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The beautiful and elegant chord diagrams were all created using MATLAB?
Indeed, they were all generated using the chord diagram plotting toolkit that I developed myself:
You can download these toolkits from the provided links.
The reason for writing this article is that many people have started using the chord diagram plotting toolkit that I developed. However, some users are unsure about customizing certain styles. As the developer, I have a good understanding of the implementation principles of the toolkit and can apply it flexibly. This has sparked the idea of challenging myself to create various styles of chord diagrams. Currently, the existing code is quite lengthy. In the future, I may integrate some of this code into the toolkit, enabling users to achieve the effects of many lines of code with just a few lines.
Without further ado, let's see the extent to which this MATLAB toolkit can currently perform.
demo 1
rng(2)
dataMat = randi([0,5], [11,5]);
dataMat(1:6,1) = 0;
dataMat([11,7],1) = [45,25];
dataMat([1,4,5,7],2) = [20,20,30,30];
dataMat(:,3) = 0;
dataMat(6,3) = 45;
dataMat(1:5,4) = 0;
dataMat([6,7],4) = [25,25];
dataMat([5,6,9],5) = [25,25,25];
colName = {'Fly', 'Beetle', 'Leaf', 'Soil', 'Waxberry'};
rowName = {'Bartomella', 'Bradyrhizobium', 'Dysgomonas', 'Enterococcus',...
'Lactococcus', 'norank', 'others', 'Pseudomonas', 'uncultured',...
'Vibrionimonas', 'Wolbachia'};
figure('Units','normalized', 'Position',[.02,.05,.6,.85])
CC = chordChart(dataMat, 'rowName',rowName, 'colName',colName, 'Sep',1/80);
CC = CC.draw();
% 修改上方方块颜色(Modify the color of the blocks above)
CListT = [0.7765 0.8118 0.5216; 0.4431 0.4706 0.3843; 0.5804 0.2275 0.4549;
0.4471 0.4039 0.6745; 0.0157 0 0 ];
for i = 1:size(dataMat, 2)
CC.setSquareT_N(i, 'FaceColor',CListT(i,:))
end
% 修改下方方块颜色(Modify the color of the blocks below)
CListF = [0.5843 0.6863 0.7843; 0.1098 0.1647 0.3255; 0.0902 0.1608 0.5373;
0.6314 0.7961 0.2118; 0.0392 0.2078 0.1059; 0.0157 0 0 ;
0.8549 0.9294 0.8745; 0.3882 0.3255 0.4078; 0.5020 0.7216 0.3843;
0.0902 0.1843 0.1804; 0.8196 0.2314 0.0706];
for i = 1:size(dataMat, 1)
CC.setSquareF_N(i, 'FaceColor',CListF(i,:))
end
% 修改弦颜色(Modify chord color)
for i = 1:size(dataMat, 1)
for j = 1:size(dataMat, 2)
CC.setChordMN(i,j, 'FaceColor',CListT(j,:), 'FaceAlpha',.5)
end
end
CC.tickState('on')
CC.labelRotate('on')
CC.setFont('FontSize',17, 'FontName','Cambria')
% CC.labelRotate('off')
% textHdl = findobj(gca,'Tag','ChordLabel');
% for i = 1:length(textHdl)
% if textHdl(i).Position(2) < 0
% if abs(textHdl(i).Position(1)) > .7
% textHdl(i).Rotation = textHdl(i).Rotation + 45;
% textHdl(i).HorizontalAlignment = 'right';
% if textHdl(i).Rotation > 90
% textHdl(i).Rotation = textHdl(i).Rotation + 180;
% textHdl(i).HorizontalAlignment = 'left';
% end
% else
% textHdl(i).Rotation = textHdl(i).Rotation + 10;
% textHdl(i).HorizontalAlignment = 'right';
% end
% end
% end
demo 2
rng(3)
dataMat = randi([1,15], [7,22]);
dataMat(dataMat < 11) = 0;
dataMat(1, sum(dataMat, 1) == 0) = 15;
colName = {'A2M', 'FGA', 'FGB', 'FGG', 'F11', 'KLKB1', 'SERPINE1', 'VWF',...
'THBD', 'TFPI', 'PLAT', 'SERPINA5', 'SERPIND1', 'F2', 'PLG', 'F12',...
'SERPINC1', 'SERPINA1', 'PROS1', 'SERPINF2', 'F13A1', 'PROC'};
rowName = {'Lung', 'Spleen', 'Liver', 'Heart',...
'Renal cortex', 'Renal medulla', 'Thyroid'};
figure('Units','normalized', 'Position',[.02,.05,.6,.85])
CC = chordChart(dataMat, 'rowName',rowName, 'colName',colName, 'Sep',1/80, 'LRadius',1.21);
CC = CC.draw();
CC.labelRotate('on')
% 单独设置每一个弦末端方块(Set individual end blocks for each chord)
% Use obj.setEachSquareF_Prop
% or obj.setEachSquareT_Prop
% F means from (blocks below)
% T means to (blocks above)
CListT = [173,70,65; 79,135,136]./255;
% Upregulated:1 | Downregulated:2
Regulated = rand([7, 22]);
Regulated = (Regulated < .8) + 1;
for i = 1:size(Regulated, 1)
for j = 1:size(Regulated, 2)
CC.setEachSquareT_Prop(i, j, 'FaceColor', CListT(Regulated(i,j),:))
end
end
% 绘制图例(Draw legend)
H1 = fill([0,1,0] + 100, [1,0,1] + 100, CListT(1,:), 'EdgeColor','none');
H2 = fill([0,1,0] + 100, [1,0,1] + 100, CListT(2,:), 'EdgeColor','none');
lgdHdl = legend([H1,H2], {'Upregulated','Downregulated'}, 'AutoUpdate','off', 'Location','best');
lgdHdl.ItemTokenSize = [12,12];
lgdHdl.Box = 'off';
lgdHdl.FontSize = 13;
% 修改下方方块颜色(Modify the color of the blocks below)
CListF = [128,108,171; 222,208,161; 180,196,229; 209,150,146; 175,201,166;
134,156,118; 175,175,173]./255;
for i = 1:size(dataMat, 1)
CC.setSquareF_N(i, 'FaceColor',CListF(i,:))
end
% 修改弦颜色(Modify chord color)
for i = 1:size(dataMat, 1)
for j = 1:size(dataMat, 2)
CC.setChordMN(i,j, 'FaceColor',CListF(i,:), 'FaceAlpha',.45)
end
end
demo 3
dataMat = rand([15,15]);
dataMat(dataMat > .15) = 0;
CList = [ 75,146,241; 252,180, 65; 224, 64, 10; 5,100,146; 191,191,191;
26, 59,105; 255,227,130; 18,156,221; 202,107, 75; 0, 92,219;
243,210,136; 80, 99,129; 241,185,168; 224,131, 10; 120,147,190]./255;
figure('Units','normalized', 'Position',[.02,.05,.6,.85])
BCC = biChordChart(dataMat, 'Arrow','on', 'CData',CList);
BCC = BCC.draw();
% 添加刻度
BCC.tickState('on')
% 修改字体，字号及颜色
BCC.setFont('FontName','Cambria', 'FontSize',17, 'Color',[0,0,.8])
demo 4
rng(5)
dataMat = randi([1,20], [5,5]);
dataMat(1,1) = 110;
dataMat(2,2) = 40;
dataMat(3,3) = 50;
dataMat(5,5) = 50;
CList1 = [164,190,158; 216,213,153; 177,192,208; 238,238,227; 249,217,153]./255;
CList2 = [247,204,138; 128,187,185; 245,135,124; 140,199,197; 252,223,164]./255;
CList = CList2;
NameList={'CHORD','CHART','MADE','BY','SLANDARER'};
figure('Units','normalized', 'Position',[.02,.05,.6,.85])
BCC = biChordChart(dataMat, 'Arrow','on', 'CData',CList, 'Sep',1/30, 'Label',NameList, 'LRadius',1.33);
BCC = BCC.draw();
% 添加刻度
BCC.tickState('on')
% 修改弦颜色(Modify chord color)
for i = 1:size(dataMat, 1)
for j = 1:size(dataMat, 2)
if dataMat(i,j) > 0
BCC.setChordMN(i,j, 'FaceAlpha',.7, 'EdgeColor',CList(i,:)./1.1)
end
end
end
% 修改方块颜色(Modify the color of the blocks)
for i = 1:size(dataMat, 1)
BCC.setSquareN(i, 'EdgeColor',CList(i,:)./1.7)
end
% 修改字体，字号及颜色
BCC.setFont('FontName','Cambria', 'FontSize',17)
BCC.tickLabelState('on')
BCC.setTickFont('FontName','Cambria', 'FontSize',9)
demo 5
dataMat=randi([1,20], [14,3]);
dataMat(11:14,1) = 0;
dataMat(6:10,2) = 0;
dataMat(1:5,3) = 0;
colName = compose('C%d', 1:3);
rowName = [compose('A%d', 1:7), compose('B%d', 7:-1:1)];
figure('Units','normalized', 'Position',[.02,.05,.6,.85])
CC = chordChart(dataMat, 'rowName',rowName, 'colName',colName, 'Sep',1/80);
CC = CC.draw();
% 修改上方方块颜色(Modify the color of the blocks above)
for i = 1:size(dataMat, 2)
CC.setSquareT_N(i, 'FaceColor',[190,190,190]./255)
end
% 修改下方方块颜色(Modify the color of the blocks below)
CListF=[255,244,138; 253,220,117; 254,179, 78; 253,190, 61;
252, 78, 41; 228, 26, 26; 178, 0, 36; 4, 84,119;
1,113,137; 21,150,155; 67,176,173; 68,173,158;
123,204,163; 184,229,162]./255;
for i = 1:size(dataMat, 1)
CC.setSquareF_N(i, 'FaceColor',CListF(i,:))
end
% 修改弦颜色(Modify chord color)
for i = 1:size(dataMat, 1)
for j = 1:size(dataMat, 2)
CC.setChordMN(i,j, 'FaceColor',CListF(i,:), 'FaceAlpha',.5)
end
end
CC.tickState('on')
CC.tickLabelState('on')
demo 6
rng(2)
dataMat = randi([0,40], [20,4]);
dataMat(rand([20,4]) < .2) = 0;
dataMat(1,3) = 500;
dataMat(20,1:4) = [140; 150; 80; 90];
colName = compose('T%d', 1:4);
rowName = compose('SL%d', 1:20);
figure('Units','normalized', 'Position',[.02,.05,.6,.85])
CC = chordChart(dataMat, 'rowName',rowName, 'colName',colName, 'Sep',1/80, 'LRadius',1.23);
CC = CC.draw();
% 修改上方方块颜色(Modify the color of the blocks above)
CListT = [0.62,0.49,0.27; 0.28,0.57,0.76
0.25,0.53,0.30; 0.86,0.48,0.34];
for i = 1:size(dataMat, 2)
CC.setSquareT_N(i, 'FaceColor',CListT(i,:))
end
% 修改下方方块颜色(Modify the color of the blocks below)
CListF = [0.94,0.84,0.60; 0.16,0.50,0.67; 0.92,0.62,0.49;
0.48,0.44,0.60; 0.48,0.44,0.60; 0.71,0.79,0.73;
0.96,0.98,0.98; 0.51,0.82,0.95; 0.98,0.70,0.82;
0.97,0.85,0.84; 0.55,0.64,0.62; 0.94,0.93,0.60;
0.98,0.90,0.85; 0.72,0.84,0.81; 0.85,0.45,0.49;
0.76,0.76,0.84; 0.59,0.64,0.62; 0.62,0.14,0.15;
0.75,0.75,0.75; 1.00,1.00,1.00];
for i = 1:size(dataMat, 1)
CC.setSquareF_N(i, 'FaceColor',CListF(i,:))
end
CC.setSquareF_N(size(dataMat, 1), 'EdgeColor','k', 'LineWidth',1)
% 修改弦颜色(Modify chord color)
for i = 1:size(dataMat, 1)
for j = 1:size(dataMat, 2)
CC.setChordMN(i,j, 'FaceColor',CListT(j,:), 'FaceAlpha',.46)
end
end
CC.tickState('on')
CC.labelRotate('on')
CC.setFont('FontSize',17, 'FontName','Cambria')
demo 7
dataMat = randi([10,10000], [10,10]);
dataMat(6:10,:) = 0;
dataMat(:,1:5) = 0;
NameList = {'BOC', 'ICBC', 'ABC', 'BOCM', 'CCB', ...
