def new_graph_page(self, type, btn): handler = None if type in self.pages: handler = self.pages[type] if handler == None: self.newPage = tk.Toplevel(self.master) self.app = GraphPage(self.newPage, type) handler = self.app btn.configure(text="Close "+type) else: handler.master.destroy() handler = None; btn.configure(text="Open "+type) self.pages[type] = handler self.update()
def plot_graph(self):
self.run_assoc_button.grid_remove()
self.progresslabel = ttk.Label(self, style = "wlabel.TLabel")
self.progresslabel.grid(column = 0, row = 4, columnspan = 2, pady = 5)
self.progress = ttk.Progressbar(self, mode = "determinate",
style = "green.Horizontal.TProgressbar")
self.progress.grid(column = 0, row = 5, pady = 5,
padx = 10, sticky = tk.W + tk.E)
self.quit.grid(column = 0, row = 4, pady = (5,0), columnspan = 1,
sticky = tk.E, padx = 10)
self.progress.update_idletasks()
if self.check_yes_no.get() == 0 or self.filetype == "unknown":
self.item_indexs = {}
self.item_indexs["p"] = self.optionlist.index(
self.fourth_drop_value.get()
)
self.item_indexs["snp"] = self.optionlist.index(
self.second_drop_value.get()
)
self.item_indexs["chr"] = self.optionlist.index(
self.first_drop_value.get()
)
self.item_indexs["bp"] = self.optionlist.index(
self.third_drop_value.get()
)
elif self.check_yes_no.get() == 1:
self.item_indexs = {}
self.item_indexs = get_assoc_columns(self.header_dict,
self.filetype, plot = "assoc")
print(self.item_indexs)
self.assoc_results.data = self.data
self.assoc_results.item_indexs = self.item_indexs
self.assoc_results = prep_assoc_data(self.assoc_results)
self.progress["maximum"] = len(self.assoc_results.chromset) + 0.001
x = threading.Thread(target=self.threaded_plot, daemon = True)
x.start()
self.assoc_page = GraphPage(master = self,
results = self.assoc_results,
plot_type = "all_chr")
self.assoc_page.grid(column = 0, row = 1)
self.table_page = TablePage(self, self.assoc_results,
self.assoc_page.canvas, self.filename)
self.table_page.grid(column = 0, row = 1, sticky = tk.NSEW)
self.assocnotebook.add(self.assoc_page, text = "Association Plot")
self.assocnotebook.add(self.table_page, text = "Data")
self.assocnotebook.select(self.assoc_page)
class Application(ttk.Frame):
def __init__(self, master=None):
super().__init__(master)
self.master = master
self.set_styles()
self.assoc_results = Assoc()
self.pack(expand = True)
self.create_widgets()
def set_styles(self):
self.style = ttk.Style()
self.style.theme_use("clam")
self.style.configure("greyframe.TFrame", background = "darkslategrey")
self["style"] = "greyframe.TFrame"
self.style.configure("wbutton.TButton", background = "white")
self.style.configure("greynote.TNotebook", background = "darkslategrey")
self.style.map("TNotebook.Tab", background=[("selected", "white")])
self.style.configure("TNotebook.Tab", background = "white")
self.style.configure("TCombobox",
background = "white",
foreground = "black")
self.style.map("TCombobox", fieldbackground=[("readonly", "white")],
foreground=[("focus","black"),("disabled", "grey")],
bordercolor=[("disabled", "white")])
self.style.configure("wframe.TFrame", background = "white")
self.style.configure("wlframe.TLabelframe",
background = "white")
self.style.configure("wlabel.TLabel",
background = "white", foreground = "black")
self.style.map("TLabel", background=[("disabled", "white")],
