function varargout = DoseResponseFit(varargin)
%DOSERESPONSEFIT M-file for DoseResponseFit.fig
% DOSERESPONSEFIT, by itself, creates a new DOSERESPONSEFIT or raises the existing
% singleton*.
%
% H = DOSERESPONSEFIT returns the handle to a new DOSERESPONSEFIT or the handle to
% the existing singleton*.
%
% DOSERESPONSEFIT('Property','Value',...) creates a new DOSERESPONSEFIT using the
% given property value pairs. Unrecognized properties are passed via
% varargin to DoseResponseFit_OpeningFcn. This calling syntax produces a
% warning when there is an existing singleton*.
%
% DOSERESPONSEFIT('CALLBACK') and DOSERESPONSEFIT('CALLBACK',hObject,...) call the
% local function named CALLBACK in DOSERESPONSEFIT.M with the given input
% arguments.
%
% *See GUI Options on GUIDE's Tools menu. Choose "GUI allows only one
% instance to run (singleton)".
%
% See also: GUIDE, GUIDATA, GUIHANDLES
% Copyright 2011 - 2012 MathWorks, Inc.
% Edit the above text to modify the response to help DoseResponseFit
% Last Modified by GUIDE v2.5 31-Oct-2012 14:37:30
% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @DoseResponseFit_OpeningFcn, ...
'gui_OutputFcn', @DoseResponseFit_OutputFcn, ...
'gui_LayoutFcn', [], ...
'gui_Callback', []);
if nargin && ischar(varargin{1})
gui_State.gui_Callback = str2func(varargin{1});
end
if nargout
[varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
else
gui_mainfcn(gui_State, varargin{:});
end
% End initialization code - DO NOT EDIT
% --- Executes just before DoseResponseFit is made visible.
function DoseResponseFit_OpeningFcn(hObject, ~, handles, varargin)
% This function has no output args, see OutputFcn.
% hObject handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% varargin unrecognized PropertyName/PropertyValue pairs from the
% command line (see VARARGIN)
% Choose default command line output for DoseResponseFit
handles.output = hObject;
handles.scatter = [];
% Update handles structure
guidata(hObject, handles);
%% Callback functions
% --- Executes on button press in push_LoadData.
function push_LoadData_Callback(hObject, ~, handles)
% hObject handle to push_LoadData (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Select Excel File(s)
[pname, fname] = uigetfile({'*.xls; *.xlsx', 'Excel File (.xls, .xlsx)'}, 'Select Data File') ;
if fname == 0
errordlg('Please select data file', 'Load Data Error')
else
% Import data
handles.Data = dataset('xlsfile', fullfile(fname, pname)) ;
% Get VarNames
handles.varNames = handles.Data.Properties.VarNames ;
% Populate list with Treatment groups
set(handles.popup_response, 'String', handles.varNames) ;
set(handles.popup_dose, 'String', handles.varNames) ;
set(handles.list_groupVars, 'String', handles.varNames) ;
% Get grpStr
handles.grpStr{1} = handles.Data.(handles.varNames{1}) ;
% Enable Fit Data button
set(handles.push_Fit, 'enable', 'on');
% Set dose and response var to first variable
handles.doseVar = handles.varNames{1} ;
handles.responseVar = handles.varNames{1} ;
handles.groupVars = handles.varNames{1} ;
set(handles.popup_dose, 'Value', 1)
set(handles.list_groupVars, 'Value', 1)
set(handles.popup_response, 'Value', 1)
% Set
set(handles.list_groupVars, 'max', length(handles.varNames) - 2)
% Set file name
set(handles.edit_fileString, 'string', fullfile(fname, pname), 'enable', 'on')
handles.fileStr = fullfile(fname, pname) ;
% Plot Dose vs. Response grouped by Treatment group (Dose of Drug A)
axes(handles.axes_plot); hold on;
try
cla
handles.scatter = gscatter(handles.Data.(handles.doseVar), handles.Data.(handles.responseVar), handles.Data.(handles.groupVars)) ;
catch
msgbox('Invalid inputs', 'Default dose and response selection are incorrect', 'error')
end
% Enable reset button
set(handles.push_LoadData, 'enable', 'off') ;
end
guidata(hObject, handles)
function edit_fileString_Callback(hObject, ~, handles)
% hObject handle to edit_fileString (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: get(hObject,'String') returns contents of edit_fileString as text
% str2double(get(hObject,'String')) returns contents of edit_fileString as a double
msgbox('Use the Load Data button to load a new file', 'Load Data', 'help')
set(hObject, 'string', handles.fileStr)
% --- Executes on selection change in popup_response.
