def __init__(self, file_dir, yml_file=None, gui=False, host_flask=False, selected_reader=MQReader.MQReader, loglevel=logging.DEBUG, configs: dict = None):
base_config = {
"has_replicates": False,
"has_groups": False,
}
if configs is None:
configs = {}
base_config.update(**configs)
configs = base_config
if gui and host_flask:
raise ValueError("Can only specify one of host_flask and gui")
if gui:
MSPGUI(file_dir=file_dir, yml_file=yml_file, loglevel=loglevel, configs=configs)
elif host_flask:
# TODO pass arguments to create app
app = create_app()
app.run(debug=True)
else:
mspinit = MSPInitializer(file_dir, yml_file, loglevel=loglevel)
mspinit.init_config()
mspinit.configs.update(configs)
mspinit.read_data()
# create plotter from initializer
mspplots = selected_reader.plotter.from_MSPInitializer(mspinit)
# create all plots and other results
mspplots.create_results()
def __init__(self,
file_dir,
yml_file=None,
gui=False,
host_flask=False,
selected_reader=MQReader.MQReader,
loglevel=logging.DEBUG,
configs: dict = None):
"""
Parameters
----------
file_dir
location where the directory/txt folder to the data can be found.
yml_file
path to the yaml config file
gui
should a GUI be compiled
host_flask
currently not implemented (should a flsk server be hosted)
selected_reader
instance of an :class:`~BaseReader` used to process data to an internal format for the plotter.
loglevel
level of the logger
configs
mapping of configuration
"""
base_config = {
"has_techrep": False,
"has_groups": False,
}
if configs is None:
configs = {}
base_config.update(**configs)
configs = base_config
if gui and host_flask:
raise ValueError("Can only specify one of host_flask and gui")
if gui:
MSPGUI(file_dir=file_dir,
yml_file=yml_file,
loglevel=loglevel,
configs=configs)
elif host_flask:
# TODO pass arguments to create app
app = create_app()
app.run(debug=True)
else:
mspinit = MSPInitializer(file_dir, yml_file, loglevel=loglevel)
mspinit.init_config()
mspinit.configs.update(configs)
mspinit.read_data()
# create plotter from initializer
mspplots = selected_reader.plotter.from_MSPInitializer(mspinit)
# create all plots and other results
mspplots.create_results()
def __init__(self,
file_dir,
yml_file=None,
loglevel=logging.DEBUG,
configs: dict = None):
super().__init__()
self.yaml_options = ["default"]
self.reader_options = {
reader.name: reader
for reader in BaseReader.__subclasses__()
}
self.selected_reader = MQReader.MQReader
self.normalize_options = ["None"] + list(default_normalizers.keys())
self.number_of_plots = 0
self.plot_settings = {}
self.intensity_options = ["lfq_log2", "raw_log2", "ibaq_log2"]
#,"lfq_normalized_log2", "raw_normalized_log2", "ibaq_normalized_log2]
self.title("mspypeline")
path_label = tk.Label(self,
text="Dir to analyze",
font="Helvetica 10 bold").grid(row=0, column=0)
yaml_label = tk.Label(self, text="Yaml file",
font="Helvetica 10 bold").grid(row=0, column=1)
reader_label = tk.Label(self,
text="File reader",
font="Helvetica 10 bold").grid(row=0, column=2)
self.dir_text = tk.StringVar(value=file_dir)
dir_button = tk.Button(
self,
textvariable=self.dir_text,
command=lambda: browsefunc(
filedialog.askdirectory,
self.dir_text,
fn_params={
"title":
"Please select a directory with MaxQuant result files"
}))
dir_button.grid(row=1, column=0)
self.yaml_text = tk.StringVar()
self.yaml_button = tk.OptionMenu(self, self.yaml_text,
*self.yaml_options)
self.yaml_button.grid(row=1, column=1)
self.reader_text = tk.StringVar(value="mqreader")
self.reader_button = tk.OptionMenu(self, self.reader_text,
*self.reader_options.keys())
self.reader_button.grid(row=1, column=2)
self.replicate_var = tk.IntVar(value=1)
replicate_button = tk.Checkbutton(
self,
text="Does the file have technical replicates?",
variable=self.replicate_var).grid(row=2, column=0)
go_proteins_label = tk.Label(self, text="Go analysis proteins").grid(
row=3, column=0)
experiments_label = tk.Label(self,
text="Pathway analysis").grid(row=3,
column=1)
design_label = tk.Label(self, text="Replicate names").grid(row=3,
column=2)
