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| Original file line number | Diff line number | Diff line change |
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| % N803_plotter_2.m - plot outputs from 'N803_model_2.m' | ||
| addpath Analyzer | ||
| addpath Data | ||
| load('N803_MCMC','C') | ||
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| % This script will generate all figure panels using the model outputs saved | ||
| % by 'collector.m' and using custom plotting function 'gridplot.m'. | ||
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| %% ======================================================================== | ||
| % BODY | ||
| % ======================================================================== | ||
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| % close all figures and undock new figures | ||
| close all | ||
| set(0,'DefaultFigureWindowStyle','normal') | ||
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| % scenario colors | ||
| Color{1} = [ 2 1 0 ]/2.4 ;% 'Fitting to both (C1)' ; | ||
| Color{2} = [ 0 1 2 ]/2.4 ;% 'Fitting to both (C2)' ; | ||
| Color{3} = [ 1 1 1 ]/5 ;% 'Fitting to Cohort 1 only' ; | ||
| Color{4} = [ 1 1 1 ]/5 ;% 'Fitting to Cohort 2 only' ; | ||
| Color{5} = [ 1 1 1 ]/5 ;% 'Webb18 Validation (naive)' ; | ||
| Color{6} = [ 1 1 1 ]/5 ;% 'Webb18 Validation (SIV)' ; | ||
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| % Loop through 'Fig' and create each figure | ||
| % NOTE: 'for' indent is removed | ||
| for Fig = 2:.5:14.5 | ||
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| clear P L | ||
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| % Declare axis specifications (see 'gridplot.m') | ||
| FigSizes = [0 0] ;% figure [x,y] size (not enforced) | ||
| Gaps = [.25 .25] ;% axes [x,y] gaps | ||
| isBroken = [1 0] ;% x-axis is broken | ||
| Margins = [.875 .5 .1 .1] ;% figure [left,bottom,right,top] margins | ||
| AxisProps.FontSize = 10 ; | ||
| AxisProps.LineWidth = 1 ; | ||
| AxisProps.TickDir = 'out' ; | ||
| AxisProps.XTickLabelRotation = 45 ; | ||
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| % Initialize some variables used for setting up 'gridplot.m' inputs | ||
| DatID = zeros(1,10) ;% used for mapping experimental data to axes | ||
| OutID = zeros(1,10) ;% used for mapping model outputs to axes | ||
| plotMed = false(1) ;% plot median line | ||
| plotCI = true(1) ;% plot 95% CI region ( OR plot whole sample ) | ||
| xSpace = 7 ;% converts days to weeks | ||
| XTickSpace = .2 ;% inches between X Tick Marks | ||
| DataColor = [1 1 1]*.55 ;% color for data points | ||
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| % Update figure settings for current figure | ||
| % NOTE: 'switch' indent is removed | ||
| switch Fig | ||
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| case {2,2.5} ; c = 1+2*rem(Fig,1) ;% Fitting (fold) ----------------------- | ||
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| S = c ;% scenario | ||
| figName = [ 'Fig2 Fitting c' num2str(c) ] ; | ||
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| YLengths = [.1 1.5 1.5] ; | ||
| P{1,3}.YLabel.String = {'Virus','fold change'} ; | ||
| P{1,2}.YLabel.String = {'{CD8+ T cells}','fold change',' '} ; | ||
