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Analyzer/copyfields.m

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+% copyfields.m - copies fields from one scalar structure to another
+%
+%     /--------------------------------------------------------------\
+%     | Date:         01/08/2023                                     |
+%     | Author:       Jonathan Cody                                  |
+%     | Affiliation:  Pienaar Computational Systems Pharmacology Lab |
+%     |               Weldon School of Biomedical Engineering        |
+%     |               Purdue University                              |
+%     \--------------------------------------------------------------/
+%
+% Copy field values from one scalar structure variable 'struc2' into
+% another structure variable 'struc1' and return struc1. If overWrite=0,
+% existing struc1 fields will not be changed, only new fields added. If a
+% struc2 field is itself a structure, 'copyfields' is called again for that
+% structure.
+%
+%% ========================================================================
+%	FUNCTION
+%  ========================================================================
+function struc1 = copyfields(struc1,struc2,overWrite)
+
+if nargin < 3 ; overWrite = 1 ; end % overwrite fields by default
+
+if isempty(struc2) ; return ; end % do nothing if struc2 is empty
+
+fields2 = fieldnames(struc2) ;% names of fields in struc2
+
+for f = 1:length(fields2)
+    if overWrite || ~isfield(struc1,fields2{f})
+        if isstruct(struc2.(fields2{f}))
+            struc1.(fields2{f}) = copyfields...
+                (struc1.(fields2{f}),struc2.(fields2{f}),overWrite) ;
+        else
+            try %#ok<TRYNC> avoid errors thrown by graphics objects
+                struc1.(fields2{f}) = struc2.(fields2{f}) ;
+            end
+        end
+    end
+end
+
+end

