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- Fix: Fixed the bug of when plot the Taxa-Functions Network, the fco…
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…us 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.
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@byemaxx
byemaxx committed Jun 18, 2024
1 parent 91dfae1 commit 9deb712
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Showing 9 changed files with 386 additions and 240 deletions.
6 changes: 6 additions & 0 deletions Docs/ChangeLog.md
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Original file line number Diff line number Diff line change
@@ -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:
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79 changes: 39 additions & 40 deletions utils/GUI.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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
}


Expand Down Expand Up @@ -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']
Expand All @@ -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):
Expand Down Expand Up @@ -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:
Expand Down Expand Up @@ -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()
Expand Down Expand Up @@ -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)
Expand Down Expand Up @@ -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()
Expand Down Expand Up @@ -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')
Expand All @@ -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

Expand Down
8 changes: 4 additions & 4 deletions utils/MetaX_GUI/MainWindow.ui
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Original file line number Diff line number Diff line change
Expand Up @@ -239,8 +239,8 @@
<rect>
<x>0</x>
<y>0</y>
<width>496</width>
<height>377</height>
<width>391</width>
<height>80</height>
</rect>
</property>
<attribute name="label">
Expand Down Expand Up @@ -5270,7 +5270,7 @@
<item row="2" column="1">
<widget class="QSpinBox" name="spinBox_co_expr_font_size">
<property name="enabled">
<bool>false</bool>
<bool>true</bool>
</property>
<property name="sizePolicy">
<sizepolicy hsizetype="Preferred" vsizetype="Fixed">
Expand Down Expand Up @@ -7192,7 +7192,7 @@
<item>
<widget class="QSpinBox" name="spinBox_network_font_size">
<property name="enabled">
<bool>false</bool>
<bool>true</bool>
</property>
<property name="minimum">
<number>1</number>
Expand Down
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