'yama', 'nikoto', 'saki', 'koto', 'kawa'};
CList = [0.63,0.75,0.88
0.67,0.84,0.75
0.85,0.78,0.88
1.00,0.92,0.93
0.92,0.63,0.64
0.57,0.67,0.75
1.00,0.65,0.44
0.72,0.73,0.40
0.65,0.57,0.58
0.92,0.94,0.96];
figure('Units','normalized', 'Position',[.02,.05,.6,.85])
BCC = biChordChart(dataMat, 'Arrow','on', 'CData',CList, 'Label',NameList);
BCC = BCC.draw();
% 修改弦颜色(Modify chord color)
for i = 1:size(dataMat, 1)
for j = 1:size(dataMat, 2)
if dataMat(i,j) > 0
BCC.setChordMN(i,j, 'FaceAlpha',.85, 'EdgeColor',CList(i,:)./1.5, 'LineWidth',.8)
end
end
end
for i = 1:size(dataMat, 1)
BCC.setSquareN(i, 'EdgeColor',CList(i,:)./1.5, 'LineWidth',1)
end
% 添加刻度、修改字体
BCC.tickState('on')
BCC.setFont('FontName','Cambria', 'FontSize',17)
demo 8
dataMat = rand([11,4]);
dataMat = round(10.*dataMat.*((11:-1:1).'+1))./10;
colName = {'A','B','C','D'};
rowName = {'Acidobacteriota', 'Actinobacteriota', 'Proteobacteria', ...
'Chloroflexi', 'Bacteroidota', 'Firmicutes', 'Gemmatimonadota', ...
'Verrucomicrobiota', 'Patescibacteria', 'Planctomyetota', 'Others'};
figure('Units','normalized', 'Position',[.02,.05,.8,.85])
CC = chordChart(dataMat, 'colName',colName, 'Sep',1/80, 'SSqRatio',30/100);% -30/100
CC = CC.draw();
% 修改上方方块颜色(Modify the color of the blocks above)
CListT = [0.93,0.60,0.62
0.55,0.80,0.99
0.95,0.82,0.18
1.00,0.81,0.91];
for i = 1:size(dataMat, 2)
CC.setSquareT_N(i, 'FaceColor',CListT(i,:))
end
% 修改下方方块颜色(Modify the color of the blocks below)
CListF = [0.75,0.73,0.86
0.56,0.83,0.78
0.00,0.60,0.20
1.00,0.49,0.02
0.78,0.77,0.95
0.59,0.24,0.36
0.98,0.51,0.45
0.96,0.55,0.75
0.47,0.71,0.84
0.65,0.35,0.16
0.40,0.00,0.64];
for i = 1:size(dataMat, 1)
CC.setSquareF_N(i, 'FaceColor',CListF(i,:))
end
% 修改弦颜色(Modify chord color)
CListC = [0.55,0.83,0.76
0.75,0.73,0.86
0.00,0.60,0.19
1.00,0.51,0.04];
for i = 1:size(dataMat, 1)
for j = 1:size(dataMat, 2)
CC.setChordMN(i,j, 'FaceColor',CListC(j,:), 'FaceAlpha',.4)
end
end
% 单独设置每一个弦末端方块(Set individual end blocks for each chord)
% Use obj.setEachSquareF_Prop
% or obj.setEachSquareT_Prop
% F means from (blocks below)
% T means to (blocks above)
for i = 1:size(dataMat, 1)
for j = 1:size(dataMat, 2)
CC.setEachSquareT_Prop(i,j, 'FaceColor', CListF(i,:))
end
end
% 添加刻度
CC.tickState('on')
% 修改字体，字号及颜色
CC.setFont('FontName','Cambria', 'FontSize',17)
% 隐藏下方标签
textHdl = findobj(gca, 'Tag','ChordLabel');
for i = 1:length(textHdl)
if textHdl(i).Position(2) < 0
set(textHdl(i), 'Visible','off')
end
end
% 绘制图例(Draw legend)
scatterHdl = scatter(10.*ones(size(dataMat,1)),10.*ones(size(dataMat,1)), ...
55, 'filled');
for i = 1:length(scatterHdl)
scatterHdl(i).CData = CListF(i,:);
end
lgdHdl = legend(scatterHdl, rowName, 'Location','best', 'FontSize',16, 'FontName','Cambria', 'Box','off');
set(lgdHdl, 'Position',[.7482,.3577,.1658,.3254])
demo 9
dataMat = randi([0,10], [5,5]);
CList1 = [0.70,0.59,0.67
0.62,0.70,0.62
0.81,0.75,0.62
0.80,0.62,0.56
0.62,0.65,0.65];
CList2 = [0.02,0.02,0.02
0.59,0.26,0.33
0.38,0.49,0.38
0.03,0.05,0.03
0.29,0.28,0.32];
CList = CList2;
NameList={'CHORD','CHART','MADE','BY','SLANDARER'};
figure('Units','normalized', 'Position',[.02,.05,.6,.85])
BCC = biChordChart(dataMat, 'Arrow','on', 'CData',CList, 'Sep',1/30, 'Label',NameList, 'LRadius',1.33);
BCC = BCC.draw();
% 修改弦颜色(Modify chord color)
for i = 1:size(dataMat, 1)
for j = 1:size(dataMat, 2)
BCC.setChordMN(i,j, 'FaceAlpha',.5)
end
end
% 修改方块颜色(Modify the color of the blocks)
for i = 1:size(dataMat, 1)
BCC.setSquareN(i, 'EdgeColor',[0,0,0], 'LineWidth',5)
end
% 添加刻度
BCC.tickState('on')
% 修改字体，字号及颜色
BCC.setFont('FontSize',17, 'FontWeight','bold')
BCC.tickLabelState('on')
BCC.setTickFont('FontSize',9)
demo 10
rng(2)
dataMat = rand([14,5]) > .3;
colName = {'phosphorylation', 'vasculature development', 'blood vessel development', ...
'cell adhesion', 'plasma membrane'};
rowName = {'THY1', 'FGF2', 'MAP2K1', 'CDH2', 'HBEGF', 'CXCR4', 'ECSCR',...