Analyzer/gridplot.m

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+% gridplot.m - creates a grid of plots (alternative to MATLAB's 'subplot')
+% 
+%     /--------------------------------------------------------------\
+%     | Date:         01/08/2023                                     |
+%     | Author:       Jonathan Cody                                  |
+%     | Affiliation:  Pienaar Computational Systems Pharmacology Lab |
+%     |               Weldon School of Biomedical Engineering        |
+%     |               Purdue University                              |
+%     \--------------------------------------------------------------/
+% 
+%% ========================================================================
+% 	INPUTS
+%  ========================================================================
+% 
+% PROPS = cell array of scalar structures that define axis properties
+%   -> Index is {left-to-right,bottom-to-top} 
+%      (EX: {2,1} is 2nd axis from the left, on the bottom)
+% 	-> See 'Axes Properties' in MATLAB help for a list of fields
+%
+% LINES = cell array that defines line data and properties
+%   -> Index is {left-to-right,bottom-to-top} (same as 'PROPS')
+%   -> Each element is a cell array of scalar structures
+%   -> Order determines plot rank ({1} is plotted on top of other lines)
+%   -> See 'linemaker.m' for a description of fields in these structures
+
+% Optional inputs are entered after 'LINES' as (string name),(value) pairs
+%   -> See line 44 for definitions and default values
+%
+%% ========================================================================
+%	OUTPUTS
+%  ========================================================================
+% 
+% figH = figure handle
+%
+% AxisH = matrix of axis handles (Index is left-to-right,bottom-to-top)
+%
+%% ========================================================================
+%	FUNCTION
+%  ========================================================================
+function [figH,AxisH] = gridplot(PROPS,LINES,varargin)
+
+[nX,nY] = size(PROPS)   ;% number of x,y axes
+
+% Set default values for optional inputs
+AxisProps = [] ;% scalar structure of properties shared by all axes
+                % -> see 'Axes Properties' in MATLAB help
+
+FigColor = [1 1 1] ;% figure background color [R G B]
+
+figName = 'figure' ;% figure name (and file name)
+
+FigSizes = [0 0] ;% figure [horizontal,vertical] size
+                  % -> axes will adapt to ensure figure size
+                  % -> (ignored in that direction if zero)
+                  % -> use 'Units' to define units
+
+imageRes  = '-r300'	 ;% image resolution (see MATLAB 'print' function)
+
+imageType = '-dtiff' ;% image file type (see MATLAB 'print' function)
+
+isBroken = [0 0] ;% treat [x,y] axes as broken axes
+                  % -> EX: [1 0] shares lines and axis properties between
+                  %    all axes in each row and hides y-axes after column 1
+                  % -> if 'FigSizes' is also set, axes lengths will be
+                  %    proportional to number of ticks
+
+Gaps = [.25 .25] ;% [horizontal,vertical] gaps between axes
+                  % -> use 'Units' to define units
+
+LineProps = [] ;% scalar structure of properties shared by all lines
+                % -> see 'linemaker.m' for a descriptions of fields
+
+Margins = [1 1 .5 .5] ;% [left,bottom,right,top] figure margins
+                       % -> use 'Units' to define units
+
+Units = 'inches' ;% length units for figure
+                  % -> see 'Figure Properties' in MATLAB help for options
+
+XLengths = ones(1,nX) ;% lengths of x-axes (left-to-right)
+                       % -> If FigSizes(1)~=0, treated as relative size
+
+YLengths = ones(1,nY) ;% lengths of y-axes (bottom-to-top)
+                       % -> If FigSizes(2)~=0, treated as relative size
+
+for n = 1:length(varargin)
+    if strcmp('AxisProps',varargin(n)) ; AxisProps = varargin{n+1} ; end
+    if strcmp('FigColor', varargin(n)) ; FigColor  = varargin{n+1} ; end
+    if strcmp('figName',  varargin(n)) ; figName   = varargin{n+1} ; end
+    if strcmp('FigSizes', varargin(n)) ; FigSizes  = varargin{n+1} ; end
+    if strcmp('imageRes', varargin(n)) ; imageRes  = varargin{n+1} ; end
+    if strcmp('imageType',varargin(n)) ; imageType = varargin{n+1} ; end
+    if strcmp('isBroken', varargin(n)) ; isBroken  = varargin{n+1} ; end
+    if strcmp('Gaps',     varargin(n)) ; Gaps      = varargin{n+1} ; end
+    if strcmp('LineProps',varargin(n)) ; LineProps = varargin{n+1} ; end
+    if strcmp('Margins',  varargin(n)) ; Margins   = varargin{n+1} ; end
+    if strcmp('Units',    varargin(n)) ; Units     = varargin{n+1} ; end
+    if strcmp('XLengths', varargin(n)) ; XLengths  = varargin{n+1} ; end
+    if strcmp('YLengths', varargin(n)) ; YLengths  = varargin{n+1} ; end
+end
+
+% If 'LINES' is not full size, make it full size
+if size(LINES,1) < nX ; LINES{nX,1} = [] ; end
+if size(LINES,2) < nY ; LINES{1,nY} = [] ; end
+
+% Update axis lengths to enforce figure size
+if FigSizes(1)~=0
+    if isBroken(1)
+        for x = 1:nX
+            XLengths(x) = length(PROPS{x,1}.XTick) ;
+        end
+    end
+    axisSpace = FigSizes(1) - (nX-1)*Gaps(1) - Margins(1) - Margins(3) ;
+    XLengths  = XLengths * axisSpace / sum(XLengths) ;
+end
+if FigSizes(2)~=0
+    if isBroken(2)
+        for y = 1:nY
+            YLengths(y) = length(PROPS{1,y}.YTick) ;
+        end
+    end
+    axisSpace = FigSizes(2) - (nY-1)*Gaps(2) - Margins(2) - Margins(4) ;
+    YLengths  = YLengths * axisSpace / sum(YLengths) ;
+end
+
+LongestAxis = max( [YLengths XLengths] ) ;% used for equalizing tick length
+
+figH = figure( 'Name'       , figName  ...
+             , 'Color'      , FigColor ...
+             , 'Units'      , Units    ...
+             , 'PaperUnits' , Units    ) ;% figure handle
+
+AxisH = gobjects(nX,nY) ;% axis handles
+
+xPos = Margins(1) ;% distance from left of figure
+
+for x = 1:nX
+
+    yPos = Margins(2) ;% distance from bottom of figure
+
+    for y = 1:nY
+
+        % Generate axis and define axis position
+        AxisH(x,y) = axes(figH,'Units',Units,...
+            'Position',[xPos yPos XLengths(x) YLengths(y)]) ;
+
+        % Modify axis per 'AxisProps' and 'PROPS{y,x}'
+        AxisH(x,y) = copyfields(AxisH(x,y),AxisProps ) ;
+        AxisH(x,y) = copyfields(AxisH(x,y),PROPS{x,y}) ;
+
+        % Copy x/y tick from bottom/left axis
+        % Hide x/y axis if y/x axis is broken
+        if x~=1
+            AxisH(x,y).YTick      = AxisH(1,y).YTick ;
+            AxisH(x,y).YTickLabel = [] ;
+            if isBroken(1)
+                AxisH(x,y).YColor = 'none' ;
+                LINES{x,y} = LINES{1,y} ;
+            end
+        end
+        if y~=1
+            AxisH(x,y).XTick      = AxisH(x,1).XTick ;
+            AxisH(x,y).XTickLabel = [] ;
+            if isBroken(2)
+                AxisH(x,y).XColor = 'none' ;
+                LINES{x,y} = LINES{x,1} ;
+            end
+        end
+
+        % Plot lines, modifying 'LINES' per 'LineProps'
+        if ~isempty(LINES{x,y})
+            for n = length(LINES{x,y}):-1:1
+                LINES{x,y}{n} = copyfields(LINES{x,y}{n},LineProps,0) ;
+                linemaker(LINES{x,y}{n}) ;
+            end
+        end
+
+        % Fit axis limits to tick marks
+        AxisH(x,y).XLim = [AxisH(x,y).XTick(1) AxisH(x,y).XTick(end)] ;
+        AxisH(x,y).YLim = [AxisH(x,y).YTick(1) AxisH(x,y).YTick(end)] ;
+
+        % Correct MATLAB's normalized tick lengths
+        AxisH(x,y).TickLength = AxisH(x,y).TickLength * ...
+            LongestAxis / max( [XLengths(x) YLengths(y)] ) ;
+
+        yPos = yPos + YLengths(y) + Gaps(2) ;
+    end
+    xPos = xPos + XLengths(x) + Gaps(1) ;
+end
+
+% Declare figure width and height
+FigSizes = [xPos yPos] - Gaps + Margins(3:4) ;
+
+% Print figure
+figH.Position  = [0 0 FigSizes] ;
+figH.PaperSize = FigSizes ;
+figH.InvertHardcopy = "off" ;
+print(figName,imageType,imageRes)
+
+end

