Showing the distribution of graphs as a bar graph attached to the plot

Hello, I wanted to reproduce the following figure.

So I ran the following code using stdshade.m package from here.

clear all

%set parameter values
am=300;
bm=1;
ar=1;
br=1;
kf=10;
kb=100;
kd=10;
%set number of reactions
Tend=3000;
%set initial conditions for # molecules and for time t 
X=zeros(Tend,3);
Y=zeros(Tend,2);
t1=zeros(Tend,1);
t2=zeros(Tend,1);
X(1,:)=[100 100 0]; Y(1,:)=[100 100]; t1(1)=0; t2(1)=0;
j=1;
k=1;
km=2000;
M1=zeros(km,600);
M2=zeros(km,600);
while k<=km
    while t1(j)<6
        %calculate propensities
        p1=am*X(j,3);
        p2=bm*X(j,1);
        p3=ar*X(j,1);
        p4=br*X(j,2);
        p5=kf*X(j,2)*X(j,3);
        p6=kb*(1-X(j,3));
        psum1=p1+p2+p3+p4+p5+p6;
        %select next reaction
        mu=rand(1);
        z1=0;z2=0;z3=0;z4=0;z5=0;z6=0;
        if 0 <= mu && mu < p1/psum1 
           z1=1;
            else if p1/psum1 <= mu && mu  < (p1+p2)/psum1
                    z2=1;
                else if (p1+p2)/psum1 <= mu && mu < (p1+p2+p3)/psum1
                        z3=1;
                    else if (p1+p2+p3)/psum1 <= mu && mu < (p1+p2+p3+p4)/psum1
                            z4=1;
                        else if (p1+p2+p3+p4)/psum1 <= mu && mu < (p1+p2+p3+p4+p5)/psum1
                                z5=0.01;
                            else
                                z6=0.01;
                            end
                        end
                    end
                end
        end
        %update state
        X(j+1,1) = X(j,1) + z1 - z2;
        X(j+1,2) = X(j,2) + z3 - z4 - z5 - z6;
        X(j+1,3) = X(j,3) - z5 + z6;
        %update time
        t1(j+1) = t1(j) + log(1/rand(1))/psum1;
        %update counter
        j=j+1;
    end
    M1(k,:)=interp1(t1(1:j),X(1:j,2),0.01:0.01:6);
    X=zeros(Tend,3);
    X(1,:)=[100 100 0];
    t1=zeros(Tend,1);
    k=k+1;
    j=1;
end
k=1;
while k<=km
    while t2(j)<6
        %calculate propensities
        p1=am*kd/(Y(j,2)+kd);
        p2=bm*Y(j,1);
        p3=ar*Y(j,1);
        p4=br*Y(j,2);
        psum2=p1+p2+p3+p4;
        %select next reaction
        mu=rand(1);
        z1=0;z2=0;z3=0;z4=0;
        if 0 <= mu && mu < p1/psum2
           z1=1;
            else if p1/psum2 <= mu && mu  < (p1+p2)/psum2
                    z2=1;
                else if (p1+p2)/psum2 <= mu && mu < (p1+p2+p3)/psum2
                        z3=1;
                    else
                        z4=1;
                    end
                end
        end
        %update state
        Y(j+1,1) = Y(j,1) + z1 - z2;
        Y(j+1,2) = Y(j,2) + z3 - z4;
        %update time
        t2(j+1) = t2(j) + log(1/rand(1))/psum2;
        %update counter
        j=j+1;
    end
    M2(k,:)=interp1(t2(1:j),Y(1:j,2),0.01:0.01:6);
    Y=zeros(Tend,2);
    Y(1,:)=[100 100];
    t2=zeros(Tend,1);
    k=k+1;
    j=1;
end
stdshade(M1,0.1,'b',0.01:0.01:6)
xlim([0 6])
ylim([0 120])
hold on
stairs(0.01:0.01:6, M1(1,1:600), 'r', 'linewidth', 2)
stairs(0.01:0.01:6, M2(1,1:600), 'b', 'linewidth', 2)
stdshade(M2,0.1,'r',0.01:0.01:6)
xlim([0 6])
ylim([0 120])
hold off
ylabel('Concentration of R')
xlabel('time')
title('R')

Now I got very similar figure, but without 'a horizontal bar graphs which shows the distribution of the plotted graphs'.

My question is: Is there any nice code or package to show a horizontal bar graphs which shows the distribution of the plotted graphs next to this figure, exactly like the first figure?

It is okay to just look 'similar', I mean, it does not need to be a bar graph but can be any type of graphs if it gives the desired informations to us clearly.

Thanks.

Answer 1

[Malay Agarwal]

Hi Kyuwon,

I understand that you want to display a bar graph along the right boundary of another plot.

The following code can help you achieve this:

• It uses the “subplot” function and manually changes the position of the bar graph to align it with the right boundary of the line graph.
• Note that since I am not sure about the data that should appear in the bar graph, I am using dummy data. Please change the data accordingly.

% Use subplot to create a subplot
ax_line = subplot(1, 2, 1);

% Your code to plot the line graph
stdshade(M1,0.1,'b',0.01:0.01:6)
xlim([0 6])
ylim([0 120])
hold on
stairs(0.01:0.01:6, M1(1,1:600), 'r', 'linewidth', 2)
stairs(0.01:0.01:6, M2(1,1:600), 'b', 'linewidth', 2)
stdshade(M2,0.1,'r',0.01:0.01:6)
xlim([0 6])
ylim([0 120])
hold off
ylabel('Concentration of R')
xlabel('time')
title('R')

% Turn off the box to remove ticks
% On the right boundary of the line plot
set(ax_line, 'box', 'off');

% Adjust the position of the line graph to remove space for y-axis ticks
lineGraphPos = get(ax_line, 'Position');
lineGraphPos(1) = 0.05; % Adjust the left position as needed
lineGraphPos(3) = lineGraphPos(3) + 0.05; % Increase the width to fill the space
set(ax_line, 'Position', lineGraphPos);

% Plot the bar graph
ax_bar = subplot(1, 2, 2);
% TODO: Change data here
values = randi([1 10], [1 10]);
barh(ax_bar, values, 'r', 'FaceColor', 'flat');

% Adjust the position of the bar graph to attach it to the line graph
barGraphPos = get(ax_bar, 'Position');
barGraphPos(1) = lineGraphPos(1) + lineGraphPos(3); % Adjust the left position
barGraphPos(3) = 0.05; % Adjust the width of the bar graph as needed
set(ax_bar, 'Position', barGraphPos);

% Remove the boundaries (spines), ticks, and labels of the bar graph
set(ax_bar, 'box', 'off', 'Color', 'none');
axis(ax_bar, 'off');

This generates the following plot:

The code can be extended to display two bar graphs as in the image attached in the question by using “hold on” after the first “barh” call, calling “barh” again with the data for the second bar graph and then using “hold off”. For example:

ax_bar = subplot(1, 2, 2);
% TODO: Change data here
values1 = randi([1, 10], [1 10]);
values2 = randi([1 10], [1 10]);
barh(ax_bar, values1, 'r', 'FaceColor', 'flat');
hold on
barh(values2, 'b', 'FaceColor', 'flat');
hold off

This results in the following graph:

Please refer to the following resources for more details:

• “subplot” documentation: https://www.mathworks.com/help/releases/R2021b/matlab/ref/subplot.html.
• “axes” properties documentation: https://www.mathworks.com/help/releases/R2021b/matlab/ref/matlab.graphics.axis.axes-properties.html.
• “barh” documentation: https://www.mathworks.com/help/releases/R2021b/matlab/ref/barh.html.

Hope this helps!