| [P{1,3}.YTick,P{1,3}.YTickLabel] = tickmaker( -3:1 , [], 1 ) ; | ||
| [P{1,2}.YTick,P{1,2}.YTickLabel] = tickmaker( 0:6 ) ; | ||
| OutID(3) = 01 ; DatID(3) = 01 ; | ||
| OutID(2) = 02 ; DatID(2) = 02 ; | ||
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| load(['N803_DataSet_' num2str(c)]) | ||
| X = {DataSet(1).X_data, DataSet(3).X_data} ; | ||
| Y = {DataSet(1).Y_data, DataSet(3).Y_data} ; | ||
| [X,Y,Sid,Cid] = prepper(X,Y,{2,[]},{2,[]},{0,0},[1 0]) ; | ||
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| if c == 1 | ||
| [P{1,1}.XTick,P{1,1}.XTickLabel] = tickmaker( -4:2:16 ) ; | ||
| [P{2,1}.XTick,P{2,1}.XTickLabel] = tickmaker( 32:2:44 ) ; | ||
| else | ||
| [P{1,1}.XTick,P{1,1}.XTickLabel] = tickmaker( -22:6:-4 ) ; | ||
| [P{2,1}.XTick,P{2,1}.XTickLabel] = tickmaker( 0:2:8 ) ; | ||
| end | ||
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| case {3,3.5} ; c = 1+2*rem(Fig,1) ;% GZB Validation ----------------------- | ||
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| S = c ;% scenario | ||
| figName = [ 'Fig3 Validation c' num2str(c) ] ; | ||
| Margins([1 3]) = .5 ; | ||
| AxisProps.XTickLabelRotation = 0 ; | ||
| % AxisProps.YAxisLocation = 'right' ; | ||
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| YLengths = [.1 1.5] ; | ||
| P{1,2}.YTick = 0:.2:1 ; | ||
| P{1,2}.YTickLabel = {'0%','20%','40%','60%','80%','100%'} ; | ||
| OutID(2) = 27 ; DatID(2) = 01 ; | ||
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| xSpace = 1 ; | ||
| XTickSpace = .15 ; | ||
| [P{1,1}.XTick,P{1,1}.XTickLabel] = tickmaker( -2:8 , [-2,-1] ) ; | ||
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| load('N803_DataSet_2') | ||
| if c == 1 | ||
| X = {DataSet(16).X_data(1:4) } ; | ||
| Y = {DataSet(16).Y_data(1:4) } ; | ||
| else | ||
| X = {DataSet(15).X_data } ; | ||
| Y = {DataSet(15).Y_data } ; | ||
| end | ||
| [X,Y,Sid,Cid] = prepper(X,Y,{[],[]},{[],[]},{[],[]},[0 0]) ; | ||
| Y{1} = Y{1}/100 ; | ||
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| case 4 ; c = 1 ;% Killing Weeds (alternate) ------------------------------- | ||
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| S = [1 2] ;% scenario | ||
| figName = 'Fig4 Killing Weeds' ; | ||
| Margins(1) = .5 ; | ||
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| YLengths = [0.2 .75 .75 1 .75] ; | ||
| [P{1,5}.YTick,P{1,5}.YTickLabel] = tickmaker( -1:2 , [], 1 ) ; | ||
| [P{1,4}.YTick,P{1,4}.YTickLabel] = tickmaker( -1:3 , [], 1 ) ; | ||
| [P{1,3}.YTick,P{1,3}.YTickLabel] = tickmaker( -3:0 , [], 1 ) ; | ||
| [P{1,2}.YTick,P{1,2}.YTickLabel] = tickmaker( -2:1 , [], 1 ) ; | ||
| OutID(5) = 58 ;% S killing rate (gS*) | ||
| OutID(4) = 29 ;% Sa | ||
| OutID(3) = 60 ;% R multiplier for gS* | ||
| OutID(2) = 4 ;% S0 | ||
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| [P{1,1}.XTick,P{1,1}.XTickLabel] = tickmaker( -1:10 ) ; | ||
| XTickSpace = .15 ; | ||
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| case 4.5 ; c = 1 ;% Cell Weeds (alternate) -------------------------------- | ||
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| S = [1 2] ;% scenario | ||
| figName = 'Fig4 Cell Weeds' ; | ||
| Margins(1) = .5 ; | ||
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| YLengths = [0.2 [3 3 4 5]*3.25/15 ] ; | ||