self.go_proteins_list = tk.Listbox(self,
selectmode="multiple",
height=5,
width=len(
max(MSPInitializer.possible_gos,
key=len)))
self.go_proteins_list.configure(exportselection=False)
for x in MSPInitializer.possible_gos:
self.go_proteins_list.insert("end", x)
self.go_proteins_list.grid(row=4, column=0)
self.pathway_list = tk.Listbox(
self,
selectmode="multiple",
height=5,
width=len(max(MSPInitializer.possible_pathways, key=len)))
self.pathway_list.configure(exportselection=False)
for x in MSPInitializer.possible_pathways:
self.pathway_list.insert("end", x)
self.pathway_list.grid(row=4, column=1)
self.experiments_list = tk.Listbox(self, height=5)
self.experiments_list.grid(row=4, column=2)
report_button = tk.Button(self,
text="Create Report",
command=lambda: self.report_button())
report_button.grid(row=5, column=0)
plot_label = tk.Label(self, text="Which plots should be created").grid(
row=6, column=0)
intensity_label = tk.Label(self, text="Intensities").grid(row=6,
column=1)
levels_label = tk.Label(self, text="Levels").grid(row=6, column=2)
self.heading_length = 7
tk.Label(self, text="Normalization plots",
font="Helvetica 10 bold").grid(row=self.heading_length +
self.number_of_plots,
column=0)
self.number_of_plots += 1
self.plot_row("Normalization overview",
"normalization_overview_all_normalizers")
self.plot_row("Heatmap overview", "heatmap_overview_all_normalizers")
tk.Label(self,
text="Choose a Normalization Method:",
font="Helvetica 10 bold").grid(row=self.heading_length +
self.number_of_plots,
column=1)
self.number_of_plots += 1
self.plot_intermediate_row("Choose a Normalization Method")
tk.Label(self,
text="Outlier detection / Comparisons",
font="Helvetica 10 bold").grid(row=self.heading_length +
self.number_of_plots,
column=0)
self.number_of_plots += 1
self.plot_row("Detection counts", "detection_counts")
self.plot_row("Number of detected proteins",
"detected_proteins_per_replicate")
self.plot_row("Venn diagrams", "venn_results")
self.plot_row("Group diagrams", "venn_groups")
self.plot_row("PCA overview", "pca_overview")
self.plot_row("Intensity histogram", "intensity_histograms")
self.plot_row("Relative std", "relative_std")
self.plot_row("Scatter replicates", "scatter_replicates")
self.plot_row("Experiment comparison", "experiment_comparison")
self.plot_row("Rank", "rank")
tk.Label(self, text="Statistical inference",
font="Helvetica 10 bold").grid(row=self.heading_length +
self.number_of_plots,
column=0)
self.number_of_plots += 1
self.plot_row("Pathway Analysis", "pathway_analysis")
#self.plot_row("Pathway Timecourse", "pathway_timecourse")
self.plot_row("Go analysis", "go_analysis")
self.plot_row("Volcano plot (R)", "r_volcano")
self.p_val_var = tk.IntVar(value=1)
pval_button = tk.Checkbutton(
self, text="Use adjusted p value", variable=self.p_val_var).grid(
row=self.heading_length + self.number_of_plots, column=1)
total_length = self.heading_length + self.number_of_plots
update_button = tk.Button(self,
text="Update",
command=lambda: self.update_button())
update_button.grid(row=total_length + 1, column=1)
start_button = tk.Button(self,
text="Start",
command=lambda: self.start_button())
start_button.grid(row=total_length + 1, column=2)
self.running_text = tk.StringVar(value="Please press Start")
self.running_label = tk.Label(
self, textvariable=self.running_text).grid(row=total_length + 2,
column=2)
# add all tracing to the variables
self.dir_text.trace("w", self.dir_setter)
self.yaml_text.trace("w", self.yaml_path_setter)
self.reader_text.trace("w", self.reader_setter)
# make the GUI resizable
self.columnconfigure(0, weight=1)
self.rowconfigure(0, weight=1)
# here we set the configurations
# constructing the class reads the yaml file once
self.mspinit = MSPInitializer(file_dir, yml_file, loglevel=loglevel)
if file_dir:
# the dir setting reads the yaml file twice, once after setting the dir, then after setting the yaml path
self.dir_text.set(file_dir)
self.mspinit.configs.update(configs)
self.mainloop()
class MSPGUI(tk.Tk):
def __init__(self,
file_dir,
yml_file=None,
