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Igemrna #193

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merged 2 commits into from
Jul 5, 2023
Merged

Igemrna #193

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464ae22
Merge pull request #189 from opencobra/master
rmtfleming Aug 17, 2022
08dd2f5
Files added in igemRNA folder
NebulaKit Aug 24, 2022
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309 changes: 309 additions & 0 deletions analysis/igemRNA/IgemRNA.m
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Original file line number Diff line number Diff line change
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global trGroup
global transcriptomicsDataSamples
global modelGroup
global mediumGroup

global thGroup
global thValueSelectionGroup
global upperThLabel
global upperThreshold

global gmGroup

global boundConstrGroup

global nonOptTasksGroup
global nonOptCompareSource
global nonOptCompareTarget
global nonOptLabel1
global nonOptLabel2

global postOptTasksGroup
global initCobraWithUpdates
global initCobraNoUpdates

addpath('Scripts');

openDlg();

function openDlg()
d = dialog('Position',[550 50 610 650],'Name','IgemRNA');

% Transcriptomics Data Input
global trGroup
trGroup = uibuttongroup('parent', d, 'Title', 'Load Transcriptomics Data','TitlePosition','lefttop','Position',[.01 .88 0.98 0.1]);
e = uicontrol('parent',trGroup, 'Style', 'edit', 'HorizontalAlignment', 'left', 'enable', 'off', 'pos', [10, 10, 470, 20]);
trDataPath = uicontrol('parent', trGroup, 'Style', 'pushbutton', 'String', 'Open', 'pos',[500, 10, 75, 20], 'Callback', {@Data_Selected,e});

% Model Input
global modelGroup
modelGroup = uibuttongroup('parent', d, 'Title', 'Load Model','TitlePosition','lefttop','Position',[.01 .78 0.98 0.1]);
e2 = uicontrol('parent',modelGroup, 'Style', 'edit', 'HorizontalAlignment', 'left', 'enable', 'off', 'pos', [10, 10, 470, 20]);
modelPath = uicontrol('parent', modelGroup, 'Style', 'pushbutton', 'String', 'Open', 'pos',[500, 10, 75, 20], 'Callback', {@Data_Selected,e2});

% Medium Data Input
global mediumGroup
mediumGroup = uibuttongroup('parent', d, 'Title', 'Load Medium Data','TitlePosition','lefttop','Position',[.01 .68 0.98 0.1]);
e3 = uicontrol('parent',mediumGroup, 'Style', 'edit', 'HorizontalAlignment', 'left', 'enable', 'off', 'pos', [10, 10, 470, 20]);
mediumDataPath = uicontrol('parent', mediumGroup, 'Style', 'pushbutton', 'String', 'Open', 'pos',[500, 10, 75, 20], 'Callback', {@Data_Selected,e3});

global thValueSelectionGroup
thValueSelectionGroup = uibuttongroup('parent',d,'Title','Global Threshold Value Selection','TitlePosition','lefttop','visible','off','Position',[.52 .48 0.47 0.2]);
lowerThLabel = uicontrol('Style', 'text', 'parent', thValueSelectionGroup, 'String', 'Lower Threshold: ', 'HorizontalAlignment', 'left', 'pos', [5 70 100 20]);
lowerThreshold = uicontrol('parent', thValueSelectionGroup, 'Style', 'edit', 'String', '0', 'HorizontalAlignment', 'left', 'pos', [120, 72, 100, 20], 'callback',@Numeric_Validate);
global upperThLabel
global upperThreshold
upperThLabel = uicontrol('visible', 'off', 'Style', 'text', 'parent', thValueSelectionGroup, 'String', 'Upper Threshold: ', 'HorizontalAlignment', 'left', 'pos', [5 40 100 20]);
upperThreshold = uicontrol('visible', 'off', 'parent', thValueSelectionGroup, 'Style', 'edit', 'HorizontalAlignment', 'left', 'pos', [120, 42, 100, 20], 'callback',@Numeric_Validate);
isExactVal = uicontrol('Style', 'Radio', 'String', 'Exact Value','pos', [5 15 100 15], 'parent',thValueSelectionGroup);
isPercentile = uicontrol('Style', 'Radio', 'String', 'Percentile','pos', [110 15 100 15], 'parent',thValueSelectionGroup);
thValueSelectionGroup.Visible = 'on';

