comboBox_others_taxa.clear() - # self.comboBox_others_taxa.addItems(taxa) - # except Exception as e: - # self.logger.write_log(f'show_others_linked error: {e}', 'e') - # QMessageBox.warning(self.MainWindow, 'Warning', f"No Linked Taxa-Func for your Input! please check your input.\n\n{e}") def update_combobox_and_label(self, current_text, type, label, comboBox): if not current_text: @@ -2772,7 +2753,7 @@ def update_combobox_and_label(self, current_text, type, label, comboBox): comboBox.addItem('') comboBox.addItems(items) except Exception as e: - QMessageBox.warning(self.MainWindow, 'Warning', f"No Linked Taxa-Func for your Input! please check your input.\n\n{e}") + QMessageBox.warning(self.MainWindow, 'Warning', f"No Linked Taxa-Functions for your Input!\n\n{e}") def remove_pep_num_str_and_strip(self, text): text = text.strip() @@ -3102,7 +3083,11 @@ def check_if_in_list(str_selected, df_type): search_results.extend(matches) # Remove duplicates from search_results in case there are overlapping matches search_results = [x for i, x in enumerate(search_results) if i == search_results.index(x)] - + + # Remove No Linked Taxa-Functions if aim_list is 'tfnet' + if search_results and aim_list == 'tfnet': + search_results = self.remove_no_linked_taxa_and_func_after_filter_tflink(search_results, type= df_type.lower()) + # show the search results in a new window, allowing user to select the valid items if search_results: self.input_window = InputWindow(self.MainWindow, input_mode=False) @@ -4919,19 +4904,23 @@ def deseq2_plot_sankey(self): - # Others Functions # + # Taxa-Functions Linkages Functions # # network def update_tfnet_select_list(self): df_type = self.comboBox_tfnet_table.currentText() if df_type == 'Taxa-Functions': self.comboBox_tfnet_select_list.clear() - self.comboBox_tfnet_select_list.addItems(self.taxa_func_list) + # remove no linked items to avoid error when plot focus list only + taxa_func_list = self.get_list_by_df_type('Taxa-Functions', remove_no_linked=True, silent=True) + self.comboBox_tfnet_select_list.addItems(taxa_func_list) elif df_type == 'Taxa': self.comboBox_tfnet_select_list.clear() - self.comboBox_tfnet_select_list.addItems(self.taxa_list) + taxa_list = self.get_list_by_df_type('Taxa', remove_no_linked=True, silent=True) + self.comboBox_tfnet_select_list.addItems(taxa_list) elif df_type == 'Functions': self.comboBox_tfnet_select_list.clear() - self.comboBox_tfnet_select_list.addItems(self.func_list) + func_list = self.get_list_by_df_type('Functions', remove_no_linked=True, silent=True) + self.comboBox_tfnet_select_list.addItems(func_list) def add_a_list_to_tfnet_focus_list(self): df_type = self.comboBox_tfnet_table.currentText() @@ -5147,7 +5136,7 @@ def get_sample_list_tflink(self): sample_list = selected_samples return sample_list - def remove_no_linked_taxa_and_func_after_filter_tflink(self, check_list:list | None = None, type:str = 'taxa'): + def remove_no_linked_taxa_and_func_after_filter_tflink(self, check_list:list | None = None, type:str = 'taxa', silent:bool = False) -> list[str] | None: # keep taxa and func only in the taxa_func_linked_dict and remove others if check_list is None: print(f'check_list is {check_list}, return None') @@ -5163,14 +5152,24 @@ def remove_no_linked_taxa_and_func_after_filter_tflink(self, check_list:list | N elif type == 'taxa-functions': return check_list else: - raise ValueError('type should be taxa, functions or taxa-functions!') + raise ValueError(f'type should be taxa, functions or taxa-functions! but got: {type}') - if removed: - QMessageBox.warning( - self.MainWindow, - 'Warning', - f'{len(removed)} {type} are removed from the list because they do not have links!