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ArrayPlotEditor.m
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ArrayPlotEditor.m
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function varargout = ArrayPlotEditor(varargin)
% ARRAYPLOTEDITOR M-file for ArrayPlotEditor.fig
% ARRAYPLOTEDITOR, by itself, creates a new ARRAYPLOTEDITOR or raises the existing
% singleton*.
%
% H = ARRAYPLOTEDITOR returns the handle to a new ARRAYPLOTEDITOR or the handle to
% the existing singleton*.
%
% ARRAYPLOTEDITOR('CALLBACK',hObject,eventData,handles,...) calls the local
% function named CALLBACK in ARRAYPLOTEDITOR.M with the given input arguments.
%
% ARRAYPLOTEDITOR('Property','Value',...) creates a new ARRAYPLOTEDITOR or raises the
% existing singleton*. Starting from the left, property value pairs are
% applied to the GUI before ArrayPlotEditor_OpeningFunction gets called. An
% unrecognized property name or invalid value makes property application
% stop. All inputs are passed to ArrayPlotEditor_OpeningFcn via varargin.
%
% *See GUI Options on GUIDE's Tools menu. Choose "GUI allows only one
% instance to run (singleton)".
%
% See also: GUIDE, GUIDATA, GUIHANDLES
% Edit the above text to modify the response to help ArrayPlotEditor
% Last Modified by GUIDE v2.5 22-Aug-2008 18:03:55
% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @ArrayPlotEditor_OpeningFcn, ...
'gui_OutputFcn', @ArrayPlotEditor_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 ArrayPlotEditor is made visible.
function ArrayPlotEditor_OpeningFcn(hObject, eventdata, handles, varargin)
% Set Window size and Position
screensize=get(0,'screensize');
winsize=get(handles.ArrayPlotEditor,'Position');
winwidth=winsize(3);
winheight=winsize(4);
screenwidth=screensize(3);
screenheight=screensize(4);
winpos=[0.5*(screenwidth-winwidth),0.5*(screenheight-winheight),winwidth,winheight];
set(handles.ArrayPlotEditor,'Position',winpos);
% Get inputs
handles.arrays=varargin{1};
handles.normarrays=varargin{2};
handles.software=varargin{3};
handles.normpfmd=varargin{4};
% Fill lists
set(handles.allArrayList,'String',handles.arrays,'Max',2,'Value',[])
set(handles.normArrayList,'String',handles.normarrays,'Value',[])
% Set some names to be displayed in the popup
if handles.software==99 % Affymetrix
handles.dispNames={'Intensity',...
'Standard Deviation',...
'PM',...
'MM',...
'BackAdjusted PM',...
'Normalized PM',...
'Expression (raw)',...
'Expression (back)',...
'Expression (norm)'};
elseif handles.software==98 % Illumina
handles.dispNames={'Expression (raw)',...
'Expression (norm)'};
else % 2-channel
handles.dispNames={'log_2 Ratio',...
'Intensity',...
'Channel 1 Foreground Mean',...
'Channel 2 Foreground Mean',...
'Channel 1 Foreground Median',...
'Channel 2 Foreground Median',...
'Channel 1 Background Mean',...
'Channel 2 Background Mean',...
'Channel 1 Background Median',...
'Channel 2 Background Median',...
'Channel 1 Foreground Standard Deviation',...
'Channel 2 Foreground Standard Deviation',...
'Channel 1 Background Standard Deviation',...
'Channel 2 Background Standard Deviation',...
'Channel 1 Foreground - Background (Mean)',...
'Channel 2 Foreground - Background (Mean)',...
'Channel 1 Foreground - Background (Median)',...
'Channel 2 Foreground - Background (Median)',...
'Channel 1 Foreground / Background (Mean)',...
'Channel 2 Foreground / Background (Mean)',...
'Channel 1 Foreground / Background (Median)',...