'ACVRL1', 'RECK', 'PNPLA6', 'CDH5', 'AMOT', 'EFNB2', 'CAV1'};
figure('Units','normalized', 'Position',[.02,.05,.9,.85])
CC = chordChart(dataMat, 'colName',colName, 'rowName',rowName, 'Sep',1/80, 'LRadius',1.2);
CC = CC.draw();
% 修改上方方块颜色(Modify the color of the blocks above)
CListT1 = [0.5686 0.1961 0.2275
0.2275 0.2863 0.3765
0.8431 0.7882 0.4118
0.4275 0.4510 0.2706
0.3333 0.2706 0.2510];
CListT2 = [0.4941 0.5490 0.4118
0.9059 0.6510 0.3333
0.8980 0.6157 0.4980
0.8902 0.5137 0.4667
0.4275 0.2824 0.2784];
CListT3 = [0.4745 0.5843 0.7569
0.4824 0.5490 0.5843
0.6549 0.7216 0.6510
0.9412 0.9216 0.9059
0.9804 0.7608 0.6863];
CListT = CListT3;
for i = 1:size(dataMat, 2)
CC.setSquareT_N(i, 'FaceColor',CListT(i,:), 'EdgeColor',[0,0,0])
end
% 修改弦颜色(Modify chord color)
for i = 1:size(dataMat, 1)
for j = 1:size(dataMat, 2)
CC.setChordMN(i,j, 'FaceColor',CListT(j,:), 'FaceAlpha',.9, 'EdgeColor',[0,0,0])
end
end
% 修改下方方块颜色(Modify the color of the blocks below)
logFC = sort(rand(1,14))*6 - 3;
for i = 1:size(dataMat, 1)
CC.setSquareF_N(i, 'CData',logFC(i), 'FaceColor','flat', 'EdgeColor',[0,0,0])
end
CMap = [ 0 0 1.0000; 0.0645 0.0645 1.0000; 0.1290 0.1290 1.0000; 0.1935 0.1935 1.0000
0.2581 0.2581 1.0000; 0.3226 0.3226 1.0000; 0.3871 0.3871 1.0000; 0.4516 0.4516 1.0000
0.5161 0.5161 1.0000; 0.5806 0.5806 1.0000; 0.6452 0.6452 1.0000; 0.7097 0.7097 1.0000
0.7742 0.7742 1.0000; 0.8387 0.8387 1.0000; 0.9032 0.9032 1.0000; 0.9677 0.9677 1.0000
1.0000 0.9677 0.9677; 1.0000 0.9032 0.9032; 1.0000 0.8387 0.8387; 1.0000 0.7742 0.7742
1.0000 0.7097 0.7097; 1.0000 0.6452 0.6452; 1.0000 0.5806 0.5806; 1.0000 0.5161 0.5161
1.0000 0.4516 0.4516; 1.0000 0.3871 0.3871; 1.0000 0.3226 0.3226; 1.0000 0.2581 0.2581
1.0000 0.1935 0.1935; 1.0000 0.1290 0.1290; 1.0000 0.0645 0.0645; 1.0000 0 0];
colormap(CMap);
try clim([-3,3]),catch,end
try caxis([-3,3]),catch,end
CBHdl = colorbar();
CBHdl.Position = [0.74,0.25,0.02,0.2];
% =========================================================================
% 交换XY轴(Swap XY axis)
patchHdl = findobj(gca, 'Type','patch');
for i = 1:length(patchHdl)
tX = patchHdl(i).XData;
tY = patchHdl(i).YData;
patchHdl(i).XData = tY;
patchHdl(i).YData = - tX;
end
txtHdl = findobj(gca, 'Type','text');
for i = 1:length(txtHdl)
txtHdl(i).Position([1,2]) = [1,-1].*txtHdl(i).Position([2,1]);
if txtHdl(i).Position(1) < 0
txtHdl(i).HorizontalAlignment = 'right';
else
txtHdl(i).HorizontalAlignment = 'left';
end
end
lineHdl = findobj(gca, 'Type','line');
for i = 1:length(lineHdl)
tX = lineHdl(i).XData;
tY = lineHdl(i).YData;
lineHdl(i).XData = tY;
lineHdl(i).YData = - tX;
end
% =========================================================================
txtHdl = findobj(gca, 'Type','text');
for i = 1:length(txtHdl)
if txtHdl(i).Position(1) > 0
txtHdl(i).Visible = 'off';
end
end
text(1.25,-.15, 'LogFC', 'FontSize',16)
text(1.25,1, 'Terms', 'FontSize',16)
patchHdl = [];
for i = 1:size(dataMat, 2)
patchHdl(i) = fill([10,11,12],[10,13,13], CListT(i,:), 'EdgeColor',[0,0,0]);
end
lgdHdl = legend(patchHdl, colName, 'Location','best', 'FontSize',14, 'FontName','Cambria', 'Box','off');
lgdHdl.Position = [.735,.53,.167,.27];
lgdHdl.ItemTokenSize = [18,8];
demo 11
rng(2)
dataMat = rand([12,12]);
dataMat(dataMat < .85) = 0;
dataMat(7,:) = 1.*(rand(1,12)+.1);
dataMat(11,:) = .6.*(rand(1,12)+.1);
dataMat(12,:) = [2.*(rand(1,10)+.1), 0, 0];
CList = [repmat([49,49,49],[10,1]); 235,28,34; 19,146,241]./255;
figure('Units','normalized', 'Position',[.02,.05,.6,.85])
BCC = biChordChart(dataMat, 'Arrow','off', 'CData',CList);
BCC = BCC.draw();
% 添加刻度
BCC.tickState('on')
% 修改字体，字号及颜色
BCC.setFont('FontName','Cambria', 'FontSize',17)
% 修改弦颜色(Modify chord color)
for i = 1:size(dataMat, 1)
for j = 1:size(dataMat, 2)
if dataMat(i,j) > 0
BCC.setChordMN(i,j, 'FaceAlpha',.78, 'EdgeColor',[0,0,0])
end
end
end
% 修改方块颜色(Modify the color of the blocks)
for i = 1:size(dataMat, 1)
BCC.setSquareN(i, 'EdgeColor',[0,0,0], 'LineWidth',2)
end
demo 12
dataMat = rand([9,9]);
dataMat(dataMat > .7) = 0;
dataMat(eye(9) == 1) = (rand([1,9])+.2).*3;
CList = [0.85,0.23,0.24
0.96,0.39,0.18
0.98,0.63,0.22
0.99,0.80,0.26
0.70,0.76,0.21
0.24,0.74,0.71
0.27,0.65,0.84
0.09,0.37,0.80
0.64,0.40,0.84];
figure('Units','normalized', 'Position',[.02,.05,.6,.85])
BCC = biChordChart(dataMat, 'Arrow','on', 'CData',CList);
BCC = BCC.draw();
% 添加刻度、刻度标签
BCC.tickState('on')
% 修改字体，字号及颜色
BCC.setFont('FontName','Cambria', 'FontSize',17)
% 修改弦颜色(Modify chord color)
for i = 1:size(dataMat, 1)
for j = 1:size(dataMat, 2)
if dataMat(i,j) > 0
BCC.setChordMN(i,j, 'FaceAlpha',.7)
end
end
end
demo 13
rng(2)
dataMat = randi([1,40], [7,4]);
dataMat(rand([7,4]) < .1) = 0;
colName = compose('MATLAB%d', 1:4);
rowName = compose('SL%d', 1:7);
figure('Units','normalized', 'Position',[.02,.05,.7,.85])
CC = chordChart(dataMat, 'rowName',rowName, 'colName',colName, 'Sep',1/80, 'LRadius',1.32);
CC = CC.draw();
% 修改上方方块颜色(Modify the color of the blocks above)
CListT = [0.49,0.64,0.53
0.75,0.39,0.35
0.80,0.74,0.42
0.40,0.55,0.66];
for i = 1:size(dataMat, 2)
CC.setSquareT_N(i, 'FaceColor',CListT(i,:))
end
% 修改下方方块颜色(Modify the color of the blocks below)
CListF = [0.91,0.91,0.97
0.62,0.95,0.66
0.91,0.61,0.20
0.54,0.45,0.82
0.99,0.76,0.81
0.91,0.85,0.83
0.53,0.42,0.43];
for i = 1:size(dataMat, 1)
CC.setSquareF_N(i, 'FaceColor',CListF(i,:))
end
% 修改弦颜色(Modify chord color)
for i = 1:size(dataMat, 1)
for j = 1:size(dataMat, 2)
CC.setChordMN(i,j, 'FaceColor',CListT(j,:), 'FaceAlpha',.46)
end
end
CC.tickState('on')
CC.tickLabelState('on')
CC.setFont('FontSize',17, 'FontName','Cambria')
CC.setTickFont('FontSize',8, 'FontName','Cambria')
% 绘制图例(Draw legend)
scatterHdl = scatter(10.*ones(size(dataMat,1)),10.*ones(size(dataMat,1)), ...
55, 'filled');
for i = 1:length(scatterHdl)
scatterHdl(i).CData = CListF(i,:);
end
lgdHdl = legend(scatterHdl, rowName, 'Location','best', 'FontSize',16, 'FontName','Cambria', 'Box','off');
set(lgdHdl, 'Position',[.77,.38,.1658,.27])
demo 14
rng(6)
dataMat = randi([1,20], [8,8]);
dataMat(dataMat > 5) = 0;
dataMat(1,:) = randi([1,15], [1,8]);
dataMat(1,8) = 40;
dataMat(8,8) = 60;
dataMat = dataMat./sum(sum(dataMat));
CList = [0.33,0.53,0.86
0.94,0.50,0.42
0.92,0.58,0.30
0.59,0.47,0.45
0.37,0.76,0.82
0.82,0.68,0.29
0.75,0.62,0.87
0.43,0.69,0.57];
NameList={'CHORD', 'CHART', 'AND', 'BICHORD',...