| [P{1,5}.YTick,P{1,5}.YTickLabel] = tickmaker( -1:4 , [], 1 ) ; | ||
| [P{1,4}.YTick,P{1,4}.YTickLabel] = tickmaker( -2:2 , [], 1 ) ; | ||
| [P{1,3}.YTick,P{1,3}.YTickLabel] = tickmaker( -3:0 , [], 1 ) ; | ||
| [P{1,2}.YTick,P{1,2}.YTickLabel] = tickmaker( 0:3 , [], 1 ) ; | ||
| OutID(5) = 39 ;% S0 activation | ||
| OutID(4) = 53 ;% V multiplier for aS* | ||
| OutID(3) = 51 ;% R multiplier for aS* | ||
| OutID(2) = 49 ;% C multiplier for aS* | ||
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| [P{1,1}.XTick,P{1,1}.XTickLabel] = tickmaker( -1:10 ) ; | ||
| XTickSpace = .15 ; | ||
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| case {13,13.5} ; c = 1+2*rem(Fig,1) ;% Single Fitting --------------------- | ||
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| S = [0 2]+c ;% scenario | ||
| figName = [ 'FigS3 Single Fitting c' num2str(c) ] ; | ||
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| YLengths = [.1 1.5 1.5] ; | ||
| P{1,3}.YLabel.String = {'Virus','fold change'} ; | ||
| P{1,2}.YLabel.String = {'{CD8+ T cells}','fold change',' '} ; | ||
| [P{1,3}.YTick,P{1,3}.YTickLabel] = tickmaker( -3:1 , [], 1 ) ; | ||
| [P{1,2}.YTick,P{1,2}.YTickLabel] = tickmaker( 0:6 ) ; | ||
| OutID(3) = 01 ; DatID(3) = 01 ; | ||
| OutID(2) = 02 ; DatID(2) = 02 ; | ||
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| load(['N803_DataSet_' num2str(c)]) | ||
| X = {DataSet(1).X_data, DataSet(3).X_data} ; | ||
| Y = {DataSet(1).Y_data, DataSet(3).Y_data} ; | ||
| [X,Y,Sid,Cid] = prepper(X,Y,{2,[]},{2,[]},{0,0},[1 0]) ; | ||
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| if c == 1 | ||
| [P{1,1}.XTick,P{1,1}.XTickLabel] = tickmaker( -4:2:16 ) ; | ||
| [P{2,1}.XTick,P{2,1}.XTickLabel] = tickmaker( 32:2:44 ) ; | ||
| else | ||
| [P{1,1}.XTick,P{1,1}.XTickLabel] = tickmaker( -22:6:-4 ) ; | ||
| [P{2,1}.XTick,P{2,1}.XTickLabel] = tickmaker( 0:2:8 ) ; | ||
| end | ||
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| case {14,14.5} ; c = 1+2*rem(Fig,1) ;% Webb Validation -------------------- | ||
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| S = 4+c ;% scenario | ||
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| figName = ['FigS4 Webb ' num2str(c) ] ; | ||
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| YLengths = [.1 1.5 1.25] ; | ||
| P{1,2}.YLabel.String = {'CD8+ T cells','per µL blood'} ; | ||
| [P{1,2}.YTick,P{1,2}.YTickLabel] = tickmaker( 0:500:3000 ) ; | ||
| OutID(2) = 21 ; DatID(2) = 3 ; | ||
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| XTickSpace = .35 ; | ||
| [P{1,1}.XTick,P{1,1}.XTickLabel] = tickmaker( -1:2 ) ; | ||
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| load('Webb_DataSet') | ||
| X = {DataSet(1).X_data, DataSet(2).X_data, DataSet(3).X_data} ; | ||
| Y = {DataSet(1).Y_data, DataSet(2).Y_data, DataSet(3).Y_data} ; | ||
| [X,Y,Sid,Cid] = prepper(X,Y,[],[],[],[]) ; | ||
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| if c == 2 | ||
| P{1,3}.YLabel.String = {'SIV RNA copies','per mL blood'} ; | ||
| [P{1,3}.YTick,P{1,3}.YTickLabel] = tickmaker( 0:5 , [], 1 ) ; | ||
| OutID(3) = 3 ; DatID(3) = 1 ; | ||
| DatID(2) = 2 ; | ||
| XTickSpace = .2 ; | ||
| [P{1,1}.XTick,P{1,1}.XTickLabel] = tickmaker( -1:18 ) ; | ||
| end | ||
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| otherwise | ||