% Thresholding Approach Radio Buttons
global thGroup
thGroup = uibuttongroup('parent',d,'Title','Thresholding Approach','TitlePosition','lefttop','visible','off','Position',[.01 .48 0.5 0.2]);
t1 = uicontrol('Style','Radio','String','Global T1 (one global)','pos',[10 70 400 15],'parent',thGroup, 'callback',{@Threshold_Approach_changed});
t2 = uicontrol('Style','Radio','String','Local T1 (one global + local)','pos',[10 50 400 15],'parent',thGroup, 'callback',{@Threshold_Approach_changed});
t3 = uicontrol('Style','Radio','String','Local T2 (two global + local)','pos',[10 30 400 15],'parent',thGroup, 'callback',{@Threshold_Approach_changed});
thGroup.Visible = 'on';

% Gene Mapping Approach Radio Buttons
global gmGroup
gmGroup = uibuttongroup('parent',d,'Title','Gene Mapping Approach (AND/OR)','TitlePosition','lefttop','visible','off','Position',[.01 .38 0.3 0.1]);
gmMinMax = uicontrol('Style','Radio','String','Min/Max','pos',[10 30 70 15],'parent',gmGroup);
gmMinSum = uicontrol('Style','Radio','String','Min/Sum','pos',[10 10 70 15],'parent',gmGroup);
gmGmMax = uicontrol('Style','Radio','String','GM/Max','pos',[90 30 70 15],'parent',gmGroup);
gmGmSum = uicontrol('Style','Radio','String','GM/Sum','pos',[90 10 70 15],'parent',gmGroup);
gmGroup.Visible = 'off';

% Bound Constraining Options
global boundConstrGroup
boundConstrGroup = uibuttongroup('parent',d,'Title','Constraining Options','TitlePosition','lefttop','visible','off','Position',[.32 .38 0.67 0.1]);
constrIrreversible = uicontrol('Style','Radio','String','Only irreversible reactions','pos',[10 30 310 15],'parent',boundConstrGroup);
consrtAll = uicontrol('Style', 'Radio', 'String', 'All reactions','pos', [10 10 310 15], 'parent',boundConstrGroup);
% Preserve growth requirements options
growthNotAffectingGeneDel = uicontrol('parent',boundConstrGroup,'Style','checkbox','String','Growth not affecting gene deletion only', 'pos',[180 30 400 15],'Enable','off');
meetMinimumGrowthReq = uicontrol('parent',boundConstrGroup,'Style','checkbox','String','Meet minimum growth requirements', 'pos',[180 10 400 15],'Enable','off');
boundConstrGroup.Visible = 'off';

global nonOptTasksGroup
global nonOptCompareSource
global nonOptCompareTarget
global nonOptLabel1
global nonOptLabel2
nonOptTasksGroup = uibuttongroup('parent',d,'Title','Non-optimization Tasks','TitlePosition','lefttop','visible','off','Position',[.01 .08 0.5 0.3]);
nonOptT1 = uicontrol('parent',nonOptTasksGroup,'Style','checkbox','String','Filter highly and lowly expressed genes', 'pos',[10 150 400 15]);
nonOptT2 = uicontrol('parent',nonOptTasksGroup,'Style','checkbox','String','Filter lowly expressed genes', 'pos',[10 130 400 15]);
nonOptT3 = uicontrol('parent',nonOptTasksGroup,'Style','checkbox','String','Filter up-/down-regulated genes between phenotypes', 'pos',[10 110 400 15],'callback',{@NonOptComparePhenotypes_changed});
nonOptLabel1 = uicontrol('visible','off','Style', 'text', 'parent', nonOptTasksGroup, 'String', 'Compare', 'HorizontalAlignment', 'left', 'pos', [10 80 45 15]);
nonOptCompareSource = uicontrol('visible','off','Style','popupmenu','parent',nonOptTasksGroup, 'String',{},'HorizontalAlignment', 'left', 'pos',[60 82 80 15]);
nonOptLabel2 = uicontrol('visible','off','Style', 'text', 'parent', nonOptTasksGroup, 'String', 'with', 'HorizontalAlignment', 'left', 'pos', [145 80 45 15]);
nonOptCompareTarget = uicontrol('visible','off','Style','popupmenu','parent',nonOptTasksGroup, 'String',{},'HorizontalAlignment', 'left', 'pos',[170 82 80 15]);