'CHART', 'MADE', 'BY', 'SLANDARER'};
figure('Units','normalized', 'Position',[.02,.05,.6,.85])
BCC = biChordChart(dataMat, 'Arrow','on', 'CData',CList, 'Sep',1/12, 'Label',NameList, 'LRadius',1.33);
BCC = BCC.draw();
% 添加刻度
BCC.tickState('on')
% 修改弦颜色(Modify chord color)
for i = 1:size(dataMat, 1)
for j = 1:size(dataMat, 2)
if dataMat(i,j) > 0
BCC.setChordMN(i,j, 'FaceAlpha',.7, 'EdgeColor',CList(i,:)./1.1)
end
end
end
% 修改方块颜色(Modify the color of the blocks)
for i = 1:size(dataMat, 1)
BCC.setSquareN(i, 'EdgeColor',CList(i,:)./1.7)
end
% 修改字体，字号及颜色
BCC.setFont('FontName','Cambria', 'FontSize',17)
BCC.tickLabelState('on')
BCC.setTickFont('FontName','Cambria', 'FontSize',9)
% 调整数值字符串格式
% Adjust numeric string format
BCC.setTickLabelFormat(@(x)[num2str(round(x*100)),'%'])
demo 15
CList = [0.81,0.72,0.83
0.69,0.82,0.89
0.17,0.44,0.64
0.70,0.85,0.55
0.03,0.57,0.13
0.97,0.67,0.64
0.84,0.09,0.12
1.00,0.80,0.46
0.98,0.52,0.01
];
figure('Units','normalized', 'Position',[.02,.05,.53,.85], 'Color',[1,1,1])
% =========================================================================
ax1 = axes('Parent',gcf, 'Position',[0,1/2,1/2,1/2]);
dataMat = rand([9,9]);
dataMat(dataMat > .4) = 0;
BCC = biChordChart(dataMat, 'Arrow','on', 'CData',CList);
BCC = BCC.draw();
BCC.tickState('on')
BCC.setFont('Visible','off')
% 修改弦颜色(Modify chord color)
for i = 1:size(dataMat, 1)
for j = 1:size(dataMat, 2)
if dataMat(i,j) > 0
BCC.setChordMN(i,j, 'FaceAlpha',.6)
end
end
end
text(-1.2,1.2, 'a', 'FontName','Times New Roman', 'FontSize',35)
% =========================================================================
ax2 = axes('Parent',gcf, 'Position',[1/2,1/2,1/2,1/2]);
dataMat = rand([9,9]);
dataMat(dataMat > .4) = 0;
dataMat = dataMat.*(1:9);
BCC = biChordChart(dataMat, 'Arrow','on', 'CData',CList);
BCC = BCC.draw();
BCC.tickState('on')
BCC.setFont('Visible','off')
% 修改弦颜色(Modify chord color)
for i = 1:size(dataMat, 1)
for j = 1:size(dataMat, 2)
if dataMat(i,j) > 0
BCC.setChordMN(i,j, 'FaceAlpha',.6)
end
end
end
text(-1.2,1.2, 'b', 'FontName','Times New Roman', 'FontSize',35)
% =========================================================================
ax3 = axes('Parent',gcf, 'Position',[0,0,1/2,1/2]);
dataMat = rand([9,9]);
dataMat(dataMat > .4) = 0;
dataMat = dataMat.*(1:9).';
BCC = biChordChart(dataMat, 'Arrow','on', 'CData',CList);
BCC = BCC.draw();
BCC.tickState('on')
BCC.setFont('Visible','off')
% 修改弦颜色(Modify chord color)
for i = 1:size(dataMat, 1)
for j = 1:size(dataMat, 2)
if dataMat(i,j) > 0
BCC.setChordMN(i,j, 'FaceAlpha',.6)
end
end
end
text(-1.2,1.2, 'c', 'FontName','Times New Roman', 'FontSize',35)
% =========================================================================
ax4 = axes('Parent',gcf, 'Position',[1/2,0,1/2,1/2]);
ax4.XColor = 'none'; ax4.YColor = 'none';
ax4.XLim = [-1,1]; ax4.YLim = [-1,1];
hold on
NameList = {'Food supply', 'Biodiversity', 'Water quality regulation', ...
'Air quality regulation', 'Erosion control', 'Carbon storage', ...
'Water retention', 'Recreation', 'Soil quality regulation'};
patchHdl = [];
for i = 1:size(dataMat, 2)
patchHdl(i) = fill([10,11,12],[10,13,13], CList(i,:), 'EdgeColor',[0,0,0]);
end
lgdHdl = legend(patchHdl, NameList, 'Location','best', 'FontSize',14, 'FontName','Cambria', 'Box','off');
lgdHdl.Position = [.625,.11,.255,.27];
lgdHdl.ItemTokenSize = [18,8];
demo 16
dataMat = rand([15,15]);
dataMat(dataMat > .2) = 0;
CList = [ 75,146,241; 252,180, 65; 224, 64, 10; 5,100,146; 191,191,191;
26, 59,105; 255,227,130; 18,156,221; 202,107, 75; 0, 92,219;
243,210,136; 80, 99,129; 241,185,168; 224,131, 10; 120,147,190]./255;
CListC = [54,69,92]./255;
CList = CList.*.6 + CListC.*.4;
figure('Units','normalized', 'Position',[.02,.05,.6,.85])
BCC = biChordChart(dataMat, 'Arrow','on', 'CData',CList);
BCC = BCC.draw();
% 添加刻度
BCC.tickState('on')
% 修改字体，字号及颜色
BCC.setFont('FontName','Cambria', 'FontSize',17, 'Color',[0,0,0])
% 修改弦颜色(Modify chord color)
for i = 1:size(dataMat, 1)
for j = 1:size(dataMat, 2)
if dataMat(i,j) > 0
BCC.setChordMN(i,j, 'FaceColor',CListC ,'FaceAlpha',.07)
end
end
end
[~, N] = max(sum(dataMat > 0, 2));
for j = 1:size(dataMat, 2)
BCC.setChordMN(N,j, 'FaceColor',CList(N,:) ,'FaceAlpha',.6)
end
You need to download following tools:
I'm excited to share some valuable resources that I've found to be incredibly helpful for anyone looking to enhance their MATLAB skills. Whether you're just starting out, studying as a student, or are a seasoned professional, these guides and books offer a wealth of information to aid in your learning journey.
Matlab Books
INTRODUCTION TO MATLAB FOR ENGINEERING STUDENTS
A Guide to MATLAB
MATLAB® Notes for Professionals book
These materials are freely available and can be a great addition to your learning resources. They cover a wide range of topics and are designed to help users at all levels to improve their proficiency in MATLAB.
Happy learning and I hope you find these resources as useful as I have!
I found this link posted on Reddit.
https://workhunty.com/job-blog/where-is-the-best-place-to-be-a-programmer/Matlab/
Let S be the closed surface composed of the hemisphere and the base Let be the electric field defined by . Find the electric flux through S. (Hint: Divide S into two parts and calculate ).
% Define the limits of integration for the hemisphere S1
theta_lim = [-pi/2, pi/2];
phi_lim = [0, pi/2];
% Perform the double integration over the spherical surface of the hemisphere S1
% Define the electric flux function for the hemisphere S1
flux_function_S1 = @(theta, phi) 2 * sin(phi);
electric_flux_S1 = integral2(flux_function_S1, theta_lim(1), theta_lim(2), phi_lim(1), phi_lim(2));
% For the base of the hemisphere S2, the electric flux is 0 since the electric
% field has no z-component at the base
electric_flux_S2 = 0;
% Calculate the total electric flux through the closed surface S
total_electric_flux = electric_flux_S1 + electric_flux_S2;
% Display the flux calculations
disp(['Electric flux through the hemisphere S1: ', num2str(electric_flux_S1)]);
disp(['Electric flux through the base of the hemisphere S2: ', num2str(electric_flux_S2)]);
disp(['Total electric flux through the closed surface S: ', num2str(total_electric_flux)]);
% Parameters for the plot
radius = 1; % Radius of the hemisphere
% Create a meshgrid for theta and phi for the plot
[theta, phi] = meshgrid(linspace(theta_lim(1), theta_lim(2), 20), linspace(phi_lim(1), phi_lim(2), 20));
% Calculate Cartesian coordinates for the points on the hemisphere
x = radius * sin(phi) .* cos(theta);
y = radius * sin(phi) .* sin(theta);
z = radius * cos(phi);
% Define the electric field components
Ex = 2 * x;
Ey = 2 * y;
Ez = 2 * z;
% Plot the hemisphere
figure;
surf(x, y, z, 'FaceAlpha', 0.5, 'EdgeColor', 'none');
hold on;
% Plot the electric field vectors
quiver3(x, y, z, Ex, Ey, Ez, 'r');
% Plot the base of the hemisphere
[x_base, y_base] = meshgrid(linspace(-radius, radius, 20), linspace(-radius, radius, 20));
z_base = zeros(size(x_base));
surf(x_base, y_base, z_base, 'FaceColor', 'cyan', 'FaceAlpha', 0.3);
% Additional plot settings
colormap('cool');
axis equal;
grid on;
xlabel('X');
ylabel('Y');
zlabel('Z');
title('Hemisphere and Electric Field');
The line integral , where C is the boundary of the square oriented counterclockwise, can be evaluated in two ways:
Using the definition of the line integral:
% Initialize the integral sum
integral_sum = 0;
% Segment C1: x = -1, y goes from -1 to 1
y = linspace(-1, 1);
x = -1 * ones(size(y));
dy = diff(y);
integral_sum = integral_sum + sum(-x(1:end-1) .* dy);
% Segment C2: y = 1, x goes from -1 to 1
x = linspace(-1, 1);
y = ones(size(x));
dx = diff(x);
integral_sum = integral_sum + sum(y(1:end-1).^2 .* dx);
% Segment C3: x = 1, y goes from 1 to -1
y = linspace(1, -1);
x = ones(size(y));
dy = diff(y);
integral_sum = integral_sum + sum(-x(1:end-1) .* dy);
% Segment C4: y = -1, x goes from 1 to -1
x = linspace(1, -1);
y = -1 * ones(size(x));
dx = diff(x);
integral_sum = integral_sum + sum(y(1:end-1).^2 .* dx);
disp(['Direct Method Integral: ', num2str(integral_sum)]);
Plotting the square path
% Define the square's vertices
vertices = [-1 -1; -1 1; 1 1; 1 -1; -1 -1];
% Plot the square
figure;
plot(vertices(:,1), vertices(:,2), '-o');
title('Square Path for Line Integral');
xlabel('x');
ylabel('y');
grid on;
axis equal;
% Add arrows to indicate the path direction (counterclockwise)
hold on;
for i = 1:size(vertices,1)-1
% Calculate direction
dx = vertices(i+1,1) - vertices(i,1);