'Channel 2 Foreground / Background (Median)'};
end
% Fill popups
set(handles.plotwhatPopup,'String',handles.dispNames)
set(handles.vsplotPopup,'String',handles.dispNames)
% Set default outputs
handles.finalarrays=''; % Default array to plot from non-normalized
handles.finalnormarrays=''; % Default array to plot from normalized
handles.plotwhat=1; % What quantity to plot
handles.plotwhatName=handles.dispNames{1}; % Its name
if handles.software==98 || handles.software==99
handles.vswhat=1;
handles.vswhatName=handles.dispNames{1};
else
handles.vswhat=3; % Plot vs what in case of single arrays
handles.vswhatName=handles.dispNames{3}; % Its name
end
handles.titles=''; % The title(s)
handles.ntitle=''; % Normalized title
handles.dispcorr=true; % Calculate correlation to put on plot
handles.logscale=false; % Plot in log2 scale
handles.displine=false; % Display a cutoff line where colors change
handles.linecut=2; % The above cutoff
handles.issingle=false; % Plot for single arrays
handles.cancel=false; % User did not press cancel
% See what happens if normalization has not been performed
if ~handles.normpfmd
set(handles.nStatic,'Enable','off')
set(handles.normArrayList,'Enable','off')
if handles.software==99
set(handles.plotwhatPopup,'String',handles.dispNames(1:2))
set(handles.vsplotPopup,'String',handles.dispNames(1:2))
elseif handles.software==98
set(handles.plotwhatPopup,'String',handles.dispNames(1))
set(handles.vsplotPopup,'String',handles.dispNames(1))
else
set(handles.plotwhatPopup,'String',handles.dispNames(3:end))
set(handles.vsplotPopup,'String',handles.dispNames(3:end))
end
end
% Update handles structure
guidata(hObject, handles);
% UIWAIT makes ArrayPlotEditor wait for user response (see UIRESUME)
uiwait(handles.ArrayPlotEditor);
% --- Outputs from this function are returned to the command line.
function varargout = ArrayPlotEditor_OutputFcn(hObject, eventdata, handles)
if (get(handles.cancelButton,'Value')==0)
delete(handles.ArrayPlotEditor);
elseif (get(handles.okButton,'Value')==0)
delete(handles.ArrayPlotEditor);
end
varargout{1}=handles.finalarrays;
varargout{2}=handles.finalnormarrays;
varargout{3}=handles.plotwhat;
varargout{4}=handles.plotwhatName;
varargout{5}=handles.vswhat;
varargout{6}=handles.vswhatName;
varargout{7}=handles.titles;
varargout{8}=handles.ntitle;
varargout{9}=handles.dispcorr;
varargout{10}=handles.logscale;
varargout{11}=handles.displine;
varargout{12}=handles.linecut;
varargout{13}=handles.issingle;
varargout{14}=handles.cancel;
function allArrayList_Callback(hObject, eventdata, handles)
if get(handles.singleRadio,'Value')==1 && length(get(hObject,'Value'))>1
set(handles.titleEdit,'Max',length(get(hObject,'Value')))
elseif get(handles.singleRadio,'Value')==1 && length(get(hObject,'Value'))==1
set(handles.titleEdit,'Max',length(get(hObject,'Value')))
end
conts=get(hObject,'String');
val=get(hObject,'Value');
if get(handles.singleRadio,'Value')==0
if length(val)>2
uiwait(warndlg('Only two arrays can be selected for an array vs array plot.','Warning'));
val=val(1:2);
set(hObject,'Value',val);
end
end
handles.finalarrays=conts(val);
if get(handles.vsRadio,'Value')==1
if handles.software==99 || handles.software==98 % Affymetrix or Illumina
set(handles.plotwhatPopup,'String',handles.dispNames(1:2))
if ismember(handles.plotwhat,3:9)
handles.plotwhat=1;
handles.plotwhatName='Intensity';
set(handles.plotwhatPopup,'Value',1)
end
else % 2-channel
% pwval=get(handles.plotwhatPopup,'Value');
set(handles.plotwhatPopup,'String',handles.dispNames(3:end))
if handles.plotwhat==1 || handles.plotwhat==2
handles.plotwhat=3;
handles.plotwhatName='Channel 1 Foreground Mean';
set(handles.plotwhatPopup,'Value',1)
% else
% set(handles.plotwhatPopup,'Value',pwval-2)
end
end
end
if get(handles.singleRadio,'Value')==1
if handles.software==99 % Affymetrix
set(handles.plotwhatPopup,'String',handles.dispNames(1:2))
set(handles.vsplotPopup,'String',handles.dispNames(1:2))
if ismember(handles.plotwhat,3:9)
handles.plotwhat=1;
handles.plotwhatName='Intensity';
set(handles.plotwhatPopup,'Value',1)
handles.vswhatName='Intensity';
set(handles.vsplotPopup,'Value',1)
end
end
end
guidata(hObject,handles);
function allArrayList_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function normArrayList_Callback(hObject, eventdata, handles)
conts=get(hObject,'String');
val=get(hObject,'Value');
if get(handles.singleRadio,'Value')==0 && length(val)>2
uiwait(warndlg('Only two arrays can be selected for an array vs array plot.','Warning'));
val=val(1:2);
set(hObject,'Value',val);