\n{len(check_list)} {type} are kept!' - ) + if removed and not silent: + removed_str = '\n'.join(removed) + if len(removed) > 10: + self.input_window = InputWindow(self.MainWindow) + self.input_window.setWindowTitle('Warning') + self.input_window.text_edit.setText( + f"[{len(removed)}] {type} are removed from the list because they do not have links!\n[{len(check_list)}] {type} are kept!\n\nRemoved {type}:\n{removed_str}" + ) + self.input_window.exec_() + + else: + QMessageBox.warning( + self.MainWindow, + 'Warning', + f'[{len(removed)}] {type} are removed from the list because they do not have links!\n[{len(check_list)}] {type} are kept!\n\nRemoved {type}:\n{removed_str}' + ) return check_list diff --git a/utils/MetaX_GUI/MainWindow.ui b/utils/MetaX_GUI/MainWindow.ui index 68d4e27..2377049 100644 --- a/utils/MetaX_GUI/MainWindow.ui +++ b/utils/MetaX_GUI/MainWindow.ui @@ -239,8 +239,8 @@ 0 0 - 496 - 377 + 391 + 80 @@ -5270,7 +5270,7 @@ - false + true @@ -7192,7 +7192,7 @@ - false + true 1 diff --git a/utils/MetaX_GUI/Setting.ui b/utils/MetaX_GUI/Setting.ui index 4803340..1f01903 100644 --- a/utils/MetaX_GUI/Setting.ui +++ b/utils/MetaX_GUI/Setting.ui @@ -24,8 +24,8 @@ 0 0 - 246 - 37 + 748 + 367 @@ -94,29 +94,6 @@ - - - - Taxa Color - - - - - - - 1 - - - 1.000000000000000 - - - 0.100000000000000 - - - 0.000000000000000 - - - @@ -156,13 +133,37 @@ - - + + - #DF8F44 + Taxa Shape + + + + + bold + + + + + normal + + + + + bolder + + + + + lighter + + + + @@ -170,6 +171,20 @@ + + + + Repulsion + + + + + + + Focus Taxa Color + + + @@ -177,38 +192,67 @@ - - + + - #B24745 + Line Curve - - + + - #6A6599 + #9aa7b1 - - + + - Line Width + #DF8F44 - - + + + + 1 + + + 1.000000000000000 + + + 0.100000000000000 + + + 0.000000000000000 + + + + + + + 100000 + + + 10 + + + 500 + + + + + - Taxa Shape + Font Weight - - + + - Function Shape + #B24745 @@ -219,10 +263,19 @@ - - - - Focus Taxa Color + + + + 1 + + + 1.000000000000000 + + + 0.100000000000000 + + + 0.500000000000000 @@ -265,13 +318,6 @@ - - - - Line opacity - - - @@ -279,26 +325,31 @@ - - + + - Line Curve + Taxa Color - - - - 1 - - - 1.000000000000000 + + + + Line opacity - - 0.100000000000000 + + + + + + #6A6599 - - 0.500000000000000 + + + + + + Line Width @@ -318,64 +369,99 @@ - - - - #9aa7b1 - - - - - + + - Repulsion - - - - - - - 100000 - - - 10 - - - 500 + Function Shape - - + + - Font Weight + Label Postion - - + + - bold + bottom - normal + top - bolder + right - lighter + left + + + + + inside + + + + + insideLeft + + + + + insideRight + + + + Text Width + + + + + + + 9999 + + + 10 + + + 300 + + + + + + + Gravity + + + + + + + 1.000000000000000 + + + 0.100000000000000 + + + 0.200000000000000 + + + diff --git a/utils/MetaX_GUI/Settings.py b/utils/MetaX_GUI/Settings.py index e1fde9c..3da8e40 100644 --- a/utils/MetaX_GUI/Settings.py +++ b/utils/MetaX_GUI/Settings.py @@ -51,7 +51,11 @@ def __init__(self, parent=None, update_branch="main", auto_check_update=True): self.ui.lineEdit_tf_link_net_line_color.textChanged.connect(self.handle_tf_link_network_changed) self.ui.spinBox_tf_link_net_repulsion.valueChanged.connect(self.handle_tf_link_network_changed) self.ui.comboBox_tf_link_net_font_weight.currentTextChanged.connect(self.handle_tf_link_network_changed) - + self.ui.comboBox_tf_link_net_label_position.currentTextChanged.connect(self.handle_tf_link_network_changed) + self.ui.spinBox_tf_link_net_text_width.valueChanged.connect(self.handle_tf_link_network_changed) + self.ui.doubleSpinBox_tf_link_net_gravity.valueChanged.connect(self.handle_tf_link_network_changed) + + def init_ui(self, update_mode, auto_check_update): if update_mode == "main": self.ui.radioButton_update_stable.setChecked(True) @@ -82,14 +86,15 @@ def