dy = vertices(i+1,2) - vertices(i,2);
% Reduce the length of the arrow for better visibility
scale = 0.2;
dx = scale * dx;
dy = scale * dy;
% Calculate the start point of the arrow
startx = vertices(i,1) + (1 - scale) * dx;
starty = vertices(i,2) + (1 - scale) * dy;
% Plot the arrow
quiver(startx, starty, dx, dy, 'MaxHeadSize', 0.5, 'Color', 'r', 'AutoScale', 'off');
end
hold off;
Apply Green's Theorem for the line integral
% Define the partial derivatives of P and Q
f = @(x, y) -1 - 2*y; % derivative of -x with respect to x is -1, and derivative of y^2 with respect to y is 2y
% Compute the double integral over the square [-1,1]x[-1,1]
integral_value = integral2(f, -1, 1, 1, -1);
disp(['Green''s Theorem Integral: ', num2str(integral_value)]);
Plotting the vector field related to Green’s theorem
% Define the grid for the vector field
[x, y] = meshgrid(linspace(-2, 2, 20), linspace(-2 ,2, 20));
% Define the vector field components
P = y.^2; % y^2 component
Q = -x; % -x component
% Plot the vector field
figure;
quiver(x, y, P, Q, 'b');
hold on; % Hold on to plot the square on the same figure
% Define the square's vertices
vertices = [-1 -1; -1 1; 1 1; 1 -1; -1 -1];
% Plot the square path
plot(vertices(:,1), vertices(:,2), '-o', 'Color', 'k'); % 'k' for black color
title('Vector Field (P = y^2, Q = -x) with Square Path');
xlabel('x');
ylabel('y');
axis equal;
% Add arrows to indicate the path direction (counterclockwise)
for i = 1:size(vertices,1)-1
% Calculate direction
dx = vertices(i+1,1) - vertices(i,1);
dy = vertices(i+1,2) - vertices(i,2);
% Reduce the length of the arrow for better visibility
scale = 0.2;
dx = scale * dx;
dy = scale * dy;
% Calculate the start point of the arrow
startx = vertices(i,1) + (1 - scale) * dx;
starty = vertices(i,2) + (1 - scale) * dy;
% Plot the arrow
quiver(startx, starty, dx, dy, 'MaxHeadSize', 0.5, 'Color', 'r', 'AutoScale', 'off');
end
hold off;
To solve a surface integral for example the over the sphere easily in MATLAB, you can leverage the symbolic toolbox for a direct and clear solution. Here is a tip to simplify the process:
  1. Use Symbolic Variables and Functions: Define your variables symbolically, including the parameters of your spherical coordinates θ and ϕ and the radius r . This allows MATLAB to handle the expressions symbolically, making it easier to manipulate and integrate them.
  2. Express in Spherical Coordinates Directly: Since you already know the sphere's equation and the relationship in spherical coordinates, define x, y, and z in terms of r , θ and ϕ directly.
  3. Perform Symbolic Integration: Use MATLAB's `int` function to integrate symbolically. Since the sphere and the function are symmetric, you can exploit these symmetries to simplify the calculation.
Here’s how you can apply this tip in MATLAB code:
% Include the symbolic math toolbox
syms theta phi
% Define the limits for theta and phi
theta_limits = [0, pi];
phi_limits = [0, 2*pi];
% Define the integrand function symbolically
integrand = 16 * sin(theta)^3 * cos(phi)^2;
% Perform the symbolic integral for the surface integral
surface_integral = int(int(integrand, theta, theta_limits(1), theta_limits(2)), phi, phi_limits(1), phi_limits(2));
% Display the result of the surface integral symbolically
disp(['The surface integral of x^2 over the sphere is ', char(surface_integral)]);
% Number of points for plotting
num_points = 100;
% Define theta and phi for the sphere's surface
[theta_mesh, phi_mesh] = meshgrid(linspace(double(theta_limits(1)), double(theta_limits(2)), num_points), ...
linspace(double(phi_limits(1)), double(phi_limits(2)), num_points));
% Spherical to Cartesian conversion for plotting
r = 2; % radius of the sphere
x = r * sin(theta_mesh) .* cos(phi_mesh);
y = r * sin(theta_mesh) .* sin(phi_mesh);
z = r * cos(theta_mesh);
% Plot the sphere
figure;
surf(x, y, z, 'FaceColor', 'interp', 'EdgeColor', 'none');
colormap('jet'); % Color scheme
shading interp; % Smooth shading
camlight headlight; % Add headlight-type lighting
lighting gouraud; % Use Gouraud shading for smooth color transitions
title('Sphere: x^2 + y^2 + z^2 = 4');
xlabel('x-axis');
ylabel('y-axis');
zlabel('z-axis');
colorbar; % Add color bar to indicate height values
axis square; % Maintain aspect ratio to be square
view([-30, 20]); % Set a nice viewing angle
Hans Scharler
Hans Scharler
Last activity il 19 Apr 2024

Starter MATLAB Script

I am often talking to new MATLAB users. I have put together one script. If you know how this script works, why, and what each line means, you will be well on your way on your MATLAB learning journey.
% Clear existing variables and close figures
clear;
close all;
% Print to the Command Window
disp('Hello, welcome to MATLAB!');
% Create a simple vector and matrix
vector = [1, 2, 3, 4, 5];
matrix = [1, 2, 3; 4, 5, 6; 7, 8, 9];
% Display the created vector and matrix
disp('Created vector:');
disp(vector);
disp('Created matrix:');
disp(matrix);
% Perform element-wise multiplication
result = vector .* 2;
% Display the result of the operation
disp('Result of element-wise multiplication of the vector by 2:');
disp(result);
% Create plot
x = 0:0.1:2*pi; % Generate values from 0 to 2*pi
y = sin(x); % Calculate the sine of these values
% Plotting
figure; % Create a new figure window
plot(x, y); % Plot x vs. y
title('Simple Plot of sin(x)'); % Give the plot a title
xlabel('x'); % Label the x-axis
ylabel('sin(x)'); % Label the y-axis
grid on; % Turn on the grid
disp('This is the end of the script. Explore MATLAB further to learn more!');
Hannah
Hannah
Last activity il 1 Apr 2024

Solar Eclipse

Although, I think I will only get to see a partial eclipse (April 8th!) from where I am at in the U.S. I will always have MATLAB to make my own solar eclipse. Just as good as the real thing.
Code (found on the @MATLAB instagram)
a=716;
v=255;
X=linspace(-10,10,a);
[~,r]=cart2pol(X,X');
colormap(gray.*[1 .78 .3]);
[t,g]=cart2pol(X+2.6,X'+1.4);
image(rescale(-1*(2*sin(t*10)+60*g.^.2),0,v))
hold on
h=exp(-(r-3)).*abs(ifft2(r.^-1.8.*cos(7*rand(a))));
h(r<3)=0;
image(v*ones(a),'AlphaData',rescale(h,0,1))
camva(3.8)
One of the privileges of working at MathWorks is that I get to hang out with some really amazing people. Steve Eddins, of ‘Steve on Image Processing’ fame is one of those people. He recently announced his retirement and before his final day, I got the chance to interview him. See what he had to say over at The MATLAB Blog The Steve Eddins Interview: 30 years of MathWorking
Before we begin, you will need to make sure you have 'sir_age_model.m' installed. Once you've downloaded this folder into your working directory, which can be located at your current folder. If you can see this file in your current folder, then it's safe to use it. If you choose to use MATLAB online or MATLAB Mobile, you may upload this to your MATLAB Drive.
This is the code for the SIR model stratified into 2 age groups (children and adults). For a detailed explanation of how to derive the force of infection by age group.
% Main script to run the SIR model simulation
% Initial state values
initial_state_values = [200000; 1; 0; 800000; 0; 0]; % [S1; I1; R1; S2; I2; R2]
% Parameters
parameters = [0.05; 7; 6; 1; 10; 1/5]; % [b; c_11; c_12; c_21; c_22; gamma]
% Time span for the simulation (3 months, with daily steps)
tspan = [0 90];
% Solve the ODE
[t, y] = ode45(@(t, y) sir_age_model(t, y, parameters), tspan, initial_state_values);
% Plotting the results
plot(t, y);
xlabel('Time (days)');
ylabel('Number of people');
legend('S1', 'I1', 'R1', 'S2', 'I2', 'R2');
title('SIR Model with Age Structure');
What was the cumulative incidence of infection during this epidemic? What proportion of those infections occurred in children?
In the SIR model, the cumulative incidence of infection is simply the decline in susceptibility.
% Assuming 'y' contains the simulation results from the ode45 function
% and 't' contains the time points
% Total cumulative incidence
total_cumulative_incidence = (y(1,1) - y(end,1)) + (y(1,4) - y(end,4));
fprintf('Total cumulative incidence: %f\n', total_cumulative_incidence);
% Cumulative incidence in children
cumulative_incidence_children = (y(1,1) - y(end,1));
% Proportion of infections in children
proportion_infections_children = cumulative_incidence_children / total_cumulative_incidence;
fprintf('Proportion of infections in children: %f\n', proportion_infections_children);
927,447 people became infected during this epidemic, 20.5% of which were children.