foreground=[("disabled","grey")])
self.style.configure("wradio.TRadiobutton", background = "white")
self.style.map("wradio.TRadiobutton",
background=[("disabled", "white")])
self.style.configure("Run.TButton", font = ("bold", 12),
background = "white")
self.style.configure("teallabel.TLabel", background = "teal",
foreground = "white", font = ("bold", 11))
self.style.configure("fancy.Vertical.TScrollbar",
background = "white",
troughcolor = "white")
self.style.configure("fancy.Horizontal.TScrollbar",
background = "white",
troughcolor = "white")
self.style.configure("Optpane.TLabelframe",
background = "white")
self.style.configure("Optlabel.TLabel",
background = "white", foreground = "black")
self.style.configure("Optheadlabel.TLabel",
background = "white", foreground = "teal")
self.style.configure("Optscrol.Horizontal.TScale",
background = "teal",
troughcolor = "white")
self.style.configure("green.Horizontal.TProgressbar",
troughcolor ='white', background='green')
def create_widgets(self):
self.quit = ttk.Button(self, text="QUIT",
command=self.master.destroy,
style = "wbutton.TButton")
self.quit.grid(column = 0, row = 10, pady = 5, columnspan = 2)
self.make_input_frame()
def make_input_frame(self):
self.assocnotebook = ttk.Notebook(self, style = "greynote.TNotebook")
self.assocnotebook.grid(column = 0, row = 1, sticky = tk.NSEW)
self.input_frame = ttk.Frame(self, padding = 10,
style = "wframe.TFrame")
self.input_frame.grid(column = 0, row = 1, sticky = tk.NSEW)
self.assocnotebook.add(self.input_frame, text = "Input")
#self.title_img = tk.PhotoImage(file = "title.gif")
#self.title_label = ttk.Label(self.input_frame, image = self.title_img,
# style = "wlabel.TLabel")
#self.title_label.grid(column = 0, row = 0, columnspan = 2, pady = 20)
self.logo_canvas = tk.Canvas(self.input_frame, bg = "white", height = 150, width = 350,
borderwidth = 0, highlightthickness = 0)
self.logo_canvas.grid(column = 0, row = 0, columnspan = 2)
self.logo_outer = self.logo_canvas.create_oval(30,30,320,130, fill = "light blue", outline = "white")
self.logo_text = self.logo_canvas.create_text(175, 75, anchor = tk.CENTER)
self.logo_canvas.itemconfig(self.logo_text, text = "GWAS Toolkit v3", font = ("courier", 25, "bold", "underline"))
self.logo_canvas.update_idletasks()
self.enter_text = ttk.Entry(self.input_frame, width = 75)
self.enter_text.insert(0, "")
self.enter_text.grid(column = 0, row = 2, padx = 5, sticky = tk.W)
self.enter_text.state(["!disabled", "readonly"])
self.entertextlabel = ttk.Label(self.input_frame,
style = "wlabel.TLabel")
self.entertextlabel["text"] = ("Enter your file name and location"
", click browse to pick file:")
self.entertextlabel.grid(column = 0, row = 1, padx = 5, sticky = tk.W)
self.browse = ttk.Button(self.input_frame, style = "wbutton.TButton")
self.browse["text"] = "Browse Files"
self.browse["command"] = self.pick_file
self.browse.grid(column = 1, row = 2, padx = 5)
self.go_button = ttk.Button(self.input_frame, style = "wbutton.TButton")
self.go_button["text"] = "Continue"
self.go_button["command"] = self.get_file_info
self.go_button.grid(column = 0, row = 3, padx = 5)
self.go_button.state(["disabled"])
def check_if_empty(self):
if self.enter_text.get() == "":
self.go_button.state(["disabled"])
elif self.enter_text.get() != "":
self.go_button.state(["!disabled"])
def pick_file(self):