handle_tf_link_network_changed(self): "taxa_focus_color": self.ui.lineEdit_tf_link_net_taxa_focus_color.text(), "func_color": self.ui.lineEdit_tf_link_net_func_color.text(), "func_focus_color": self.ui.lineEdit_tf_link_net_func_focus_color.text(), - "line_opacity": self.ui.doubleSpinBox_tf_link_net_line_opacity.value(), "line_width": self.ui.doubleSpinBox_tf_link_net_line_width.value(), "line_curve": self.ui.doubleSpinBox_tf_link_net_line_curve.value(), "line_color": self.ui.lineEdit_tf_link_net_line_color.text(), - 'repulsion': self.ui.spinBox_tf_link_net_repulsion.value(), - 'font_weight': self.ui.comboBox_tf_link_net_font_weight.currentText() + 'font_weight': self.ui.comboBox_tf_link_net_font_weight.currentText(), + 'label_position': self.ui.comboBox_tf_link_net_label_position.currentText(), + 'text_width': self.ui.spinBox_tf_link_net_text_width.value(), + 'gravity': self.ui.doubleSpinBox_tf_link_net_gravity.value(), } self.tf_link_net_params_dict_changed.emit(network_params_dict) diff --git a/utils/MetaX_GUI/Ui_MainWindow.py b/utils/MetaX_GUI/Ui_MainWindow.py index b194a2e..8f51c6b 100644 --- a/utils/MetaX_GUI/Ui_MainWindow.py +++ b/utils/MetaX_GUI/Ui_MainWindow.py @@ -145,7 +145,7 @@ def setupUi(self, metaX_main): self.toolBox_2.setMaximumSize(QtCore.QSize(1677, 16777215)) self.toolBox_2.setObjectName("toolBox_2") self.page_2 = QtWidgets.QWidget() - self.page_2.setGeometry(QtCore.QRect(0, 0, 496, 377)) + self.page_2.setGeometry(QtCore.QRect(0, 0, 391, 80)) self.page_2.setObjectName("page_2") self.gridLayout_27 = QtWidgets.QGridLayout(self.page_2) self.gridLayout_27.setObjectName("gridLayout_27") @@ -2764,7 +2764,7 @@ def setupUi(self, metaX_main): self.label_162.setObjectName("label_162") self.formLayout.setWidget(2, QtWidgets.QFormLayout.LabelRole, self.label_162) self.spinBox_co_expr_font_size = QtWidgets.QSpinBox(self.tab_5) - self.spinBox_co_expr_font_size.setEnabled(False) + self.spinBox_co_expr_font_size.setEnabled(True) sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Preferred, QtWidgets.QSizePolicy.Fixed) sizePolicy.setHorizontalStretch(0) sizePolicy.setVerticalStretch(0) @@ -3779,7 +3779,7 @@ def setupUi(self, metaX_main): self.label_163.setObjectName("label_163") self.horizontalLayout_69.addWidget(self.label_163) self.spinBox_network_font_size = QtWidgets.QSpinBox(self.tab_9) - self.spinBox_network_font_size.setEnabled(False) + self.spinBox_network_font_size.setEnabled(True) self.spinBox_network_font_size.setMinimum(1) self.spinBox_network_font_size.setProperty("value", 10) self.spinBox_network_font_size.setObjectName("spinBox_network_font_size") diff --git a/utils/MetaX_GUI/Ui_Setting.py b/utils/MetaX_GUI/Ui_Setting.py index 5665757..bde7ffc 100644 --- a/utils/MetaX_GUI/Ui_Setting.py +++ b/utils/MetaX_GUI/Ui_Setting.py @@ -20,7 +20,7 @@ def setupUi(self, Settings): self.toolBox = QtWidgets.QToolBox(Settings) self.toolBox.setObjectName("toolBox") self.page = QtWidgets.QWidget() - self.page.setGeometry(QtCore.QRect(0, 0, 246, 37)) + self.page.setGeometry(QtCore.QRect(0, 0, 748, 367)) self.page.setObjectName("page") self.gridLayout_3 = QtWidgets.QGridLayout(self.page) self.gridLayout_3.setObjectName("gridLayout_3") @@ -52,16 +52,6 @@ def setupUi(self, Settings): self.gridLayout_4.addWidget(self.label, 0, 0, 1, 1) self.gridLayout_6 = QtWidgets.QGridLayout() self.gridLayout_6.setObjectName("gridLayout_6") - self.label_7 = QtWidgets.QLabel(self.page_2) - self.label_7.setObjectName("label_7") - self.gridLayout_6.addWidget(self.label_7, 0, 2, 1, 1) - self.doubleSpinBox_tf_link_net_line_curve = QtWidgets.QDoubleSpinBox(self.page_2) - self.doubleSpinBox_tf_link_net_line_curve.setDecimals(1) - self.doubleSpinBox_tf_link_net_line_curve.setMaximum(1.0) - self.doubleSpinBox_tf_link_net_line_curve.setSingleStep(0.1) - self.doubleSpinBox_tf_link_net_line_curve.setProperty("value", 0.0) - self.doubleSpinBox_tf_link_net_line_curve.setObjectName("doubleSpinBox_tf_link_net_line_curve") - self.gridLayout_6.addWidget(self.doubleSpinBox_tf_link_net_line_curve, 2, 3, 1, 