end
handles.finalnormarrays=conts(val);
guidata(hObject,handles);
function normArrayList_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function clearAll_Callback(hObject, eventdata, handles)
set(handles.allArrayList,'Value',[])
set(handles.titleEdit,'Max',1)
handles.finalarrays='';
if get(handles.vsRadio,'Value')==1 || get(handles.singleRadio,'Value')==1
set(handles.plotwhatPopup,'String',handles.dispNames,'Value',1)
set(handles.vsplotPopup,'String',handles.dispNames,'Value',1)
handles.plotwhat=1;
if handles.software~=99
handles.plotwhatName='log_2 Ratio';
else
handles.plotwhatName='Intensity';
end
end
guidata(hObject,handles);
function clearNorm_Callback(hObject, eventdata, handles)
set(handles.normArrayList,'Value',[])
handles.finalnormarrays='';
guidata(hObject,handles);
function singleRadio_Callback(hObject, eventdata, handles)
if get(hObject,'Value')==1
handles.issingle=true;
set(handles.hStatic,'Visible','on')
set(handles.vStatic,'Visible','on')
if handles.software~=99 && handles.software~=98
set(handles.nStatic,'Enable','off')
set(handles.normArrayList,'Enable','off')
set(handles.ntitleEdit,'Enable','off')
end
set(handles.allArrayList,'Max',length(handles.arrays))
set(handles.vsStatic,'Enable','on')
set(handles.vsplotPopup,'Enable','on')
if handles.software~=99 && handles.software~=98
set(handles.plotwhatPopup,'String',handles.dispNames(3:end))
set(handles.vsplotPopup,'String',handles.dispNames(3:end))
if handles.plotwhat==1 || handles.plotwhat==2
handles.plotwhat=3;
handles.plotwhatName='Channel 1 Foreground Mean';
end
else
if ~isempty(handles.finalarrays)
set(handles.plotwhatPopup,'String',handles.dispNames(1:2))
set(handles.vsplotPopup,'String',handles.dispNames(1:2))
if ismember(handles.plotwhat,3:9)
handles.plotwhat=1;
handles.plotwhatName='Intensity';
end
end
end
end
guidata(hObject,handles);
function vsRadio_Callback(hObject, eventdata, handles)
if get(hObject,'Value')==1
handles.issingle=false;
set(handles.hStatic,'Visible','off')
set(handles.vStatic,'Visible','off')
if handles.normpfmd
set(handles.nStatic,'Enable','on')
set(handles.normArrayList,'Enable','on')
end
set(handles.allArrayList,'Max',2)
set(handles.plotwhatPopup,'String',handles.dispNames);
set(handles.vsStatic,'Enable','off');
set(handles.vsplotPopup,'Enable','off');
set(handles.ntitleEdit,'Enable','on')
end
guidata(hObject,handles);
function plotwhatPopup_Callback(hObject, eventdata, handles)
contents=get(hObject,'String');
val=get(hObject,'Value');
if get(handles.singleRadio,'Value')==1 || ~isempty(handles.finalarrays)
if handles.software~=99 && handles.software~=98
val=val+2;
end
end
handles.plotwhat=val;
handles.plotwhatName=handles.dispNames{val};
% Handle the case of QuantArray where there is no Median - CORRECT THIS!!!
if ismember(val,[5 6 9 10 17 18 21 22]) && handles.software==1;
uiwait(errordlg({'The image analysis software you have used (QuantArray) does not',...
'support signal median values. Please select means instead.'},...
'Bad Input','modal'));
set(hObject,'Value',1)
if get(handles.singleRadio,'Value')==1
handles.plotwhat=3;
handles.plotwhatName=contents{3};
else
handles.plotwhat=1;
handles.plotwhatName=contents{1};
end
elseif ismember(val,3:22) && handles.software==100 % External data
uiwait(errordlg({'You have imported external data. The information provided is not',...
'sufficient to support other than ratio (or intensity) plots.'},...
'Bad Input','modal'));
set(hObject,'Value',1)
handles.plotwhat=1;
handles.plotwhatName=contents{1};
end
guidata(hObject,handles);
function plotwhatPopup_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
% --- Executes on selection change in vsplotPopup.
function vsplotPopup_Callback(hObject, eventdata, handles)
contents=get(hObject,'String');
val=get(hObject,'Value');
if handles.software~=99 && handles.software~=98
val=val+2;
end
handles.vswhat=val;
handles.vswhatName=contents{val};
% Handle the case of QuantArray where there is no Median - CORRECT THIS!!!
if ismember(val,[3 4 7 8 15 16 19 20]) && handles.software==1;
uiwait(errordlg({'The image analysis software you have used (QuantArray) does not',...
'support signal median values. Please select means instead.'},...
'Bad Input','modal'));
set(hObject,'Value',1)
if get(handles.singleRadio,'Value')==1
handles.vswhat=3;
handles.vswhatName=contents{3};
else
handles.vswhat=1;
handles.vswhatName=contents{1};
end
elseif ismember(val,1:20) && handles.software==100 % External data
uiwait(errordlg({'You have imported external data. The information provided is not',...