filename = tk.filedialog.askopenfilename(defaultextension = ".assoc",
filetypes=[("ASSOC", ".assoc"),
("TEXT", ".txt")],
title = "Choose Data File")
self.enter_text.state(["!readonly"])
self.enter_text.delete(0, "end")
self.enter_text.insert(0, filename)
self.enter_text.state(["readonly"])
self.check_if_empty()
def get_file_info(self):
file_location = self.enter_text.get()
self.header_dict, self.data = get_data(file_location)
self.filename = ""
self.filename = get_simple_filename(file_location)
file_format_query, self.filetype = find_file_type(self.header_dict)
self.assoc_check_frame(self.filename, file_format_query)
def assoc_check_frame(self, name, file_format_query):
self.browse.grid_remove()
self.go_button.grid_remove()
check_labeltitle = ttk.Label(self.input_frame, text = "Data Check",
style = "wlabel.TLabel")
self.checkframe = ttk.LabelFrame(self.input_frame, text = "Data Check",
style = "wlframe.TLabelframe",
labelwidget = check_labeltitle)
self.checkframe.grid(column = 0, row = 3, sticky = tk.N + tk.W + tk.E,
padx = 10, pady = 10)
self.checkframe["padding"] = 10
self.checkframe.configure(borderwidth = 2)
self.data_info = ttk.Label(self.checkframe, style = "wlabel.TLabel")
self.data_info["text"] = f"There are {len(self.data)} rows in {name}"
self.data_info.grid(column = 0, row = 0, sticky = tk.N + tk.S + tk.E + tk.W)
self.format_query_message = ttk.Label(self.checkframe,
style = "wlabel.TLabel")
self.format_query_message["text"] = "\n" + file_format_query
self.format_query_message.grid(column = 0, row = 1, sticky = tk.W)
if self.filetype != "unknown":
self.check_yes_no = tk.IntVar()
self.yes_check = ttk.Radiobutton(self.checkframe, text = "Yes",
style = "wradio.TRadiobutton")
self.yes_check.grid(column = 0, row = 2, sticky = tk.W, pady = 5)
self.yes_check["variable"] = self.check_yes_no
self.yes_check["value"] = 1
self.no_check = ttk.Radiobutton(self.checkframe, text = "No",
style = "wradio.TRadiobutton")
self.no_check.grid(column = 0, row = 2, pady = 5)
self.no_check["variable"] = self.check_yes_no
self.no_check["value"] = 0
self.check_go = ttk.Button(self.checkframe, text = "Continue",
style = "wbutton.TButton")
self.check_go.grid(column = 0, row = 3, pady = 10, padx = 5,
sticky = tk.W)
self.check_go["command"] = self.check_input
elif self.filetype == "unknown":
self.user_manual_input()
def check_input(self):
if self.check_yes_no.get() == 0:
self.user_manual_input()
elif self.check_yes_no.get() == 1:
self.prep_to_run()
def user_manual_input(self):
if self.filetype != "unknown":
self.yes_check.state(["disabled"])
self.no_check.state(["disabled"])
self.check_go.grid_remove()
user_input_titlelabel = ttk.Label(self.input_frame,
style = "wlabel.TLabel",
text = "Manual Data Column Input")
self.user_input_col_frame = ttk.LabelFrame(self.input_frame,
style = "wlframe.TLabelframe",
labelwidget = user_input_titlelabel)
self.user_input_col_frame.grid(column = 0, row = 3, rowspan = 2,
sticky = tk.N + tk.W + tk.E + tk.S,
padx = 10, pady = 10)
self.user_input_col_frame["padding"] = 10
self.user_input_message = ttk.Label(self.user_input_col_frame,
style = "wlabel.TLabel")
self.user_input_message["text"] = ("Please input the header of the "
"column that contains the following:")
self.user_input_message.grid(column = 0, row = 0, sticky = tk.W)
self.optionlist = []
for key, value in self.header_dict.items():