1) self.comboBox_tf_link_net_taxa_sahpe = QtWidgets.QComboBox(self.page_2) self.comboBox_tf_link_net_taxa_sahpe.setObjectName("comboBox_tf_link_net_taxa_sahpe") self.comboBox_tf_link_net_taxa_sahpe.addItem("") @@ -72,36 +62,66 @@ def setupUi(self, Settings): self.comboBox_tf_link_net_taxa_sahpe.addItem("") self.comboBox_tf_link_net_taxa_sahpe.addItem("") self.gridLayout_6.addWidget(self.comboBox_tf_link_net_taxa_sahpe, 0, 1, 1, 1) - self.lineEdit_tf_link_net_func_color = QtWidgets.QLineEdit(self.page_2) - self.lineEdit_tf_link_net_func_color.setObjectName("lineEdit_tf_link_net_func_color") - self.gridLayout_6.addWidget(self.lineEdit_tf_link_net_func_color, 1, 3, 1, 1) + self.label_5 = QtWidgets.QLabel(self.page_2) + self.label_5.setObjectName("label_5") + self.gridLayout_6.addWidget(self.label_5, 0, 0, 1, 1) + self.comboBox_tf_link_net_font_weight = QtWidgets.QComboBox(self.page_2) + self.comboBox_tf_link_net_font_weight.setObjectName("comboBox_tf_link_net_font_weight") + self.comboBox_tf_link_net_font_weight.addItem("") + self.comboBox_tf_link_net_font_weight.addItem("") + self.comboBox_tf_link_net_font_weight.addItem("") + self.comboBox_tf_link_net_font_weight.addItem("") + self.gridLayout_6.addWidget(self.comboBox_tf_link_net_font_weight, 3, 5, 1, 1) self.lineEdit_tf_link_net_taxa_color = QtWidgets.QLineEdit(self.page_2) self.lineEdit_tf_link_net_taxa_color.setObjectName("lineEdit_tf_link_net_taxa_color") self.gridLayout_6.addWidget(self.lineEdit_tf_link_net_taxa_color, 0, 3, 1, 1) + self.label_15 = QtWidgets.QLabel(self.page_2) + self.label_15.setObjectName("label_15") + self.gridLayout_6.addWidget(self.label_15, 2, 4, 1, 1) + self.label_9 = QtWidgets.QLabel(self.page_2) + self.label_9.setObjectName("label_9") + self.gridLayout_6.addWidget(self.label_9, 0, 4, 1, 1) self.label_10 = QtWidgets.QLabel(self.page_2) self.label_10.setObjectName("label_10") self.gridLayout_6.addWidget(self.label_10, 1, 2, 1, 1) + self.label_14 = QtWidgets.QLabel(self.page_2) + self.label_14.setObjectName("label_14") + self.gridLayout_6.addWidget(self.label_14, 2, 2, 1, 1) + self.lineEdit_tf_link_net_line_color = QtWidgets.QLineEdit(self.page_2) + self.lineEdit_tf_link_net_line_color.setObjectName("lineEdit_tf_link_net_line_color") + self.gridLayout_6.addWidget(self.lineEdit_tf_link_net_line_color, 3, 3, 1, 1) + self.lineEdit_tf_link_net_func_color = QtWidgets.QLineEdit(self.page_2) + self.lineEdit_tf_link_net_func_color.setObjectName("lineEdit_tf_link_net_func_color") + self.gridLayout_6.addWidget(self.lineEdit_tf_link_net_func_color, 1, 3, 1, 1) + self.doubleSpinBox_tf_link_net_line_curve = QtWidgets.QDoubleSpinBox(self.page_2) + self.doubleSpinBox_tf_link_net_line_curve.setDecimals(1) + self.doubleSpinBox_tf_link_net_line_curve.setMaximum(1.0) + self.doubleSpinBox_tf_link_net_line_curve.setSingleStep(0.1) + self.doubleSpinBox_tf_link_net_line_curve.setProperty("value", 0.0) + self.doubleSpinBox_tf_link_net_line_curve.setObjectName("doubleSpinBox_tf_link_net_line_curve") + self.gridLayout_6.addWidget(self.doubleSpinBox_tf_link_net_line_curve, 2, 3, 1, 1) + self.spinBox_tf_link_net_repulsion = QtWidgets.QSpinBox(self.page_2) + self.spinBox_tf_link_net_repulsion.setMaximum(100000) + self.spinBox_tf_link_net_repulsion.setSingleStep(10) + self.spinBox_tf_link_net_repulsion.setProperty("value", 500) + self.spinBox_tf_link_net_repulsion.setObjectName("spinBox_tf_link_net_repulsion") + self.gridLayout_6.addWidget(self.spinBox_tf_link_net_repulsion, 2, 5, 1, 1) + self.label_16 = QtWidgets.QLabel(self.page_2) + self.label_16.setObjectName("label_16") + self.gridLayout_6.addWidget(self.label_16, 3, 4, 1, 1) self.lineEdit_tf_link_net_func_focus_color = QtWidgets.QLineEdit(self.page_2) self.lineEdit_tf_link_net_func_focus_color.setObjectName("lineEdit_tf_link_net_func_focus_color") self.gridLayout_6.addWidget(self.lineEdit_tf_link_net_func_focus_color, 