Which age group was most affected by the epidemic?
To answer this, we can calculate the proportion of children and adults that became infected.
% Assuming 'y' contains the simulation results from the ode45 function
% and 't' contains the time points
% Proportion of children that became infected
initial_children = 200000; % initial number of susceptible children
final_susceptible_children = y(end,1); % final number of susceptible children
proportion_infected_children = (initial_children - final_susceptible_children) / initial_children;
fprintf('Proportion of children that became infected: %f\n', proportion_infected_children);
% Proportion of adults that became infected
initial_adults = 800000; % initial number of susceptible adults
final_susceptible_adults = y(end,4); % final number of susceptible adults
proportion_infected_adults = (initial_adults - final_susceptible_adults) / initial_adults;
fprintf('Proportion of adults that became infected: %f\n', proportion_infected_adults);
Throughout this epidemic, 95% of all children and 92% of all adults were infected. Children were therefore slightly more affected in proportion to their population size, even though the majority of infections occurred in adults.
Are you going to be in the path of totality? How can you predict, track, and simulate the solar eclipse using MATLAB?
The latest release is pretty much upon us. Official annoucements will be coming soon and the eagle-eyed among you will have started to notice some things shifting around on the MathWorks website as we ready for this.
The pre-release has been available for a while. Maybe you've played with it? I have...I've even been quietly using it to write some of my latest blog posts...and I have several queued up for publication after MathWorks officially drops the release.
At the time of writing, this page points to the pre-release highlights. Prerelease Release Highlights - MATLAB & Simulink (mathworks.com)
What excites you about this release? why?
The stationary solutions of the Klein-Gordon equation refer to solutions that are time-independent, meaning they remain constant over time. For the non-linear Klein-Gordon equation you are discussing:
Stationary solutions arise when the time derivative term, , is zero, meaning the motion of the system does not change over time. This leads to a static differential equation:
This equation describes how particles in the lattice interact with each other and how non-linearity affects the steady state of the system.
The solutions to this equation correspond to the various possible stable equilibrium states of the system, where each represents different static distribution patterns of displacements . The specific form of these stationary solutions depends on the system parameters, such as κ , ω, and β , as well as the initial and boundary conditions of the problem.
To find these solutions in a more specific form, one might need to solve the equation using analytical or numerical methods, considering the different cases that could arise in such a non-linear system.
By interpreting the equation in this way, we can relate the dynamics described by the discrete Klein - Gordon equation to the behavior of DNA molecules within a biological system . This analogy allows us to understand the behavior of DNA in terms of concepts from physics and mathematical modeling .
% Parameters
numBases = 100; % Number of spatial points
omegaD = 0.2; % Common parameter for the equation
% Preallocate the array for the function handles
equations = cell(numBases, 1);
% Initial guess for the solution
initialGuess = 0.01 * ones(numBases, 1);
% Parameter sets for kappa and beta
paramSets = [0.1, 0.05; 0.5, 0.05; 0.1, 0.2];
% Prepare figure for subplot
figure;
set(gcf, 'Position', [100, 100, 1200, 400]); % Set figure size
% Newton-Raphson method parameters
maxIterations = 1000;
tolerance = 1e-10;
% Set options for fsolve to use the 'levenberg-marquardt' algorithm
options = optimoptions('fsolve', 'Algorithm', 'levenberg-marquardt', 'MaxIterations', maxIterations, 'FunctionTolerance', tolerance);
for i = 1:size(paramSets, 1)
kappa = paramSets(i, 1);
beta = paramSets(i, 2);
% Define the equations using a function
for n = 2:numBases-1
equations{n} = @(x) -kappa * (x(n+1) - 2 * x(n) + x(n-1)) - omegaD^2 * (x(n) - beta * x(n)^3);
end
% Boundary conditions with specified fixed values
someFixedValue1 = 10; % Replace with actual value if needed
someFixedValue2 = 10; % Replace with actual value if needed
equations{1} = @(x) x(1) - someFixedValue1;
equations{numBases} = @(x) x(numBases) - someFixedValue2;
% Combine all equations into a single function
F = @(x) cell2mat(cellfun(@(f) f(x), equations, 'UniformOutput', false));
% Solve the system of equations using fsolve with the specified options
x_solution = fsolve(F, initialGuess, options);
norm(F(x_solution))
% Plot the solution in a subplot
subplot(1, 3, i);
plot(x_solution, 'o-', 'LineWidth', 2);
grid on;
xlabel('n', 'FontSize', 12);
ylabel('x[n]', 'FontSize', 12);
title(sprintf('\\kappa = %.2f, \\beta = %.2f', kappa, beta), 'FontSize', 14);
end
% Improve overall aesthetics
sgtitle('Stationary States for Different \kappa and \beta Values', 'FontSize', 16); % Super title for the figure
In the second plot, the elasticity constant κis increased to 0.5, representing a system with greater stiffness . This parameter influences how resistant the system is to deformation, implying that a higher κ makes the system more resilient to changes . By increasing κ, we are essentially tightening the interactions between adjacent units in the model, which could represent, for instance, stronger bonding forces in a physical or biological system .
In the third plot the nonlinearity coefficient β is increased to 0.2 . This adjustment enhances the nonlinear interactions within the system, which can lead to more complex dynamic behaviors, especially in systems exhibiting bifurcations or chaos under certain conditions .
The following expression
gives the solution for the Helmholtz problem. On the circular disc with center 0 and radius a. For the plot in 3-dimensional graphics of the solutions on Matlab for and then calculate some eigenfunctions with the following expression.
It could be better to separate functions with and as follows
diska = 1; % Radius of the disk
mmax = 2; % Maximum value of m
nmax = 2; % Maximum value of n
% Function to find the k-th zero of the n-th Bessel function
% This function uses a more accurate method for initial guess
besselzero = @(n, k) fzero(@(x) besselj(n, x), [(k-(n==0))*pi, (k+1-(n==0))*pi]);
% Define the eigenvalue k[m, n] based on the zeros of the Bessel function
k = @(m, n) besselzero(n, m);
% Define the functions uc and us using Bessel functions
% These functions represent the radial part of the solution
uc = @(r, t, m, n) cos(n * t) .* besselj(n, k(m, n) * r);
us = @(r, t, m, n) sin(n * t) .* besselj(n, k(m, n) * r);
% Generate data for demonstration
data = zeros(5, 3);
for m = 1:5
for n = 0:2
data(m, n+1) = k(m, n); % Storing the eigenvalues
end
end
% Display the data
disp(data);
% Plotting all in one figure
figure;
plotIndex = 1;
for n = 0:nmax
for m = 1:mmax
subplot(nmax + 1, mmax, plotIndex);
[X, Y] = meshgrid(linspace(-diska, diska, 100), linspace(-diska, diska, 100));
R = sqrt(X.^2 + Y.^2);
T = atan2(Y, X);
Z = uc(R, T, m, n); % Using uc for plotting
% Ensure the plot is only within the disk
Z(R > diska) = NaN;
mesh(X, Y, Z);
title(sprintf('uc: n=%d, m=%d', n, m));
colormap('jet');
plotIndex = plotIndex + 1;
end
end
First, I felt that the three answers provided by a user in this thread might have been generated by AI. How do you think?
https://www.mathworks.com/matlabcentral/answers/2094551-calculation-of-rms-like-dc-signal-for-a-sinusoidal-signal-using-simulink-algorithm
Second, I found that "Responsible usage of generative AI tools, such as ChatGPT, is allowed in MATLAB Answers."
https://www.mathworks.com/matlabcentral/content/community-guidelines.html
If the answers are indeed AI generated, then the user didn't do "clearly indicating when AI generated content is incorporated".
That leads to my question that how do we enforce the guideline.
I am not against using AI for answers but in this case, I felt the answering text is mentioning all the relevant words but missing the point. For novice users who are seeking answers, this would be misleading and waste of time.
Zhaoxu Liu / slandarer
Zhaoxu Liu / slandarer
Last activity il 15 Mar 2024

Happy Pi Day !!

Happy Pi Day!
3.14 π Day has arrived, and this post provides some very cool pi implementations and complete MATLAB code.
https://www.mathworks.com/matlabcentral/fileexchange/126210-happy-pi-day
Firstly, in order to obtain the first n decimal places of pi, we need to write the following code (to prevent inaccuracies, we need to take a few more tails and perform another operation of taking the first n decimal places when needed):
function Pi=getPi(n)
if nargin<1,n=3;end
Pi=char(vpa(sym(pi),n+10));
Pi=abs(Pi)-48;
Pi=Pi(3:n+2);
end
With this function to obtain the decimal places of pi, our visualization journey has begun~Step by step, from simple to complex~(Please try to use newer versions of MATLAB to run, at least R17b)
1 Pie chart
Just calculate the proportion of each digit to the first 1500 decimal places:
% 获取pi前1500位小数
Pi=getPi(1500);
% 统计各个数字出现次数
numNum=find([diff(sort(Pi)),1]);
numNum=[numNum(1),diff(numNum)];
% 配色列表
CM=[20,164,199;43,187,170;53,165,81;189,190,28;248,167,22;
232,74,27;244,57,99;240,118,177;168,109,195;78,125,187]./255;
% 绘图并修饰
pieHdl=pie(numNum);
set(gcf,'Color',[1,1,1],'Position',[200,100,620,620]);
for i=1:2:20
pieHdl(i).EdgeColor=[1,1,1];
pieHdl(i).LineWidth=1;
pieHdl(i).FaceColor=CM((i+1)/2,:);
end
for i=2:2:20
pieHdl(i).Color=CM(i/2,:);
pieHdl(i).FontWeight='bold';
pieHdl(i).FontSize=14;
end
% 绘制图例并修饰
lgdHdl=legend(num2cell('0123456789'));
lgdHdl.FontWeight='bold';
lgdHdl.FontSize=11;
lgdHdl.TextColor=[.5,.5,.5];
lgdHdl.Location='southoutside';
lgdHdl.Box='off';
lgdHdl.NumColumns=10;
lgdHdl.ItemTokenSize=[20,15];
title("VISUALIZING \pi 'Pi' Chart | 1500 digits",'FontSize',18,...
