I figured it out. had to adjust the axis ratios
%%Graphing Fluorescent Intensity
clc;
clear all;
close all;
fontSize = 16;
%
% Calculate the mean gray level.
grayImage = imread('alignedImage.png');
meanAlongEachColumn = mean(grayImage);
%
% Plot the aligned image
h=figure;
subplot(2,1,1);
alignPlot = subplot(2,1,1);
topAxs = gca;
photoAxsRatio = get(topAxs,'PlotBoxAspectRatio');
imshow('alignedImage.png');
axis on;
title('Aligned Image', 'FontSize', fontSize);
%
% Plot the Fluorsecent Intensity
subplot(2,1,2);
fluorPlot = subplot(2,1,2);
botAxs = gca;
%
plot(meanAlongEachColumn, 'k-', 'LineWidth', 2);
title('Fluorescent Intensity', 'FontSize', fontSize);
xlabel('Position');
ylabel('Fluorescent Intensity');
% adjust ratios
botAxsRatio = photoAxsRatio;
botAxsRatio(2) = photoAxsRatio(2)/1.88; % NOTE: not exactly 3...
set(botAxs,'PlotBoxAspectRatio', botAxsRatio)
%
% Find current position [x,y,width,height]
pos1 = get(alignPlot, 'Position');
pos2 = get(fluorPlot, 'Position');
%
% Set width of second axes equal to first
pos2(3) = pos1(3);
set(alignPlot,'Position',pos1);
% Save plot
saveas(h,'graphfluor.png');