1, 5, 1, 1) - self.lineEdit_tf_link_net_taxa_focus_color = QtWidgets.QLineEdit(self.page_2) - self.lineEdit_tf_link_net_taxa_focus_color.setObjectName("lineEdit_tf_link_net_taxa_focus_color") - self.gridLayout_6.addWidget(self.lineEdit_tf_link_net_taxa_focus_color, 0, 5, 1, 1) - self.label_11 = QtWidgets.QLabel(self.page_2) - self.label_11.setObjectName("label_11") - self.gridLayout_6.addWidget(self.label_11, 2, 0, 1, 1) - self.label_5 = QtWidgets.QLabel(self.page_2) - self.label_5.setObjectName("label_5") - self.gridLayout_6.addWidget(self.label_5, 0, 0, 1, 1) - self.label_6 = QtWidgets.QLabel(self.page_2) - self.label_6.setObjectName("label_6") - self.gridLayout_6.addWidget(self.label_6, 1, 0, 1, 1) self.label_8 = QtWidgets.QLabel(self.page_2) self.label_8.setObjectName("label_8") self.gridLayout_6.addWidget(self.label_8, 1, 4, 1, 1) - self.label_9 = QtWidgets.QLabel(self.page_2) - self.label_9.setObjectName("label_9") - self.gridLayout_6.addWidget(self.label_9, 0, 4, 1, 1) + self.doubleSpinBox_tf_link_net_line_opacity = QtWidgets.QDoubleSpinBox(self.page_2) + self.doubleSpinBox_tf_link_net_line_opacity.setDecimals(1) + self.doubleSpinBox_tf_link_net_line_opacity.setMaximum(1.0) + self.doubleSpinBox_tf_link_net_line_opacity.setSingleStep(0.1) + self.doubleSpinBox_tf_link_net_line_opacity.setProperty("value", 0.5) + self.doubleSpinBox_tf_link_net_line_opacity.setObjectName("doubleSpinBox_tf_link_net_line_opacity") + self.gridLayout_6.addWidget(self.doubleSpinBox_tf_link_net_line_opacity, 3, 1, 1, 1) self.comboBox_tf_link_net_func_shape = QtWidgets.QComboBox(self.page_2) self.comboBox_tf_link_net_func_shape.setObjectName("comboBox_tf_link_net_func_shape") self.comboBox_tf_link_net_func_shape.addItem("") @@ -112,22 +132,21 @@ def setupUi(self, Settings): self.comboBox_tf_link_net_func_shape.addItem("") self.comboBox_tf_link_net_func_shape.addItem("") self.gridLayout_6.addWidget(self.comboBox_tf_link_net_func_shape, 1, 1, 1, 1) - self.label_12 = QtWidgets.QLabel(self.page_2) - self.label_12.setObjectName("label_12") - self.gridLayout_6.addWidget(self.label_12, 3, 0, 1, 1) self.label_13 = QtWidgets.QLabel(self.page_2) self.label_13.setObjectName("label_13") self.gridLayout_6.addWidget(self.label_13, 3, 2, 1, 1) - self.label_14 = QtWidgets.QLabel(self.page_2) - self.label_14.setObjectName("label_14") - self.gridLayout_6.addWidget(self.label_14, 2, 2, 1, 1) - self.doubleSpinBox_tf_link_net_line_opacity = QtWidgets.QDoubleSpinBox(self.page_2) - self.doubleSpinBox_tf_link_net_line_opacity.setDecimals(1) - self.doubleSpinBox_tf_link_net_line_opacity.setMaximum(1.0) - self.doubleSpinBox_tf_link_net_line_opacity.setSingleStep(0.1) - self.doubleSpinBox_tf_link_net_line_opacity.setProperty("value", 0.5) - self.doubleSpinBox_tf_link_net_line_opacity.setObjectName("doubleSpinBox_tf_link_net_line_opacity") - self.gridLayout_6.addWidget(self.doubleSpinBox_tf_link_net_line_opacity, 3, 1, 1, 1) + self.label_7 = QtWidgets.QLabel(self.page_2) + self.label_7.setObjectName("label_7") + self.gridLayout_6.addWidget(self.label_7, 0, 2, 1, 1) + self.label_12 = QtWidgets.QLabel(self.page_2) + self.label_12.setObjectName("label_12") + self.gridLayout_6.addWidget(self.label_12, 3, 0, 1, 1) + self.lineEdit_tf_link_net_taxa_focus_color = QtWidgets.QLineEdit(self.page_2) + self.lineEdit_tf_link_net_taxa_focus_color.setObjectName("lineEdit_tf_link_net_taxa_focus_color") + self.gridLayout_6.addWidget(self.lineEdit_tf_link_net_taxa_focus_color, 0, 5, 1, 1) + self.label_11 = QtWidgets.QLabel(self.page_2) + self.label_11.setObjectName("label_11") + self.gridLayout_6.addWidget(self.label_11, 2, 0, 1, 1) self.doubleSpinBox_tf_link_net_line_width = QtWidgets.QDoubleSpinBox(self.page_2) self.doubleSpinBox_tf_link_net_line_width.setDecimals(1) self.doubleSpinBox_tf_link_net_line_width.setMinimum(0.1) @@ -135,28 +154,40 @@ def setupUi(self, Settings): self.doubleSpinBox_tf_link_net_line_width.setProperty("value", 3.0) self.doubleSpinBox_tf_link_net_line_width.setObjectName("doubleSpinBox_tf_link_net_line_width") self.gridLayout_6.addWidget(self.doubleSpinBox_tf_link_net_line_width, 2, 1, 1, 1) - self.lineEdit_tf_link_net_line_color = QtWidgets.QLineEdit(self.page_2) - self.lineEdit_tf_link_net_line_color.setObjectName("lineEdit_tf_link_net_line_color") - self.gridLayout_6.addWidget(self.lineEdit_tf_link_net_line_color, 3, 3, 1, 1) - self.label_15 = QtWidgets.QLabel(self.page_2) - self.label_15.setObjectName("label_15") - self.gridLayout_6.addWidget(self.label_15, 2, 4, 1, 1) - self.spinBox_tf_link_net_repulsion = QtWidgets.QSpinBox(self.page_2) - self.spinBox_tf_link_net_repulsion.setMaximum(100000) - self.spinBox_tf_link_net_repulsion.setSingleStep(10) - self.spinBox_tf_link_net_repulsion.setProperty("value", 500) - self.spinBox_tf_link_net_repulsion.setObjectName("spinBox_tf_link_net_repulsion") - self.gridLayout_6.addWidget(self.spinBox_tf_link_net_repulsion, 2, 5, 1, 1) - self.label_16 = QtWidgets.QLabel(self.page_2) - self.label_16.setObjectName("label_16") - self.gridLayout_6.addWidget(self.label_16, 3, 4, 1, 1) - self.comboBox_tf_link_net_font_weight = QtWidgets.QComboBox(self.page_2) - self.comboBox_tf_link_net_font_weight.setObjectName("comboBox_tf_link_net_font_weight") - self.comboBox_tf_link_net_font_weight.addItem("") - self.comboBox_tf_link_net_font_weight.addItem("") - self.comboBox_tf_link_net_font_weight.addItem("") - self.comboBox_tf_link_net_font_weight.addItem("") - self.gridLayout_6.addWidget(self.comboBox_tf_link_net_font_weight, 3, 5, 1, 1) + self.label_6 = QtWidgets.QLabel(self.page_2) + self.label_6.setObjectName("label_6") + self.gridLayout_6.addWidget(self.label_6, 1, 0, 1, 1) + self.label_17 = QtWidgets.QLabel(self.page_2) + self.label_17.setObjectName("label_17") + self.gridLayout_6.addWidget(self.label_17, 4, 0, 1, 1) + self.comboBox_tf_link_net_label_position = QtWidgets.QComboBox(self.page_2) + self.comboBox_tf_link_net_label_position.setObjectName("comboBox_tf_link_net_label_position") + self.comboBox_tf_link_net_label_position.addItem("") + self.comboBox_tf_link_net_label_position.addItem("") + self.comboBox_tf_link_net_label_position.addItem("") + self.comboBox_tf_link_net_label_position.addItem("") + self.comboBox_tf_link_net_label_position.addItem("") + self.comboBox_tf_link_net_label_position.addItem("") + self.comboBox_tf_link_net_label_position.addItem("") + self.gridLayout_6.addWidget(self.comboBox_tf_link_net_label_position, 4, 1, 1, 1) + self.label_18 = QtWidgets.QLabel(self.page_2) + self.label_18.setObjectName("label_18") + self.gridLayout_6.addWidget(self.label_18, 4, 2, 1, 1) + self.spinBox_tf_link_net_text_width = QtWidgets.QSpinBox(self.page_2) + self.spinBox_tf_link_net_text_width.setMaximum(9999) + self.spinBox_tf_link_net_text_width.setSingleStep(10) + self.spinBox_tf_link_net_text_width.setProperty("value", 300) + self.spinBox_tf_link_net_text_width.setObjectName("spinBox_tf_link_net_text_width") + self.gridLayout_6.addWidget(self.spinBox_tf_link_net_text_width, 4, 3, 1, 1) + self.label_19 = QtWidgets.QLabel(self.page_2) + self.label_19.setObjectName("label_19") + self.gridLayout_6.addWidget(self.label_19, 4, 4, 1, 1) + self.doubleSpinBox_tf_link_net_gravity = QtWidgets.QDoubleSpinBox(self.page_2) + self.doubleSpinBox_tf_link_net_gravity.setMaximum(1.0) + self.doubleSpinBox_tf_link_net_gravity.setSingleStep(0.1) + self.doubleSpinBox_tf_link_net_gravity.setProperty("value", 0.2) + self.doubleSpinBox_tf_link_net_gravity.setObjectName("doubleSpinBox_tf_link_net_gravity") + self.gridLayout_6.addWidget(self.doubleSpinBox_tf_link_net_gravity, 