'sufficient to support other than ratio (or intensity) plots.'},...
'Bad Input','modal'));
set(hObject,'Value',1)
handles.vswhat=1;
handles.vswhatName=contents{1};
end
guidata(hObject,handles);
% --- Executes during object creation, after setting all properties.
function vsplotPopup_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function titleEdit_Callback(hObject, eventdata, handles)
tit=cellstr(get(hObject,'String'));
len=length(get(handles.allArrayList,'Value'));
if length(tit)~=len
uiwait(errordlg({'Please provide a number of titles equal to the number of arrays',...
['you selected (',num2str(len),') or else leave the field completely'],...
'empty for automated title generation.'},'Bad Input'));
set(hObject,'String','')
handles.titles='';
else
handles.titles=tit;
end
guidata(hObject,handles);
function titleEdit_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function ntitleEdit_Callback(hObject, eventdata, handles)
handles.ntitle=cellstr(get(hObject,'String'));
guidata(hObject,handles);
function ntitleEdit_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function dispCorrCheck_Callback(hObject, eventdata, handles)
if get(hObject,'Value')==1
handles.dispcorr=true;
else
handles.dispcorr=false;
end
guidata(hObject,handles);
function logScaleCheck_Callback(hObject, eventdata, handles)
if get(hObject,'Value')==1
handles.logscale=true;
else
handles.logscale=false;
end
guidata(hObject,handles);
function dispFoldCheck_Callback(hObject, eventdata, handles)
if get(hObject,'Value')==1
handles.displine=true;
set(handles.fStatic,'Enable','on')
set(handles.foldChangeEdit,'Enable','on')
else
handles.displine=false;
set(handles.fStatic,'Enable','off')
set(handles.foldChangeEdit,'Enable','off')
end
guidata(hObject,handles);
function foldChangeEdit_Callback(hObject, eventdata, handles)
fc=str2double(get(hObject,'String'));
if isnan(fc) || fc<=0
uiwait(errordlg('The cutoff line must be a positive value.',...
'Bad Input'));
set(hObject,'String','2');
handles.linecut=str2double(get(hObject,'String'));
elseif get(handles.logScaleCheck,'Value')==1
if fc==1
uiwait(errordlg('The cutoff line must not equal to 1 when ploting in log scale.',...
'Bad Input'));
set(hObject,'String','2');
handles.linecut=str2double(get(hObject,'String'));
end
else
handles.linecut=fc;
end
guidata(hObject,handles);
function foldChangeEdit_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function okButton_Callback(hObject, eventdata, handles)
% Check that for array vs array at least two have been selected
if get(handles.singleRadio,'Value')==0 && ...
(length(get(handles.allArrayList,'Value'))==1 || length(get(handles.normArrayList,'Value'))==1)
uiwait(warndlg('At least two arrays must be selected for an array vs array plot.','Warning'));
return
end
% Check that we won't get an error because of plotting incompatible data
if handles.issingle && handles.software==99
if (ismember(handles.plotwhatName,handles.dispNames(1:2)) && ismember(handles.vswhatName,handles.dispNames(3:9))) || ...
(ismember(handles.plotwhatName,handles.dispNames(3:6)) && ismember(handles.vswhatName,handles.dispNames([1,2,7:9]))) || ...
(ismember(handles.plotwhatName,handles.dispNames(7:9)) && ismember(handles.vswhatName,handles.dispNames(1:6)))
uiwait(warndlg([handles.plotwhatName,' can''t be plotted against ',handles.vswhatName,...
' because they are not of same size!'],'Warning'));
return
end
end
if handles.software==99 % Other ID's for Affymetrix
handles.plotwhat=handles.plotwhat+100;
handles.vswhat=handles.vswhat+100;
elseif handles.software==98
handles.plotwhat=handles.plotwhat+200+1;
handles.vswhat=handles.vswhat+200+1;
end
guidata(hObject,handles);
uiresume(handles.ArrayPlotEditor);
function cancelButton_Callback(hObject, eventdata, handles)
% Resume defaults
handles.finalarrays=handles.arrays(1);
handles.finalnormarrays=handles.normarrays(1);
handles.plotwhat=1;
handles.plotwhatName=handles.dispNames{1};
handles.vswhat=3;
if handles.software~=99 && handles.software~=98
handles.vswhatName=handles.dispNames{3};
else
handles.vswhatName=handles.dispNames{1};
end
handles.titles='';
handles.ntitle='';
handles.dispcorr=true;
handles.logscale=false;
handles.displine=false;
handles.linecut=[];
handles.issingle=false;
handles.cancel=true; % User pressed cancel
guidata(hObject,handles);
uiresume(handles.ArrayPlotEditor);