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- Fix: Fixed the of test result table, the t-statistic was reversed.
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- New: adde z-score for heatmap scale.
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@byemaxx
byemaxx committed Aug 9, 2024
1 parent 923b0b1 commit 003f32c
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7 changes: 7 additions & 0 deletions Docs/ChangeLog.md
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Original file line number Diff line number Diff line change
@@ -1,3 +1,10 @@
# Version: 1.109.10
## Date: 2024-08-9
### Changes:
- Fix: Fixed the of test result table, the t-statistic was reversed.
- New: adde z-score for heatmap scale.


# Version: 1.109.9
## Date: 2024-08-7
### Changes:
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39 changes: 20 additions & 19 deletions metax/gui/main_gui.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1175,7 +1175,7 @@ def save_set_multi_table_settings(self):

def export_log_file(self):
log_path = os.path.join(self.metax_home_path, "MetaX.log")
if os.path.exists(path):
if os.path.exists(log_path):
#select a file to save
# default output path is self.last_path
file_path, _ = QFileDialog.getSaveFileName(self.MainWindow, "Export log file", self.last_path, "Log file (*.log)")
Expand Down Expand Up @@ -2238,15 +2238,12 @@ def change_event_comboBox_top_heatmap_table(self):
# selected_table_name = sender.currentText()
selected_table_name = self.comboBox_top_heatmap_table.currentText()

scale_method_list = [self.comboBox_top_heatmap_scale.itemText(i) for i in range(self.comboBox_top_heatmap_scale.count())]

if 'dunnett' in selected_table_name or 'deseq2' in selected_table_name:
self.spinBox_top_heatmap_number.setEnabled(False)
self.pushButton_plot_top_heatmap.setText('Plot Heatmap')
self.pushButton_get_top_cross_table.setText('Get Heatmap Table')
# add 'all' to comboBox_top_heatmap_scale.
if 'all' not in scale_method_list:
self.comboBox_top_heatmap_scale.addItem('all')


if 'dunnett_test' in selected_table_name:
self.comboBox_top_heatmap_sort_type.setEnabled(False)
Expand Down Expand Up @@ -2295,9 +2292,7 @@ def change_event_comboBox_top_heatmap_table(self):
self.pushButton_get_top_cross_table.setText('Get Top Table')
self.comboBox_top_heatmap_sort_type.setEnabled(True)
self.spinBox_top_heatmap_number.setEnabled(True)
# remove 'all' from comboBox_top_heatmap_scale.
if 'all' in scale_method_list:
self.comboBox_top_heatmap_scale.removeItem(scale_method_list.index('all'))




Expand Down Expand Up @@ -4292,6 +4287,7 @@ def plot_top_heatmap(self):
pvalue = round(pvalue, 4)
cmap = self.comboBox_top_heatmap_cmap.currentText()
scale = self.comboBox_top_heatmap_scale.currentText()
scale_method = self.comboBox_top_heatmap_scale_method.currentText()
rename_taxa = self.checkBox_top_heatmap_rename_taxa.isChecked()
rename_sample = self.checkBox_top_heatmap_rename_sample.isChecked()
show_all_labels = (self.checkBox_top_heatmap_show_all_labels_x.isChecked(), self.checkBox_top_heatmap_show_all_labels_y.isChecked())
Expand Down Expand Up @@ -4326,7 +4322,7 @@ def plot_top_heatmap(self):
fig_size=fig_size, pvalue=pvalue, cmap=cmap,
scale = scale, col_cluster = col_luster, row_cluster = row_luster,
rename_taxa=rename_taxa, font_size=font_size,
show_all_labels = show_all_labels)
show_all_labels = show_all_labels, scale_method = scale_method)
elif table_name.startswith('deseq2all'):
p_type = self.comboBox_top_heatmap_sort_type.currentText()
three_levels_df_type = self.comboBox_cross_3_level_plot_df_type.currentText()
Expand All @@ -4338,7 +4334,8 @@ def plot_top_heatmap(self):
scale = scale, col_cluster = col_luster, row_cluster = row_luster,
rename_taxa=rename_taxa, font_size=font_size,
show_all_labels = show_all_labels,return_type = 'fig', p_type = p_type,
three_levels_df_type = three_levels_df_type,remove_zero_col = remove_zero_col
three_levels_df_type = three_levels_df_type,remove_zero_col = remove_zero_col,
scale_method = scale_method
)

# if fig is a tuple
Expand All @@ -4356,7 +4353,8 @@ def plot_top_heatmap(self):
scale = scale, col_cluster = col_luster, row_cluster = row_luster,
rename_taxa=rename_taxa, font_size=font_size,
show_all_labels = show_all_labels,return_type = 'fig',
three_levels_df_type = three_levels_df_type,remove_zero_col = remove_zero_col
three_levels_df_type = three_levels_df_type,remove_zero_col = remove_zero_col,
scale_method = scale_method
)