self.optionlist.append(f"Column {int(value) + 1}: '{key}'")
self.firstlabel = ttk.Label(self.user_input_col_frame,
text = "The chromosome number:",
style = "wlabel.TLabel")
self.firstlabel.grid(column = 0, row = 1, sticky = tk.W, pady = 5,
padx = 5)
self.first_drop_value = tk.StringVar()
self.first_drop_value.set(self.optionlist[0])
self.firstoptions = ttk.Combobox(self.user_input_col_frame,
textvariable = self.first_drop_value,
values = self.optionlist)
self.firstoptions.state(["!disabled", "readonly"])
self.firstoptions.grid(column = 1, row = 1, sticky = tk.E, pady = 5)
self.secondlabel = ttk.Label(self.user_input_col_frame,
text = "The SNP name / ID:",
style = "wlabel.TLabel")
self.secondlabel.grid(column = 0, row = 2, sticky = tk.W, pady = 5,
padx = 5)
self.second_drop_value = tk.StringVar()
self.second_drop_value.set(self.optionlist[1])
self.secondoptions = ttk.Combobox(self.user_input_col_frame,
textvariable = self.second_drop_value,
values = self.optionlist)
self.secondoptions.state(["!disabled", "readonly"])
self.secondoptions.grid(column = 1, row = 2, sticky = tk.E, pady = 5)
self.thirdlabel = ttk.Label(self.user_input_col_frame,
text = "The bp position:",
style = "wlabel.TLabel")
self.thirdlabel.grid(column = 0, row = 3, sticky = tk.W, pady = 5,
padx = 5)
self.third_drop_value = tk.StringVar()
self.third_drop_value.set(self.optionlist[2])
self.thirdoptions = ttk.Combobox(self.user_input_col_frame,
textvariable = self.third_drop_value,
values = self.optionlist)
self.thirdoptions.state(["!disabled", "readonly"])
self.thirdoptions.grid(column = 1, row = 3, sticky = tk.E, pady = 5)
self.fourthlabel = ttk.Label(self.user_input_col_frame,
text = "The p-value from the association"
" analysis:",
style = "wlabel.TLabel")
self.fourthlabel.grid(column = 0, row = 4, sticky = tk.W, pady = 5,
padx = 5)
self.fourth_drop_value = tk.StringVar()
self.fourth_drop_value.set(self.optionlist[3])
self.fourthoptions = ttk.Combobox(self.user_input_col_frame,
textvariable = self.fourth_drop_value,
values = self.optionlist)
self.fourthoptions.state(["!disabled", "readonly"])
self.fourthoptions.grid(column = 1, row = 4, sticky = tk.E, pady = 5)
self.input_go = ttk.Button(self.user_input_col_frame,
text = "Continue",
style = "wbutton.TButton")
self.input_go.grid(column = 0, row = 5, sticky = tk.W, pady = 5,
padx = 5)
self.input_go["command"] = self.prep_to_run
def prep_to_run(self):
if self.check_yes_no.get() == 0 or self.filetype == "unknown":
self.input_go.grid_remove()
self.firstoptions.state(["disabled"])
self.secondoptions.state(["disabled"])
self.thirdoptions.state(["disabled"])
self.fourthoptions.state(["disabled"])
elif self.check_yes_no.get() == 1:
self.yes_check.state(["disabled"])
self.no_check.state(["disabled"])
self.check_go.grid_remove()
self.run_assoc_button = ttk.Button(self, style = "Run.TButton")
self.run_assoc_button["text"] = "Plot Graph"
self.run_assoc_button.grid(column = 0, row = 4, columnspan = 2,
pady = 10)
self.run_assoc_button["command"] = self.plot_graph
def plot_graph(self):
self.run_assoc_button.grid_remove()
self.progresslabel = ttk.Label(self, style = "wlabel.TLabel")
self.progresslabel.grid(column = 0, row = 4, columnspan = 2, pady = 5)
self.progress = ttk.Progressbar(self, mode = "determinate",
style = "green.Horizontal.TProgressbar")
self.progress.grid(column = 0, row = 5, pady = 5,