global postOptTasksGroup
global postOptLabel1
global postOptCompareSource
global postOptLabel2
global postOptCompareTarget
global initCobraWithUpdates
global initCobraNoUpdates
postOptTasksGroup = uibuttongroup('parent',d,'Title','Post-optimization Tasks','TitlePosition','lefttop','visible','off','Position',[.52 .08 0.47 0.3]);
useExistingModels = uicontrol('parent',postOptTasksGroup,'Style','checkbox','String','Use existing context-specific models','fontweight', 'bold', 'pos',[10 165 400 15]);
postOptT1 = uicontrol('parent',postOptTasksGroup,'Style','checkbox','String','Filter non-flux reactions', 'pos',[10 148 400 15]);
postOptT2 = uicontrol('parent',postOptTasksGroup,'Style','checkbox','String','Filter rate limitting reactions', 'pos',[10 131 400 15],'callback',{@PostOpt_changed});
postOptT3 = uicontrol('parent',postOptTasksGroup,'Style','checkbox','String','Calculate flux shifts between phenotypes', 'pos',[10 114 400 15],'callback',{@PostOpt_changed});
postOptLabel1 = uicontrol('visible','off','Style', 'text', 'parent', postOptTasksGroup, 'String', 'Compare', 'HorizontalAlignment', 'left', 'pos', [10 90 45 15]);
postOptCompareSource = uicontrol('visible','off','Style','popupmenu','parent',postOptTasksGroup, 'String',{},'HorizontalAlignment', 'left', 'pos',[60 92 80 15]);
postOptLabel2 = uicontrol('visible','off','Style', 'text', 'parent', postOptTasksGroup, 'String', 'with', 'HorizontalAlignment', 'left', 'pos', [145 90 45 15]);
postOptCompareTarget = uicontrol('visible','off','Style','popupmenu','parent',postOptTasksGroup, 'String',{},'HorizontalAlignment', 'left', 'pos',[170 92 80 15]);

% Objective select
objectiveFuctionLabel = uicontrol('Style', 'text', 'parent', postOptTasksGroup, 'String', 'Objective function Id: ', 'HorizontalAlignment', 'left', 'pos', [10 60 110 20]);
objectiveFunction = uicontrol('parent', postOptTasksGroup, 'String','r_1761', 'Style', 'edit', 'HorizontalAlignment', 'left', 'pos', [120, 63, 140, 20]);
%Biomass exclusion
excludeBiomass = uicontrol('parent',postOptTasksGroup,'Style','checkbox','String','Exclude biomass', 'pos',[10 40 110 20]);
biomassId = uicontrol('parent', postOptTasksGroup, 'String','r_4041', 'Style', 'edit', 'HorizontalAlignment', 'left', 'pos', [120, 45, 140, 20]);

initCobraNoUpdates = uicontrol('visible','off','Style','Radio','String','Initialize CobraToolbox Without Updates','pos',[10 20 400 15],'parent',postOptTasksGroup);
initCobraWithUpdates = uicontrol('visible','off','Style', 'Radio', 'String', 'Initialize CobraToolbox With Updates','pos', [10 5 400 15], 'parent',postOptTasksGroup);

Okbtn = uicontrol('parent', d, 'Style', 'pushbutton', 'String', 'OK', 'pos',[445, 10, 75, 20], 'Callback', {@OK});
Cancelbtn = uicontrol('parent', d, 'Style', 'pushbutton', 'String', 'Close', 'pos',[520, 10, 75, 20], 'Callback', 'delete(gcf)');
end

function Data_Selected(sender, event, textInput)
global postOptTasksGroup
global transcriptomicsDataSamples
global nonOptTasksGroup
global gmGroup
global boundConstrGroup
global initCobraWithUpdates
global initCobraNoUpdates
[FileName, FilePath] = uigetfile({'*.xlsx; *.xls'});
if ~ischar(FileName)
return;
end
set(textInput, 'String', fullfile(FilePath, FileName));
disp(textInput.Parent());
if contains(textInput.Parent().Title,"Model")
postOptTasksGroup.Visible = 'on';
gmGroup.Visible = 'on';
boundConstrGroup.Visible = 'on';
initCobraWithUpdates.Visible = 'on';
initCobraNoUpdates.Visible = 'on';
end
if contains(textInput.Parent().Title,"Transcriptomics")
trDataPath = textInput.String;
[theMessage, sheetNames] = xlsfinfo(trDataPath);
transcriptomicsDataSamples = sheetNames;
nonOptTasksGroup.Visible = 'on';
end
end

function PostOpt_changed(sender, event)
disp(sender);
global postOptCompareSource
global postOptCompareTarget
global postOptLabel1
global postOptLabel2
global transcriptomicsDataSamples

if contains(sender.String, 'flux shifts')
if sender.Value == 1
postOptCompareSource.String = transcriptomicsDataSamples;
postOptCompareTarget.String = [transcriptomicsDataSamples 'All'];
postOptCompareSource.Visible = 'on';
postOptCompareTarget.Visible = 'on';
postOptLabel1.Visible = 'on';
postOptLabel2.Visible = 'on';
else
postOptCompareSource.Visible = 'off';
postOptCompareTarget.Visible = 'off';
postOptLabel1.Visible = 'off';
postOptLabel2.Visible = 'off';
end
end
end