'FontName','Times New Roman','Color',[.5,.5,.5])
2 line chart
Calculate the change in the proportion of each number:
% 获取pi前1500位小数
Pi=getPi(1500);
% 计算比例变化
Ratio=cumsum(Pi==(0:9)',2);
Ratio=Ratio./sum(Ratio);
D=1:length(Ratio);
% 配色列表
CM=[20,164,199;43,187,170;53,165,81;189,190,28;248,167,22;
232,74,27;244,57,99;240,118,177;168,109,195;78,125,187]./255;
hold on
% 循环绘图
for i=1:10
plot(D(20:end),Ratio(i,20:end),'Color',[CM(i,:),.6],'LineWidth',1.8)
end
% 坐标区域修饰
ax=gca;box on;grid on
ax.YLim=[0,.2];
ax.YTick=0:.05:.2;
ax.XTick=0:200:1400;
ax.YTickLabel={'0%','5%','10%','15%','20%'};
ax.XMinorTick='on';
ax.YMinorTick='on';
ax.LineWidth=.8;
ax.GridLineStyle='-.';
ax.FontName='Cambria';
ax.FontSize=11;
ax.XLabel.String='Decimals';
ax.YLabel.String='Proportion';
ax.XLabel.FontSize=13;
ax.YLabel.FontSize=13;
% 绘制图例并修饰
lgdHdl=legend(num2cell('0123456789'));
lgdHdl.NumColumns=5;
lgdHdl.FontWeight='bold';
lgdHdl.FontSize=11;
lgdHdl.TextColor=[.5,.5,.5];
3 stacked area diagram
% 获取pi前500位小数
Pi=getPi(500);
% 计算比例变化
Ratio=cumsum(Pi==(0:9)',2);
Ratio=Ratio./sum(Ratio);
% 配色列表
CM=[231,98,84;239,138,71;247,170,88;255,208,111;255,230,183;
170,220,224;114,188,213;82,143,173;55,103,149;30,70,110]./255;
% 绘制堆叠面积图
hold on
areaHdl=area(Ratio');
for i=1:10
areaHdl(i).FaceColor=CM(i,:);
areaHdl(i).FaceAlpha=.9;
end
% 图窗和坐标区域修饰
set(gcf,'Position',[200,100,720,420]);
ax=gca;
ax.YLim=[0,1];
ax.XMinorTick='on';
ax.YMinorTick='on';
ax.LineWidth=.8;
ax.FontName='Cambria';
ax.FontSize=11;
ax.TickDir='out';
ax.XLabel.String='Decimals';
ax.YLabel.String='Proportion';
ax.XLabel.FontSize=13;
ax.YLabel.FontSize=13;
ax.Title.String='Area Chart of Proportion — 500 digits';
ax.Title.FontSize=14;
% 绘制图例并修饰
lgdHdl=legend(num2cell('0123456789'));
lgdHdl.NumColumns=5;
lgdHdl.FontSize=11;
lgdHdl.Location='southeast';
4 connected stacked bar chart
% 获取pi前100位小数
Pi=getPi(100);
% 计算比例变化
Ratio=cumsum(Pi==(0:9)',2);
Ratio=Ratio./sum(Ratio);
X=Ratio(:,10:10:80)';
barHdl=bar(X,'stacked','BarWidth',.2);
CM=[231,98,84;239,138,71;247,170,88;255,208,111;255,230,183;
170,220,224;114,188,213;82,143,173;55,103,149;30,70,110]./255;
for i=1:10
barHdl(i).FaceColor=CM(i,:);
end
% 以下是生成连接的部分
hold on;axis tight
yEndPoints=reshape([barHdl.YEndPoints]',length(barHdl(1).YData),[])';
zeros(1,length(barHdl(1).YData));
yEndPoints=[zeros(1,length(barHdl(1).YData));yEndPoints];
barWidth=barHdl(1).BarWidth;
for i=1:length(barHdl)
for j=1:length(barHdl(1).YData)-1
y1=min(yEndPoints(i,j),yEndPoints(i+1,j));
y2=max(yEndPoints(i,j),yEndPoints(i+1,j));
if y1*y2<0
ty=yEndPoints(find(yEndPoints(i+1,j)*yEndPoints(1:i,j)>=0,1,'last'),j);
y1=min(ty,yEndPoints(i+1,j));
y2=max(ty,yEndPoints(i+1,j));
end
y3=min(yEndPoints(i,j+1),yEndPoints(i+1,j+1));
y4=max(yEndPoints(i,j+1),yEndPoints(i+1,j+1));
if y3*y4<0
ty=yEndPoints(find(yEndPoints(i+1,j+1)*yEndPoints(1:i,j+1)>=0,1,'last'),j+1);
y3=min(ty,yEndPoints(i+1,j+1));
y4=max(ty,yEndPoints(i+1,j+1));
end
fill([j+.5.*barWidth,j+1-.5.*barWidth,j+1-.5.*barWidth,j+.5.*barWidth],...
[y1,y3,y4,y2],barHdl(i).FaceColor,'FaceAlpha',.4,'EdgeColor','none');
end
end
% 图窗和坐标区域修饰
set(gcf,'Position',[200,100,720,420]);
ax=gca;box off
ax.YLim=[0,1];
ax.XMinorTick='on';
ax.YMinorTick='on';
ax.LineWidth=.8;
ax.FontName='Cambria';
ax.FontSize=11;
ax.TickDir='out';
ax.XTickLabel={'10','20','30','40','50','60','70','80'};
ax.XLabel.String='Decimals';
ax.YLabel.String='Proportion';
ax.XLabel.FontSize=13;
ax.YLabel.FontSize=13;
ax.Title.String='Area Chart of Proportion — 10-80 digits';
ax.Title.FontSize=14;
% 绘制图例并修饰
lgdHdl=legend(barHdl,num2cell('0123456789'));
lgdHdl.NumColumns=5;
lgdHdl.FontSize=11;
lgdHdl.Location='southeast';
5 bichord chart
Need to use this tool:
https://www.mathworks.com/matlabcentral/fileexchange/121043-digraph-chord-chart
% 构建连接矩阵
dataMat=zeros(10,10);
Pi=getPi(1001);
for i=1:1000
dataMat(Pi(i)+1,Pi(i+1)+1)=dataMat(Pi(i)+1,Pi(i+1)+1)+1;
end
BCC=biChordChart(dataMat,'Arrow','on','Label',num2cell('0123456789'));
BCC=BCC.draw();
% 添加刻度
BCC.tickState('on')
% 修改字体，字号及颜色
BCC.setFont('FontName','Cambria','FontSize',17)
set(gcf,'Position',[200,100,820,820]);
6 Gravity simulation diagram
Imagine each decimal as a small ball with a mass of
For example, if, the weight of ball 0 is 1, ball 9 is 1.2589, the initial velocity of the ball is 0, and it is attracted by other balls. Gravity follows the inverse square law, and if the balls are close enough, they will collide and their value will become
After adding, take the mod, add the velocity direction proportionally, and recalculate the weight.
Pi=[3,getPi(71)];K=.18;
% 基础配置
CM=[239,32,120;239,60,52;247,98,32;255,182,60;247,235,44;
142,199,57;55,180,70;0,170,239;40,56,146;147,37,139]./255;
T=linspace(0,2*pi,length(Pi)+1)';
T=T(1:end-1);
ct=linspace(0,2*pi,100);
cx=cos(ct).*.027;
cy=sin(ct).*.027;
% 初始数据
Pi=Pi(:);
N=Pi;
X=cos(T);Y=sin(T);
VX=T.*0;VY=T.*0;
PX=X;PY=Y;
% 未碰撞时初始质量
getM=@(x)(x+1).^K;
M=getM(N);
% 绘制初始圆圈
hold on
for i=1:length(N)
fill(cx+X(i),cy+Y(i),CM(N(i)+1,:),'EdgeColor','w','LineWidth',1)
end
for k=1:800
% 计算加速度
Rn2=1./squareform(pdist([X,Y])).^2;
Rn2(eye(length(X))==1)=0;
MRn2=Rn2.*(M');
AX=X'-X;AY=Y'-Y;
normXY=sqrt(AX.^2+AY.^2);
AX=AX./normXY;AX(eye(length(X))==1)=0;
AY=AY./normXY;AY(eye(length(X))==1)=0;
AX=sum(AX.*MRn2,2)./150000;
AY=sum(AY.*MRn2,2)./150000;
% 计算速度及新位置
VX=VX+AX;X=X+VX;PX=[PX,X];
VY=VY+AY;Y=Y+VY;PY=[PY,Y];
% 检测是否有碰撞
R=squareform(pdist([X,Y]));
R(triu(ones(length(X)))==1)=inf;
[row,col]=find(R<=0.04);
if length(X)==1
break;
end
if ~isempty(row)
% 碰撞的点合为一体
XC=(X(row)+X(col))./2;YC=(Y(row)+Y(col))./2;
VXC=(VX(row).*M(row)+VX(col).*M(col))./(M(row)+M(col));
VYC=(VY(row).*M(row)+VY(col).*M(col))./(M(row)+M(col));
PC=nan(length(row),size(PX,2));
NC=mod(N(row)+N(col),10);
% 删除碰撞点并绘图
uniNum=unique([row;col]);
X(uniNum)=[];VX(uniNum)=[];
Y(uniNum)=[];VY(uniNum)=[];
for i=1:length(uniNum)
plot(PX(uniNum(i),:),PY(uniNum(i),:),'LineWidth',2,'Color',CM(N(uniNum(i))+1,:))
end
PX(uniNum,:)=[];PY(uniNum,:)=[];N(uniNum,:)=[];
% 绘制圆形
for i=1:length(XC)
fill(cx+XC(i),cy+YC(i),CM(NC(i)+1,:),'EdgeColor','w','LineWidth',1)
end
% 补充合体点
X=[X;XC];Y=[Y;YC];VX=[VX;VXC];VY=[VY;VYC];
PX=[PX;PC];PY=[PY;PC];N=[N;NC];M=getM(N);
end
end
for i=1:size(PX,1)
plot(PX(i,:),PY(i,:),'LineWidth',2,'Color',CM(N(i)+1,:))
end
text(-1,1,{['Num=',num2str(length(Pi))];['K=',num2str(K)]},'FontSize',13,'FontName','Cambria')
% 图窗及坐标区域修饰
set(gcf,'Position',[200,100,820,820]);
ax=gca;
ax.Position=[0,0,1,1];
ax.DataAspectRatio=[1,1,1];
ax.XLim=[-1.1,1.1];
ax.YLim=[-1.1,1.1];
ax.XTick=[];
ax.YTick=[];
ax.XColor='none';
ax.YColor='none';
7 forest chart
The method comes from
http://mkweb.bcgsc.ca/pi/piday2021
The digits of π are shown as a forest. Each tree in the forest represents the digits of π up to the next 9. The first 10 trees are "grown" from the digit sets 314159, 2653589, 79, 3238462643383279, 50288419, 7169, 39, 9, 3751058209, and 749.