padx = 10, sticky = tk.W + tk.E)
self.quit.grid(column = 0, row = 4, pady = (5,0), columnspan = 1,
sticky = tk.E, padx = 10)
self.progress.update_idletasks()
if self.check_yes_no.get() == 0 or self.filetype == "unknown":
self.item_indexs = {}
self.item_indexs["p"] = self.optionlist.index(
self.fourth_drop_value.get()
)
self.item_indexs["snp"] = self.optionlist.index(
self.second_drop_value.get()
)
self.item_indexs["chr"] = self.optionlist.index(
self.first_drop_value.get()
)
self.item_indexs["bp"] = self.optionlist.index(
self.third_drop_value.get()
)
elif self.check_yes_no.get() == 1:
self.item_indexs = {}
self.item_indexs = get_assoc_columns(self.header_dict,
self.filetype, plot = "assoc")
print(self.item_indexs)
self.assoc_results.data = self.data
self.assoc_results.item_indexs = self.item_indexs
self.assoc_results = prep_assoc_data(self.assoc_results)
self.progress["maximum"] = len(self.assoc_results.chromset) + 0.001
x = threading.Thread(target=self.threaded_plot, daemon = True)
x.start()
self.assoc_page = GraphPage(master = self,
results = self.assoc_results,
plot_type = "all_chr")
self.assoc_page.grid(column = 0, row = 1)
self.table_page = TablePage(self, self.assoc_results,
self.assoc_page.canvas, self.filename)
self.table_page.grid(column = 0, row = 1, sticky = tk.NSEW)
self.assocnotebook.add(self.assoc_page, text = "Association Plot")
self.assocnotebook.add(self.table_page, text = "Data")
self.assocnotebook.select(self.assoc_page)
def threaded_plot(self):
for chrom in self.assoc_results.chromset:
chrom_snpcount = len(self.assoc_results.chrom_snpnum[chrom])
self.progresslabel["text"] = (f"Plotting: chr{chrom} "
f"({chrom_snpcount} SNPs)")
self.progresslabel.update_idletasks()
self.assoc_results = plot_assoc_chr(self.assoc_results, chrom)
self.progress.step()
self.progress.update_idletasks()
self.progress.grid_remove()
self.progresslabel.grid_remove()
self.quit.grid(column = 0, row = 6, pady = 5, columnspan = 2,
sticky = tk.N)
self.assoc_results = plot_assoc_graph(self.assoc_results)
self.assoc_results.fig.subplots_adjust(left = 0.07, right = 0.98,
top = 0.92)
self.assoc_page.canvas.draw_idle()
self.assoc_page.graph_option_pane.update_text_options()
self.assoc_page.graph_option_pane.update_y_axis_option()
self.table_page.make_results_table(50)
self.table_page.make_option_and_info_panel()
def add_graph(name=None):
cur_num = len(graph_list)
name = f"Graph {cur_num}" if name is None else name
graph_list.append(GraphPage(name))
tab_list.append(dcc.Tab(label=name, value=f"tab_{cur_num}"))
import dash
import dash_html_components as html
import dash_core_components as dcc
from dash.dependencies import Input, Output
from graph_page import GraphPage
app = dash.Dash(__name__)
graph_num = -1
graph_list = [GraphPage("Settings Page"), GraphPage("Graph 1")]
tab_list = [
dcc.Tab(label="Settings", value="tab_0"),
dcc.Tab(label="Graph 1", value="tab_1")
]
drop_list = [dcc.Dropdown(id="x_drop"), dcc.Dropdown(id="y_drop", multi=True)]
def add_graph(name=None):
cur_num = len(graph_list)
name = f"Graph {cur_num}" if name is None else name
graph_list.append(GraphPage(name))
tab_list.append(dcc.Tab(label=name, value=f"tab_{cur_num}"))
app.layout = html.Div([
dcc.Tabs(id="graph-tabs", value="tab_0"),
html.Button("Add Graph", id="button"),
html.Div(id='tab-display'),
html.Div(id='tmp')
],
id='app-container')