function NonOptComparePhenotypes_changed(sender, event)
global nonOptCompareSource
global nonOptCompareTarget
global nonOptLabel1
global nonOptLabel2
global transcriptomicsDataSamples
if sender.Value == 1
nonOptCompareSource.String = transcriptomicsDataSamples;
nonOptCompareTarget.String = [transcriptomicsDataSamples 'All'];
nonOptCompareSource.Visible = 'on';
nonOptCompareTarget.Visible = 'on';
nonOptLabel1.Visible = 'on';
nonOptLabel2.Visible = 'on';
else
nonOptCompareSource.Visible = 'off';
nonOptCompareTarget.Visible = 'off';
nonOptLabel1.Visible = 'off';
nonOptLabel2.Visible = 'off';
end
end

function Threshold_Approach_changed(sender, event)
global upperThLabel
global upperThreshold
if contains(sender.String, "T2")
upperThLabel.Visible = 'on';
upperThreshold.Visible = 'on';
else
upperThLabel.Visible = 'off';
upperThreshold.Visible = 'off';
end
end

function Numeric_Validate(src,eventdata)
str=get(src,'String');
if isempty(str2num(str))
set(src,'string','0');
warndlg('Input must be numerical');
end
end

function OK(~,~)
data = {};
global trGroup
global modelGroup
global mediumGroup

global thGroup
global thValueSelectionGroup

global gmGroup
global boundConstrGroup

global nonOptTasksGroup
global postOptTasksGroup

%Supplied data files
data.trDataPath = trGroup.Children(2).String;
data.modelPath = modelGroup.Children(2).String;
data.mediumDataPath = mediumGroup.Children(2).String;

%Thresholding approach
data.globalT1 = thGroup.Children(3).Value;
data.localT1 = thGroup.Children(2).Value;
data.localT2 = thGroup.Children(1).Value;

%Global threshold values
data.lowerGlobal = thValueSelectionGroup.Children(5).String;
data.upperGlobal = thValueSelectionGroup.Children(3).String;
data.exact = thValueSelectionGroup.Children(2).Value;
data.percentile = thValueSelectionGroup.Children(1).Value;

%Gene mapping approach
% data.gmMAX = gmGroup.Children(2).Value;
% data.gmSUM = gmGroup.Children(1).Value;
data.gmGmSum = gmGroup.Children(1).Value;
data.gmGmMax = gmGroup.Children(2).Value;
data.gmMinSum = gmGroup.Children(3).Value;
data.gmMinMax = gmGroup.Children(4).Value;

%Bound constraining options
data.constrIrreversible = boundConstrGroup.Children(4).Value;
data.constrAll = boundConstrGroup.Children(3).Value;
data.meetMinimumGrowthReq = boundConstrGroup.Children(1).Value;
data.growthNotAffectingGeneDel = boundConstrGroup.Children(2).Value;

%Non-optimization tasks
data.filterHighlyLowlyExpressedGenes = nonOptTasksGroup.Children(7).Value;
data.filterLowlyExpressedGenes = nonOptTasksGroup.Children(6).Value;
data.ComparePhenotypeGenes = nonOptTasksGroup.Children(5).Value;
data.nonOptCompareSource = {};
if length(nonOptTasksGroup.Children(3).String()) > 0
data.nonOptCompareSource = nonOptTasksGroup.Children(3).String(nonOptTasksGroup.Children(3).Value);
end
data.nonOptCompareTarget = {};
if length(nonOptTasksGroup.Children(1).String())
data.nonOptCompareTarget = nonOptTasksGroup.Children(1).String(nonOptTasksGroup.Children(1).Value);
end

%Post-optimization tasks
data.useExistingModels = postOptTasksGroup.Children(14).Value;
data.filterNonFluxReactions = postOptTasksGroup.Children(13).Value;
data.filterRateLimittingReactions = postOptTasksGroup.Children(12).Value;
data.calculateFluxShifts = postOptTasksGroup.Children(11).Value;
data.fluxShiftsSource = {};
if length(postOptTasksGroup.Children(9).String()) > 0
data.fluxShiftsSource = postOptTasksGroup.Children(9).String(postOptTasksGroup.Children(9).Value);
end
data.fluxShiftsTarget = {};
if length(postOptTasksGroup.Children(7).String()) > 0
data.fluxShiftsTarget = postOptTasksGroup.Children(7).String(postOptTasksGroup.Children(7).Value);
end

data.objectiveFunction = postOptTasksGroup.Children(5).String;
data.excludeBiomassEquation = postOptTasksGroup.Children(4).Value;
data.biomassId = postOptTasksGroup.Children(3).String;

data.initCobraWithUpdates = postOptTasksGroup.Children(1).Value;
data.initCobraNoUpdates = postOptTasksGroup.Children(2).Value;

main(data);
end
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