function popup_response_Callback(hObject, ~, handles)
% hObject handle to popup_response (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
contents = cellstr(get(hObject,'String')) ;
handles.responseVar = contents{get(hObject,'Value')} ;
try
if isfield(handles, 'scatter'), delete(handles.scatter) ; handles = rmfield(handles, 'scatter'); end
hold on
handles.scatter = gscatter(handles.Data.(handles.doseVar), handles.Data.(handles.responseVar), handles.grpStr);
catch
msgbox('Invalid Dose or Response inputs', 'Invalid Input', 'error')
end
guidata(hObject, handles)
% --- Executes on selection change in popup_dose.
function popup_dose_Callback(hObject, ~, handles)
% hObject handle to popup_dose (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
contents = cellstr(get(hObject,'String')) ;
handles.doseVar = contents{get(hObject,'Value')} ;
try
if isfield(handles, 'scatter'), delete(handles.scatter) ; handles = rmfield(handles, 'scatter'); end
hold on
handles.scatter = gscatter(handles.Data.(handles.doseVar), handles.Data.(handles.responseVar), handles.grpStr);
catch
msgbox('Invalid Dose or Response inputs', 'Invalid Input', 'error')
end
guidata(hObject, handles)
% --- Executes on selection change in list_groupVars.
function list_groupVars_Callback(hObject, ~, handles)
% hObject handle to list_groupVars (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
contents = cellstr(get(hObject,'String')) ;
handles.groupVars = contents(get(hObject,'Value'));
grpStr = cell(1,length(handles.groupVars));
for i = 1:length(handles.groupVars)
grpStr{i} = handles.Data.(handles.groupVars{i}) ;
end
handles.grpStr = grpStr ;
try
if isfield(handles, 'scatter'), delete(handles.scatter) ; handles = rmfield(handles, 'scatter'); end
hold on
handles.scatter = gscatter(handles.Data.(handles.doseVar), handles.Data.(handles.responseVar), handles.grpStr);
catch
msgbox('Incorrect Dose or Response input', 'Invalid inputs', 'error')
end
guidata(hObject, handles)
% --- Executes on button press in push_Fit.
function push_Fit_Callback(hObject, ~, handles)
% hObject handle to push_Fit (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Temporary variable: Get dose response data for selected groups
subjID = unique(handles.Data.SubjID);
% Create results dataset
results = dataset ;
% Preaallocate
results.subjID = subjID ;
results.EC50 = nan(size(subjID)) ;
results.Emax = nan(size(subjID)) ;
for j = 1:length(handles.groupVars)
if iscell(handles.Data.(handles.groupVars{j}))
results.(handles.groupVars{j}) = cell(size(subjID)) ;
elseif isnumeric(handles.Data.(handles.groupVars{j}))
results.(handles.groupVars{j}) = nan(size(subjID)) ;
end
end
model = cell(1, 2) ;
for i = 1:length(subjID)
ds = handles.Data(handles.Data.SubjID == subjID(i), :) ;
try
model{i, 2} = createFit(ds.(handles.doseVar), ds.(handles.responseVar), [.7, .7, .7]) ;
model{i, 1} = subjID(i) ;
% compile results
results.EC50(i) = model{i, 2}.EC50 ;
results.Emax(i) = model{i, 2}.Emax ;
catch
msgbox('Could not fit data. Setting EC50 & Emax to nan for current ID.', 'Fitting Error', 'error', 'replace')
end
for j = 1:length(handles.groupVars)
if length(unique(ds.(handles.groupVars{j})) ) == 1
results.(handles.groupVars{j})(i) = unique(ds.(handles.groupVars{j})) ;
else
results.(handles.groupVars{j})(i) = nan ;
msgbox('Grouping variable must have one unique value per subject. setting value to nan', ...