# if fig is a tuple
Expand Down Expand Up @@ -4388,13 +4386,14 @@ def plot_top_heatmap(self):
top_number=top_num, value_type=value_type, fig_size=fig_size,
col_cluster = col_luster, row_cluster = row_luster,
pvalue=pvalue, cmap=cmap, rename_taxa=rename_taxa, font_size=font_size, title=title,
show_all_labels = show_all_labels)
show_all_labels = show_all_labels, scale = scale, scale_method = scale_method)
else:
fig = HeatmapPlot(self.tfa, **self.heatmap_params_dict).plot_basic_heatmap_of_test_res(df=df, top_number=top_num,
value_type=value_type, fig_size=fig_size, pvalue=pvalue,
scale = scale, col_cluster = col_luster, row_cluster = row_luster,
cmap = cmap, rename_taxa=rename_taxa, font_size=font_size,
show_all_labels = show_all_labels, rename_sample = rename_sample)
show_all_labels = show_all_labels, rename_sample = rename_sample,
sort_by = sort_by, scale_method = scale_method)

except Exception as e:
error_message = traceback.format_exc()
Expand All @@ -4413,6 +4412,7 @@ def get_top_cross_table(self):
pvalue = self.doubleSpinBox_top_heatmap_pvalue.value()
pvalue = round(pvalue, 4)
scale = self.comboBox_top_heatmap_scale.currentText()
scale_method = self.comboBox_top_heatmap_scale_method.currentText()
rename_taxa = self.checkBox_top_heatmap_rename_taxa.isChecked()
col_luster = self.checkBox_cross_heatmap_col_cluster.isChecked()
row_luster = self.checkBox_cross_heatmap_row_cluster.isChecked()
Expand All @@ -4429,7 +4429,7 @@ def get_top_cross_table(self):
if table_name.startswith('dunnett_test'):
df_top_cross = HeatmapPlot(self.tfa, **self.heatmap_params_dict).get_heatmap_table_of_dunnett_res(df = df, pvalue=pvalue,scale = scale,
col_cluster = col_luster, row_cluster = row_luster,
rename_taxa=rename_taxa)
rename_taxa=rename_taxa, scale_method = scale_method)
elif 'deseq2all' in table_name:
p_type = self.comboBox_top_heatmap_sort_type.currentText()
df_top_cross = HeatmapPlot(self.tfa, **self.heatmap_params_dict).plot_heatmap_of_all_condition_res(df = df, res_df_type='deseq2',
Expand All @@ -4439,15 +4439,15 @@ def get_top_cross_table(self):
col_cluster = col_luster, row_cluster = row_luster,
rename_taxa=rename_taxa, return_type = 'table', p_type = p_type,
three_levels_df_type = self.comboBox_cross_3_level_plot_df_type.currentText(),
remove_zero_col = remove_zero_col
remove_zero_col = remove_zero_col, scale_method = scale_method
)
elif 'dunnettAllCondtion' in table_name:
df_top_cross = HeatmapPlot(self.tfa, **self.heatmap_params_dict).plot_heatmap_of_all_condition_res(df = df, res_df_type='dunnett',
pvalue=pvalue,scale = scale,
col_cluster = col_luster, row_cluster = row_luster,
rename_taxa=rename_taxa, return_type = 'table',
three_levels_df_type = self.comboBox_cross_3_level_plot_df_type.currentText(),
remove_zero_col = remove_zero_col
remove_zero_col = remove_zero_col, scale_method = scale_method
)


Expand All @@ -4456,12 +4456,13 @@ def get_top_cross_table(self):
df_top_cross = HeatmapPlot(self.tfa, **self.heatmap_params_dict).get_top_across_table(df=df, top_number=top_num,
col_cluster = col_luster, row_cluster = row_luster,
value_type=value_type, pvalue=pvalue,
rename_taxa=rename_taxa)
else:
rename_taxa=rename_taxa, scale = scale, scale_method = scale_method)
else: # get result of test and anova of [taxa, functions, peptides and custom table]
# get the intensity of the result items which are significant
df_top_cross = HeatmapPlot(self.tfa, **self.heatmap_params_dict).get_top_across_table_basic(df=df, top_number=top_num,
col_cluster = col_luster, row_cluster = row_luster,
value_type=value_type, pvalue=pvalue,
scale = scale, rename_taxa=rename_taxa)
scale = scale, rename_taxa=rename_taxa, scale_method = scale_method)
except ValueError as e:
QMessageBox.warning(self.MainWindow, 'Warning', f'No significant results.\n\n{e}')
return None
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