Analyzer/linemaker.m

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+% linemaker.m - plots lines to current axis, with a variety of options
+%
+%     /--------------------------------------------------------------\
+%     | Date:         01/08/2023                                     |
+%     | Author:       Jonathan Cody                                  |
+%     | Affiliation:  Pienaar Computational Systems Pharmacology Lab |
+%     |               Weldon School of Biomedical Engineering        |
+%     |               Purdue University                              |
+%     \--------------------------------------------------------------/
+%
+%% ========================================================================
+% 	INPUTS
+%  ========================================================================
+%
+% s = structure variable that defines line
+%   -> At minimum, s must contain fields 'X' and 'Y' (data)
+%   -> See 'Line Properties' in MATLAB help for a list of fields
+%   -> Additional optional fields are defined on line 35
+%
+%% ========================================================================
+%	OUTPUTS
+%  ========================================================================
+%
+% Handles = cell array of line handles
+%
+%% ========================================================================
+%	FUNCTION
+%  ========================================================================
+function Handles = linemaker(s)
+hold on
+
+X = s.X ;% data x-values (each column is different line)
+Y = s.Y ;% data y-values (each column is different line)
+
+% Set default values for optional fields in 's'
+CensorID  = [] ;% index in Y to mark as censored (white marker face)
+                % -> use only with single line of marked data points
+
+ColorMap  = [] ;% [R1 G1 B1 ; R2 G2 B2 ; etc.] matrix of line colors
+                % -> similar to MATLAB's 'colormap'
+
+ErrorBars = [] ;% vector of error bar lengths (same size as Y)
+                % -> using with 'CensorID' will generate a trivial warning
+
+FillColor = [] ;% [R G B (transparency)] fill color between first two lines
+
+GradENDS  = [] ;% [R1 G1 B1 ; R2 G2 B2] corresponding to min(1) and max(2)
+                % of values in 'GradGuide' (alternative to 'ColorMap')
+
+GradGuide = [] ;% interpolation vector between GradENDS(1,:) and (2,:) 
+                % -> must be the same length as the number of lines
+
+if isfield(s,'CensorID')  ; CensorID  = s.CensorID  ; end
+if isfield(s,'ColorMap')  ; ColorMap  = s.ColorMap  ; end
+if isfield(s,'ErrorBars') ; ErrorBars = s.ErrorBars ; end
+if isfield(s,'FillColor') ; FillColor = s.FillColor ; end
+if isfield(s,'GradENDS')  ; GradENDS  = s.GradENDS  ; end
+if isfield(s,'GradGuide') ; GradGuide = s.GradGuide ; end
+
+% Plot lines and modify per 's'
+if ~isempty(ErrorBars)
+    Handles = errorbar(X,Y,ErrorBars) ;
+else
+    Handles = plot(X,Y) ;
+end
+for n = 1:length(Handles)
+    Handles(n) = copyfields(Handles(n),s) ;
+end
+
+% Color line based on 'ColorMap
+if ~isempty(ColorMap)
+    for n = 1:length(Handles)
+        Handles(n).Color = ColorMap(n,:) ;
+    end
+end
+
+% Color line based on 'GradGuide' and 'GradENDS'
+if ~isempty(GradGuide)
+    G = ( GradGuide - min(GradGuide) ) / range(GradGuide) ;
+    for n = 1:length(Handles)
+        Handles(n).Color = ...
+            GradENDS(1,:) + ( GradENDS(2,:) - GradENDS(1,:) )*G(n) ;
+    end
+end
+
+% Mark specified points as hidden
+if ~isempty(CensorID)
+    Handles(n+1) = copyobj(Handles(n),ancestor(Handles(n),'axes')) ;
+    Handles(n+1).XData = Handles(n).XData(CensorID) ;
+    Handles(n+1).YData = Handles(n).YData(CensorID) ;
+    Handles(n+1).LineStyle = 'none' ;
+    Handles(n+1).MarkerFaceColor = [1 1 1] ;
+end
+
+% Shade region between lines
+if ~isempty(FillColor)
+    XPATCH = [ Handles(1).XData' ; flip(Handles(2).XData') ] ;
+    YPATCH = [ Handles(1).YData' ; flip(Handles(2).YData') ] ;
+    Handles(n+1) = patch( XPATCH, YPATCH, FillColor(1:3) ...
+                        , 'FaceAlpha' , FillColor(4)     ...
+                        , 'LineStyle' , 'none'           ) ;
+end
+
+hold off
+end