4, 5, 1, 1) self.gridLayout_4.addLayout(self.gridLayout_6, 2, 3, 1, 1) self.gridLayout_8 = QtWidgets.QGridLayout() self.gridLayout_8.setObjectName("gridLayout_8") @@ -218,7 +249,6 @@ def retranslateUi(self, Settings): self.toolBox.setItemText(self.toolBox.indexOf(self.page), _translate("Settings", "General")) self.label_4.setText(_translate("Settings", "Taxa-Functions Link Network")) self.label.setText(_translate("Settings", "HeatMap")) - self.label_7.setText(_translate("Settings", "Taxa Color")) self.comboBox_tf_link_net_taxa_sahpe.setItemText(0, _translate("Settings", "circle")) self.comboBox_tf_link_net_taxa_sahpe.setItemText(1, _translate("Settings", "rect")) self.comboBox_tf_link_net_taxa_sahpe.setItemText(2, _translate("Settings", "roundRect")) @@ -226,16 +256,21 @@ def retranslateUi(self, Settings): self.comboBox_tf_link_net_taxa_sahpe.setItemText(4, _translate("Settings", "diamond")) self.comboBox_tf_link_net_taxa_sahpe.setItemText(5, _translate("Settings", "pin")) self.comboBox_tf_link_net_taxa_sahpe.setItemText(6, _translate("Settings", "arrow")) - self.lineEdit_tf_link_net_func_color.setText(_translate("Settings", "#DF8F44")) + self.label_5.setText(_translate("Settings", "Taxa Shape")) + self.comboBox_tf_link_net_font_weight.setItemText(0, _translate("Settings", "bold")) + self.comboBox_tf_link_net_font_weight.setItemText(1, _translate("Settings", "normal")) + self.comboBox_tf_link_net_font_weight.setItemText(2, _translate("Settings", "bolder")) + self.comboBox_tf_link_net_font_weight.setItemText(3, _translate("Settings", "lighter")) self.lineEdit_tf_link_net_taxa_color.setText(_translate("Settings", "#374E55")) + self.label_15.setText(_translate("Settings", "Repulsion")) + self.label_9.setText(_translate("Settings", "Focus Taxa Color")) self.label_10.setText(_translate("Settings", "Func Color")) + self.label_14.setText(_translate("Settings", "Line Curve")) + self.lineEdit_tf_link_net_line_color.setText(_translate("Settings", "#9aa7b1")) + self.lineEdit_tf_link_net_func_color.setText(_translate("Settings", "#DF8F44")) + self.label_16.setText(_translate("Settings", "Font Weight")) self.lineEdit_tf_link_net_func_focus_color.setText(_translate("Settings", "#B24745")) - self.lineEdit_tf_link_net_taxa_focus_color.setText(_translate("Settings", "#6A6599")) - self.label_11.setText(_translate("Settings", "Line Width")) - self.label_5.setText(_translate("Settings", "Taxa Shape")) - self.label_6.setText(_translate("Settings", "Function Shape")) self.label_8.setText(_translate("Settings", "Focus Func Color")) - self.label_9.setText(_translate("Settings", "Focus Taxa Color")) self.comboBox_tf_link_net_func_shape.setItemText(0, _translate("Settings", "rect")) self.comboBox_tf_link_net_func_shape.setItemText(1, _translate("Settings", "circle")) self.comboBox_tf_link_net_func_shape.setItemText(2, _translate("Settings", "roundRect")) @@ -243,16 +278,22 @@ def retranslateUi(self, Settings): self.comboBox_tf_link_net_func_shape.setItemText(4, _translate("Settings", "diamond")) self.comboBox_tf_link_net_func_shape.setItemText(5, _translate("Settings", "pin")) self.comboBox_tf_link_net_func_shape.setItemText(6, _translate("Settings", "arrow")) - self.label_12.setText(_translate("Settings", "Line opacity")) self.label_13.setText(_translate("Settings", "Line Color")) - self.label_14.setText(_translate("Settings", "Line Curve")) - self.lineEdit_tf_link_net_line_color.setText(_translate("Settings", "#9aa7b1")) - self.label_15.setText(_translate("Settings", "Repulsion")) - self.label_16.setText(_translate("Settings", "Font Weight")) - self.comboBox_tf_link_net_font_weight.setItemText(0, _translate("Settings", "bold")) - self.comboBox_tf_link_net_font_weight.setItemText(1, _translate("Settings", "normal")) - self.comboBox_tf_link_net_font_weight.setItemText(2, _translate("Settings", "bolder")) - self.comboBox_tf_link_net_font_weight.setItemText(3, _translate("Settings", "lighter")) + self.label_7.setText(_translate("Settings", "Taxa