loglevel=logging.DEBUG,
configs: dict = None):
super().__init__()
self.yaml_options = ["default"]
self.reader_options = {
reader.name: reader
for reader in BaseReader.__subclasses__()
}
self.selected_reader = MQReader.MQReader
self.normalize_options = ["None"] + list(default_normalizers.keys())
self.number_of_plots = 0
self.plot_settings = {}
self.intensity_options = ["lfq_log2", "raw_log2", "ibaq_log2"]
#,"lfq_normalized_log2", "raw_normalized_log2", "ibaq_normalized_log2]
self.title("mspypeline")
path_label = tk.Label(self,
text="Dir to analyze",
font="Helvetica 10 bold").grid(row=0, column=0)
yaml_label = tk.Label(self, text="Yaml file",
font="Helvetica 10 bold").grid(row=0, column=1)
reader_label = tk.Label(self,
text="File reader",
font="Helvetica 10 bold").grid(row=0, column=2)
self.dir_text = tk.StringVar(value=file_dir)
dir_button = tk.Button(
self,
textvariable=self.dir_text,
command=lambda: browsefunc(
filedialog.askdirectory,
self.dir_text,
fn_params={
"title":
"Please select a directory with MaxQuant result files"
}))
dir_button.grid(row=1, column=0)
self.yaml_text = tk.StringVar()
self.yaml_button = tk.OptionMenu(self, self.yaml_text,
*self.yaml_options)
self.yaml_button.grid(row=1, column=1)
self.reader_text = tk.StringVar(value="mqreader")
self.reader_button = tk.OptionMenu(self, self.reader_text,
*self.reader_options.keys())
self.reader_button.grid(row=1, column=2)
self.replicate_var = tk.IntVar(value=1)
replicate_button = tk.Checkbutton(
self,
text="Does the file have technical replicates?",
variable=self.replicate_var).grid(row=2, column=0)
go_proteins_label = tk.Label(self, text="Go analysis proteins").grid(
row=3, column=0)
experiments_label = tk.Label(self,
text="Pathway analysis").grid(row=3,
column=1)
design_label = tk.Label(self, text="Replicate names").grid(row=3,
column=2)
self.go_proteins_list = tk.Listbox(self,
selectmode="multiple",
height=5,
width=len(
max(MSPInitializer.possible_gos,
key=len)))
self.go_proteins_list.configure(exportselection=False)
for x in MSPInitializer.possible_gos:
self.go_proteins_list.insert("end", x)
self.go_proteins_list.grid(row=4, column=0)
self.pathway_list = tk.Listbox(
self,
selectmode="multiple",
height=5,
width=len(max(MSPInitializer.possible_pathways, key=len)))
self.pathway_list.configure(exportselection=False)
for x in MSPInitializer.possible_pathways:
self.pathway_list.insert("end", x)
self.pathway_list.grid(row=4, column=1)
self.experiments_list = tk.Listbox(self, height=5)
self.experiments_list.grid(row=4, column=2)
report_button = tk.Button(self,
text="Create Report",
command=lambda: self.report_button())
report_button.grid(row=5, column=0)
plot_label = tk.Label(self, text="Which plots should be created").grid(
row=6, column=0)
intensity_label = tk.Label(self, text="Intensities").grid(row=6,
column=1)
levels_label = tk.Label(self, text="Levels").grid(row=6, column=2)
self.heading_length = 7
tk.Label(self, text="Normalization plots",
font="Helvetica 10 bold").grid(row=self.heading_length +
self.number_of_plots,
column=0)
self.number_of_plots += 1
self.plot_row("Normalization overview",
"normalization_overview_all_normalizers")
self.plot_row("Heatmap overview", "heatmap_overview_all_normalizers")
tk.Label(self,
text="Choose a Normalization Method:",
font="Helvetica 10 bold").grid(row=self.heading_length +
self.number_of_plots,
column=1)
self.number_of_plots += 1
self.plot_intermediate_row("Choose a Normalization Method")
tk.Label(self,
text="Outlier detection / Comparisons",
font="Helvetica 10 bold").grid(row=self.heading_length +
self.number_of_plots,
column=0)
self.number_of_plots += 1
self.plot_row("Detection counts", "detection_counts")
self.plot_row("Number of detected proteins",
"detected_proteins_per_replicate")
self.plot_row("Venn diagrams", "venn_results")
self.plot_row("Group diagrams", "venn_groups")
self.plot_row("PCA overview", "pca_overview")
self.plot_row("Intensity histogram", "intensity_histograms")
self.plot_row("Relative std", "relative_std")
self.plot_row("Scatter replicates", "scatter_replicates")