| continue | ||
| end | ||
|
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| [nXaxes,nYaxes] = size(P) ;% number of [x,y] axes | ||
|
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| % Plot doses | ||
| if OutID(1) == 0 | ||
| [P{1,1}.YTick,P{1,1}.YTickLabel] = tickmaker( [0 .5] , [0 .5] ) ; | ||
| L{1,1}{1}.X = C(S(1)).Dose / xSpace ; | ||
| L{1,1}{1}.Y = 0.1*ones(size(C(S(1)).Dose)) ; | ||
| L{1,1}{1}.LineStyle = 'none' ; | ||
| L{1,1}{1}.Marker = '^' ; | ||
| L{1,1}{1}.MarkerSize = 5 ; | ||
| L{1,1}{1}.MarkerEdgeColor = 'none' ; | ||
| L{1,1}{1}.MarkerFaceColor = 'k' ; | ||
| if any(Fig == [4,4.5]) % for Weeds plots | ||
| L{1,1}{1}.MarkerFaceColor = Color{S(1)} ; | ||
| L{1,1}{2} = L{1,1}{1} ; | ||
| L{1,1}{2}.X = C(S(2)).Dose / xSpace ; | ||
| L{1,1}{2}.Y = 0.3*ones(size(C(S(2)).Dose)) ; | ||
| L{1,1}{2}.MarkerFaceColor = Color{S(2)} ; | ||
| end | ||
| end | ||
|
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| % Plot model outputs | ||
| for y = 1:length(YLengths) | ||
| o = OutID(y) ; | ||
| if o == 0 ; continue ; end | ||
| lid = 0 ; | ||
| for s = S | ||
| lid = lid + 1 ; | ||
| L{1,y}{lid}.X = C(s).X / xSpace ; | ||
| L{1,y}{lid}.Color = Color{s} ; | ||
| L{1,y}{lid}.Y = [ C(s).YSummary(o).lo95 C(s).YSummary(o).hi95 ] ; | ||
| L{1,y}{lid}.LineWidth = .5 ; | ||
| L{1,y}{lid}.FillColor = [ Color{s} .4 ] ; | ||
| end | ||
| end | ||
|
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| % Plot data | ||
| dataLine.MarkerEdgeColor = DataColor ; | ||
| dataLine.MarkerFaceColor = DataColor ; | ||
| dataLine.Color = DataColor ; | ||
| dataLine.LineWidth = 1 ; | ||
| dataLine.LineStyle = ':' ; | ||
| DataMarkers = repmat ( {'o','^','s'} , 1 , 5 ) ; | ||
| MarkerSize = repmat ( [ 4 , 4 , 5 ]/2 , 1 , 5 ) ; | ||
| for y = 1:length(YLengths) | ||
| d = DatID(y) ; | ||
| if d == 0 ; continue ; end | ||
| if OutID(y) == 0 ; lid = 0 ; end | ||
| for r = 1:Sid{d}(end) | ||
| subMods.X = X{d}(Sid{d}==r)/xSpace ; | ||
| subMods.Y = Y{d}(Sid{d}==r) ; | ||
| subMods.CensorID = Cid{d}(Sid{d}==r) ; | ||
| subMods.Marker = DataMarkers{r} ; | ||
| subMods.MarkerSize = MarkerSize(r) ; | ||
| L{1,y}{lid+r} = copyfields(subMods,dataLine) ; | ||
| if any(Fig == [14,14.5]) | ||
| if d == 2 ; L{1,y}{lid+r}.ErrorBars = ... | ||
| [104,205,0,0,130,157,124,0,170,580] ; | ||
| elseif d == 3 ; L{1,y}{lid+r}.ErrorBars = ... | ||
| [191,183,156,109,69,178,94,59] ; | ||
| end | ||
| L{1,y}{lid+r}.Marker = 's' ; | ||
| L{1,y}{lid+r}.MarkerSize = 5 ; | ||
| L{1,y}{lid+r}.CensorID = [] ; | ||
| break | ||
| end | ||
| end | ||
| end | ||
|
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| % Set [x,y] axes lengths bases on number of ticks | ||
| for x = 1:nXaxes | ||
| XLengths(x) = ( length(P{x,1}.XTick) - 1 ) * XTickSpace ; %#ok<SAGROW> | ||
| end | ||
|
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| % Make and save plots | ||
| gridplot(P,L ... | ||
| ,'AxisProps', AxisProps ... | ||
| ,'figName' , figName ... | ||
| ,'FigSizes' , FigSizes ... | ||
| ,'Gaps' , Gaps ... | ||
| ,'imageRes' , '-r300' ... | ||
| ,'isBroken' , isBroken ... | ||
| ,'Margins' , Margins ... | ||
| ,'XLengths' , XLengths ... | ||
| ,'YLengths' , YLengths ... | ||
| ) ; | ||
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| end |