'Invalid grouping variable', 'error', 'replace')
end
end
end
handles.model = model ;
handles.results = results;
% Enable Reset & ANOVA buttons
set(handles.push_Analyze , 'Enable', 'on')
set(handles.push_export , 'Enable', 'on')
% Disable selection button
set(handles.popup_response, 'enable', 'off')
set(handles.popup_dose , 'enable', 'off')
set(handles.list_groupVars, 'enable', 'off')
set(handles.push_Fit , 'enable', 'off')
% Update GUIDATA
guidata(hObject, handles)
% --- Executes on button press in push_export.
function push_export_Callback(hObject, eventdata, handles)
% hObject handle to push_export (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Select Excel File(s)
[pname, fname] = uiputfile({'*.xlsx; *.xls', 'Excel File (.xls, .xlsx)'}, 'Select Data File') ;
if fname == 0
errordlg('Please select data file', 'Load Data Error')
else
export(handles.results, 'xlsfile', fullfile(fname, pname));
end
winopen(fullfile(fname, pname))
% --- Executes on button press in push_Analyze.
function push_Analyze_Callback(hObject, ~, handles)
% hObject handle to push_Analyze (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
grpStr = cell(1,length(handles.groupVars));
for i = 1:length(handles.groupVars)
grpStr{i} = handles.results.(handles.groupVars{i}) ;
end
try
anovan(handles.results.EC50(:), grpStr, 'varnames', handles.groupVars)
catch
errordlg('Could not perform ANOVA. Check results dataset')
end
guidata(hObject, handles)
% --- Executes on button press in push_reset.
function push_reset_Callback(hObject, ~, handles)
% hObject handle to push_reset (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Clear axes
cla ; delete(legend)
% Remove Data
if isfield(handles, 'results') , handles = rmfield(handles, 'results') ; end
if isfield(handles, 'Data') , handles = rmfield(handles, 'Data') ; end
if isfield(handles, 'varNames') , handles = rmfield(handles, 'varNames') ; end
if isfield(handles, 'grpStr') , handles = rmfield(handles, 'grpStr') ; end
if isfield(handles, 'doseVar') , handles = rmfield(handles, 'doseVar') ; end
if isfield(handles, 'groupVars') , handles = rmfield(handles, 'groupVars') ; end
if isfield(handles, 'fileStr') , handles = rmfield(handles, 'fileStr') ; end
if isfield(handles, 'model') , handles = rmfield(handles, 'model') ; end
if isfield(handles, 'scatter') , handles = rmfield(handles, 'scatter') ; end
if isfield(handles, 'results') , handles = rmfield(handles, 'results') ; end
% Empty selects
set(handles.list_groupVars, 'value', 1, 'string', {''}) ;
set(handles.popup_dose, 'value', 1, 'string', {''});
set(handles.popup_response, 'value', 1, 'string', {''}) ;
set(handles.edit_fileString, 'string', {''}) ;
% Enable/Disable buttons
set(handles.push_Fit , 'enable', 'off');
set(handles.push_Analyze, 'enable', 'off');
set(handles.push_export, 'enable', 'off');
set(handles.push_LoadData , 'enable', 'on');
set(handles.popup_response, 'enable', 'on') ;
set(handles.popup_dose, 'enable', 'on') ;
set(handles.list_groupVars, 'enable', 'on') ;
%% Create functions
% --- Executes during object creation, after setting all properties.
function axes_plot_CreateFcn(hObject, eventdata, handles)
% --- Executes during object creation, after setting all properties.
function popup_dose_CreateFcn(hObject, eventdata, handles)
% hObject handle to popup_dose (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: popupmenu controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
% --- Executes during object creation, after setting all properties.
function edit_fileString_CreateFcn(hObject, eventdata, handles)
% hObject handle to edit_fileString (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: edit controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
% --- Executes during object creation, after setting all properties.
function popup_response_CreateFcn(hObject, eventdata, handles)
% hObject handle to popup_response (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: popupmenu controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
% --- Outputs from this function are returned to the command line.
function varargout = DoseResponseFit_OutputFcn(hObject, eventdata, handles)
% varargout cell array for returning output args (see VARARGOUT);
% hObject handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Get default command line output from handles structure
varargout{1} = handles.output;
% --- Executes during object creation, after setting all properties.
function list_groupVars_CreateFcn(hObject, eventdata, handles)
% hObject handle to list_groupVars (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: listbox controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