self.plot_row("Experiment comparison", "experiment_comparison")
self.plot_row("Rank", "rank")
tk.Label(self, text="Statistical inference",
font="Helvetica 10 bold").grid(row=self.heading_length +
self.number_of_plots,
column=0)
self.number_of_plots += 1
self.plot_row("Pathway Analysis", "pathway_analysis")
#self.plot_row("Pathway Timecourse", "pathway_timecourse")
self.plot_row("Go analysis", "go_analysis")
self.plot_row("Volcano plot (R)", "r_volcano")
self.p_val_var = tk.IntVar(value=1)
pval_button = tk.Checkbutton(
self, text="Use adjusted p value", variable=self.p_val_var).grid(
row=self.heading_length + self.number_of_plots, column=1)
total_length = self.heading_length + self.number_of_plots
update_button = tk.Button(self,
text="Update",
command=lambda: self.update_button())
update_button.grid(row=total_length + 1, column=1)
start_button = tk.Button(self,
text="Start",
command=lambda: self.start_button())
start_button.grid(row=total_length + 1, column=2)
self.running_text = tk.StringVar(value="Please press Start")
self.running_label = tk.Label(
self, textvariable=self.running_text).grid(row=total_length + 2,
column=2)
# add all tracing to the variables
self.dir_text.trace("w", self.dir_setter)
self.yaml_text.trace("w", self.yaml_path_setter)
self.reader_text.trace("w", self.reader_setter)
# make the GUI resizable
self.columnconfigure(0, weight=1)
self.rowconfigure(0, weight=1)
# here we set the configurations
# constructing the class reads the yaml file once
self.mspinit = MSPInitializer(file_dir, yml_file, loglevel=loglevel)
if file_dir:
# the dir setting reads the yaml file twice, once after setting the dir, then after setting the yaml path
self.dir_text.set(file_dir)
self.mspinit.configs.update(configs)
self.mainloop()
def dir_setter(self, *args):
start_dir = self.dir_text.get()
if os.path.split(start_dir)[1] == "txt":
start_dir = os.path.split(start_dir)[0]
self.mspinit.start_dir = start_dir
self.update_yaml_options()
def update_yaml_options(self):
if self.mspinit.has_yml_file():
self.yaml_text.set("file")
self.yaml_options = ["default", "file"]
# next steps should also be done hy what the update button does?
else:
self.yaml_text.set("default")
self.yaml_options = ["default"]
self.yaml_button["menu"].delete(0, "end")
for op in self.yaml_options:
self.yaml_button["menu"].add_command(label=op,
command=tk._setit(
self.yaml_text, op))
def update_listboxes(self):
# delete all experiments then add from file
self.experiments_list.delete(0, "end")
for op in self.mspinit.configs.get(self.selected_reader.name,
{}).get("all_replicates", []):
self.experiments_list.insert("end", op)
# clear selection then select from configs
for i, pathway in enumerate(MSPInitializer.possible_pathways):
self.pathway_list.select_clear(i)
if self.mspinit.configs.get("pathways"):
for pathway in self.mspinit.configs.get("pathways"):
self.pathway_list.select_set(
MSPInitializer.possible_pathways.index(pathway))
# clear selection then select from configs
for i, go in enumerate(MSPInitializer.possible_gos):
self.go_proteins_list.select_clear(i)
if self.mspinit.configs.get("go_terms"):
for go in self.mspinit.configs.get("go_terms"):
self.go_proteins_list.select_set(
MSPInitializer.possible_gos.index(go))
def yaml_path_setter(self, *args):
self.mspinit.file_path_yaml = self.yaml_text.get()
# get the reader class by the saved name
self.selected_reader = self.reader_options.get(
self.mspinit.configs.get("selected_reader", "mqreader"))
reader_settings = self.mspinit.configs.get(self.selected_reader.name,
{})
level_names = reader_settings.get("level_names", [])
level_names = {i: name for i, name in enumerate(level_names)}
levels = reader_settings.get("levels", 0)
for plot_name in self.selected_reader.plotter.possible_plots:
plot_settings_name = plot_name + "_settings"
plot_settings = self.mspinit.configs.get(plot_settings_name, {})
var_name = plot_name.replace("plot_", "") + "_var"
int_name = var_name.replace("var", "int")
levels_name = var_name.replace("var", "levels")