Color")) + self.label_12.setText(_translate("Settings", "Line opacity")) + self.lineEdit_tf_link_net_taxa_focus_color.setText(_translate("Settings", "#6A6599")) + self.label_11.setText(_translate("Settings", "Line Width")) + self.label_6.setText(_translate("Settings", "Function Shape")) + self.label_17.setText(_translate("Settings", "Label Postion")) + self.comboBox_tf_link_net_label_position.setItemText(0, _translate("Settings", "bottom")) + self.comboBox_tf_link_net_label_position.setItemText(1, _translate("Settings", "top")) + self.comboBox_tf_link_net_label_position.setItemText(2, _translate("Settings", "right")) + self.comboBox_tf_link_net_label_position.setItemText(3, _translate("Settings", "left")) + self.comboBox_tf_link_net_label_position.setItemText(4, _translate("Settings", "inside")) + self.comboBox_tf_link_net_label_position.setItemText(5, _translate("Settings", "insideLeft")) + self.comboBox_tf_link_net_label_position.setItemText(6, _translate("Settings", "insideRight")) + self.label_18.setText(_translate("Settings", "Text Width")) + self.label_19.setText(_translate("Settings", "Gravity")) self.label_2.setText(_translate("Settings", "Linkage Method")) self.comboBox_heatmap_linkage_method.setCurrentText(_translate("Settings", "average")) self.comboBox_heatmap_linkage_method.setItemText(0, _translate("Settings", "average")) diff --git a/utils/TaxaFuncPloter/network_plot.py b/utils/TaxaFuncPloter/network_plot.py index 8101791..2cee8bd 100644 --- a/utils/TaxaFuncPloter/network_plot.py +++ b/utils/TaxaFuncPloter/network_plot.py @@ -20,7 +20,10 @@ def __init__(self, tfobj, co_network_focus_color="#B24745", co_network_normal_color="#79af97", font_weight="normal", - theme="white" + theme="white", + label_position="bottom", + text_width = 300, + gravity = 0.2 ): @@ -48,6 +51,9 @@ def __init__(self, tfobj, self.co_network_normal_color = co_network_normal_color self.theme = theme + self.label_position = label_position + self.text_width = text_width + self.gravity = gravity def modify_focus_list(self, focus_list): @@ -219,21 +225,21 @@ def plot_tflink_network(self, sample_list:list = None, width:int = 12, height:in links, categories, repulsion=self.repulsion, + gravity= self.gravity, is_focusnode=True, is_layout_animation=True, - friction=0.6, linestyle_opts=opts.LineStyleOpts( curve=self.line_curve, opacity=self.line_opacity, width=self.line_width, color=self.line_color ), - # itemstyle_opts=opts.ItemStyleOpts(border_width=0.5, border_color="rgba(0,0,0,0.5)", opacity=0.8), - gravity=0.05, label_opts=opts.LabelOpts( is_show=self.show_labels, - position="right", + position=self.label_position, color="auto", formatter="{b}", font_size=self.font_size, - font_weight=self.font_weight + font_weight=self.font_weight, + overflow = 'break', + text_width = self.text_width ), ) .set_global_opts( @@ -393,15 +399,18 @@ def plot_co_expression_network(self, df_type:str= 'taxa', corr_method:str = 'pea nodes, links, categories=categories, + gravity= self.gravity, repulsion=self.repulsion, is_layout_animation=True, label_opts=opts.LabelOpts( is_show=self.show_labels, font_size=self.font_size, - position="right", + position=self.label_position, color="auto", formatter="{b}", - font_weight=self.font_weight + font_weight=self.font_weight, + overflow = 'break', + text_width = self.text_width ), linestyle_opts=opts.LineStyleOpts( opacity=self.line_opacity, diff --git a/utils/version.py b/utils/version.py index df4e6d1..fc032ef 100644 --- a/utils/version.py +++ b/utils/version.py @@ -1,2 +1,2 @@ -__version__ = '1.107.4' +__version__ = '1.107.5' API_version = '1' \ No newline at end of file