# update all settings in the GUI
self.plot_settings[int_name].set(
plot_settings.get("create_plot", False))
plot_intensities = plot_settings.get("dfs_to_use", [])
self.plot_settings[var_name].update_selection(plot_intensities)
plot_levels = plot_settings.get("levels", [])
selected_levels = self.plot_settings[levels_name]
selected_levels.update_options(
[level_names.get(l, l) for l in range(levels)])
selected_levels.update_selection(
[level_names.get(pl, pl) for pl in plot_levels])
self.replicate_var.set(self.mspinit.configs.get("has_techrep", True))
self.p_val_var.set(
self.mspinit.configs.get("plot_r_volcano_settings",
{}).get("adj_pval", False))
self.normalizer_text.set(
self.mspinit.configs.get("selected_normalizer", "None"))
self.update_listboxes()
def reader_setter(self, *args):
self.selected_reader = self.reader_options[self.reader_text.get()]
def update_button(self):
self.mspinit.configs["has_techrep"] = bool(self.replicate_var.get())
self.mspinit.configs["selected_reader"] = str(self.reader_text.get())
self.mspinit.configs["selected_normalizer"] = str(
self.normalizer_text.get())
reader_settings = self.mspinit.configs.get(self.selected_reader.name,
{})
level_names = reader_settings.get("level_names", [])
level_names = {name: i for i, name in enumerate(level_names)}
for plot_name in self.selected_reader.plotter.possible_plots:
plot_settings = plot_name + "_settings"
var_name = plot_name.replace("plot_", "") + "_var"
int_name = var_name.replace("var", "int")
levels_name = var_name.replace("var", "levels")
selected_settings = {
"create_plot":
bool(self.plot_settings[int_name].get()),
"dfs_to_use": [
k for k, v in
self.plot_settings[var_name].get_selection().items() if v
],
"levels": [
level_names.get(k, k) for k, v in
self.plot_settings[levels_name].get_selection().items()
if v
]
}
additional_settings = self.mspinit.configs.get(plot_settings, {})
additional_settings = {
k: v
for k, v in additional_settings.items()
if k != "create_plot" and k != "dfs_to_use" and k != "levels"
}
selected_settings.update(additional_settings)
self.mspinit.configs.update({plot_settings: selected_settings})
gos = self.go_proteins_list.curselection()
gos = [MSPInitializer.possible_gos[int(go)] for go in gos]
pathways = self.pathway_list.curselection()
pathways = [
MSPInitializer.possible_pathways[int(pathway)]
for pathway in pathways
]
self.mspinit.configs["plot_r_volcano_settings"]["adj_pval"] = bool(
self.p_val_var.get())
self.mspinit.configs["go_terms"] = gos
self.mspinit.configs["pathways"] = pathways
self.mspinit.init_config()
self.mspinit.read_data()
self.update_listboxes()
self.update_yaml_options()
def start_button(self):
self.running_text.set("Creating Plots")
self.update()
self.update_button()
mspplots = self.selected_reader.plotter.from_MSPInitializer(
self.mspinit)
mspplots.create_results()
self.running_text.set("Please press Start")
def report_button(self):
self.running_text.set("Creating Report")
self.update()
self.update_button()
mspplots = self.selected_reader.plotter.from_MSPInitializer(
self.mspinit)
mspplots.create_report()
self.running_text.set("Please press Start")
def plot_intermediate_row(self, text: str):
row = self.heading_length + self.number_of_plots
int_var = tk.IntVar(value=1)
self.normalizer_text = tk.StringVar(value="None")
self.normalizer_button = tk.OptionMenu(self, self.normalizer_text,
*self.normalize_options)
self.normalizer_button.grid(row=row, column=1)
self.number_of_plots += 1
def plot_row(self, text: str, plot_name: str):
row = self.heading_length + self.number_of_plots
int_var = tk.IntVar(value=1)
tk.Checkbutton(self, text=text, variable=int_var).grid(row=row,
column=0)
intensity_list = MultiSelectOptionMenu(self, self.intensity_options,
"Select Intensities")
intensity_list.grid(row=row, column=1)
level_list = MultiSelectOptionMenu(self, button_text="Select Levels")
level_list.grid(row=row, column=2)
self.number_of_plots += 1
self.plot_settings.update({
f"{plot_name}_int": int_var,
f"{plot_name}_var": intensity_list,
f"{plot_name}_levels": level_list
})