BRANCHES
The first digit of a tree controls how many branches grow from the trunk of the tree. For example, the first tree's first digit is 3, so you see 3 branches growing from the trunk.
The next digit's branches grow from the end of a branch of the previous digit in left-to-right order. This process continues until all the tree's digits have been used up.
Each tree grows from a set of consecutive digits sampled from the digits of π up to the next 9. The first tree, shown here, grows from 314159. Each of the digits determine how many branches grow at each fork in the tree — the branches here are colored by their corresponding digit to illustrate this. Leaves encode the digits in a left-to-right order. The digit 9 spawns a flower on one of the branches of the previous digit. The branching exception is 0, which terminates the current branch — 0 branches grow!
LEAVES AND FLOWERS
The tree's digits themselves are drawn as circular leaves, color-coded by the digit.
The leaf exception is 9, which causes one of the branches of the previous digit to sprout a flower! The petals of the flower are colored by the digit before the 9 and the center is colored by the digit after the 9, which is on the next tree. This is how the forest propagates.
The colors of a flower are determined by the first digit of the next tree and the penultimate digit of the current tree. If the current tree only has one digit, then that digit is used. Leaves are placed at the tips of branches in a left-to-right order — you can "easily" read them off. Additionally, the leaves are distributed within the tree (without disturbing their left-to-right order) to spread them out as much as possible and avoid overlap. This order is deterministic.
The leaf placement exception are the branch set that sprouted the flower. These are not used to grow leaves — the flower needs space!
function PiTree(X,pos,D)
lw=2;
theta=pi/2+(rand(1)-.5).*pi./12;
% 树叶及花朵颜色
CM=[237,32,121;237,62,54;247,99,33;255,183,59;245,236,43;
141,196,63;57,178,74;0,171,238;40,56,145;146,39,139]./255;
hold on
if all(X(1:end-2)==0)
endSet=[pos,pos,theta];
else
kplot(pos(1)+[0,cos(theta)],pos(2)+[0,sin(theta)],lw./.6)
endSet=[pos,pos+[cos(theta),sin(theta)],theta];
% 计算层级
Layer=0;
for i=1:length(X)
Layer=[Layer,ones(1,X(i)).*i];
end
% 计算树枝
if D
for i=1:length(X)-2
if X(i)==0 % 若数值为0则不长树枝
newSet=endSet(1,:);
elseif X(i)==1 % 若数值为1则一长一短两个树枝
tTheta=endSet(1,5);
tTheta=linspace(tTheta+pi/8,tTheta-pi/8,2)'+(rand([2,1])-.5).*pi./8;
newSet=repmat(endSet(1,3:4),[X(i),1]);
newSet=[newSet.*[1;1],newSet+[cos(tTheta),sin(tTheta)].*.7^Layer(i).*[1;.1],tTheta];
else % 其他情况数值为几长几个树枝
tTheta=endSet(1,5);
tTheta=linspace(tTheta+pi/5,tTheta-pi/5,X(i))'+(rand([X(i),1])-.5).*pi./8;
newSet=repmat(endSet(1,3:4),[X(i),1]);
newSet=[newSet,newSet+[cos(tTheta),sin(tTheta)].*.7^Layer(i),tTheta];
end
% 绘制树枝
for j=1:size(newSet,1)
kplot(newSet(j,[1,3]),newSet(j,[2,4]),lw.*.6^Layer(i))
end
endSet=[endSet;newSet];
endSet(1,:)=[];
end
end
end
% 计算叶子和花朵位置
FLSet=endSet(:,3:4);
[~,FLInd]=sort(FLSet(:,1));
FLSet=FLSet(FLInd,:);
[~,tempInd]=sort(rand([1,size(FLSet,1)]));
tempInd=sort(tempInd(1:length(X)-2));
flowerInd=tempInd(randi([1,length(X)-2],[1,1]));
leafInd=tempInd(tempInd~=flowerInd);
% 绘制树叶
for i=1:length(leafInd)
scatter(FLSet(leafInd(i),1),FLSet(leafInd(i),2),70,'filled','CData',CM(X(i)+1,:))
end
% 绘制花朵
for i=1:5
% if ~D
% tC=CM(X(end)+1,:);
% else
% tC=CM(X(end-2)+1,:);
% end
scatter(FLSet(flowerInd,1)+cos(pi*2*i/5).*.18,FLSet(flowerInd,2)+sin(pi*2*i/5).*.18,60,...
'filled','CData',CM(X(end-2)+1,:),'MarkerEdgeColor',[1,1,1])
end
scatter(FLSet(flowerInd,1),FLSet(flowerInd,2),60,'filled','CData',CM(X(end)+1,:),'MarkerEdgeColor',[1,1,1])
drawnow;%axis tight
% =========================================================================
function kplot(XX,YY,LW,varargin)
LW=linspace(LW,LW*.6,10);%+rand(1,20).*LW./10;
XX=linspace(XX(1),XX(2),11)';
XX=[XX(1:end-1),XX(2:end)];
YY=linspace(YY(1),YY(2),11)';
YY=[YY(1:end-1),YY(2:end)];
for ii=1:10
plot(XX(ii,:),YY(ii,:),'LineWidth',LW(ii),'Color',[.1,.1,.1])
end
end
end
main part:
Pi=[3,getPi(800)];
pos9=[0,find(Pi==9)];
set(gcf,'Position',[200,50,900,900],'Color',[1,1,1]);
ax=gca;hold on
ax.Position=[0,0,1,1];
ax.DataAspectRatio=[1,1,1];
ax.XLim=[.5,36];
ax.XTick=[];
ax.YTick=[];
ax.XColor='none';
ax.YColor='none';
for j=1:8
for i=1:11
n=i+(j-1)*11;
if n<=85
tPi=Pi((pos9(n)+1):pos9(n+1)+1);
if length(tPi)>2
PiTree(tPi,[0+i*3,0-j*4],true);
else
PiTree([Pi(pos9(n)),tPi],[0+i*3,0-j*4],false);
end
end
end
end
8 random walk
n=1200;
% 获取pi前n位小数
Pi=getPi(n);
CM=[239,65,75;230,115,48;229,158,57;232,136,85;239,199,97;
144,180,116;78,166,136;81,140,136;90,118,142;43,121,159]./255;
hold on
endPoint=[0,0];
t=linspace(0,2*pi,100);
T=linspace(0,2*pi,11)+pi/2;
fill(endPoint(1)+cos(t).*.5,endPoint(2)+sin(t).*.5,CM(Pi(1)+1,:),'EdgeColor','none')
for i=1:n
theta=T(Pi(i)+1);
plot(endPoint(1)+[0,cos(theta)],endPoint(2)+[0,sin(theta)],'Color',[CM(Pi(i)+1,:),.8],'LineWidth',1.2);
endPoint=endPoint+[cos(theta),sin(theta)];
end
fill(endPoint(1)+cos(t).*.5,endPoint(2)+sin(t).*.5,CM(Pi(n)+1,:),'EdgeColor','none')
% 图窗和坐标区域修饰
set(gcf,'Position',[200,100,820,820]);
ax=gca;
ax.XTick=[];
ax.YTick=[];
ax.Color=[0,0,0];
ax.DataAspectRatio=[1,1,1];
ax.XLim=[-30,5];
ax.YLim=[-5,40];
% 绘制图例
endPoint=[1,35];
for i=1:10
theta=T(i);
plot(endPoint(1)+[0,cos(theta).*2],endPoint(2)+[0,sin(theta).*2],'Color',[CM(i,:),.8],'LineWidth',3);
text(endPoint(1)+cos(theta).*2.7,endPoint(2)+sin(theta).*2.7,num2str(i-1),'Color',[1,1,1].*.7,...
'FontSize',12,'FontWeight','bold','FontName','Cambria','HorizontalAlignment','center')
end
text(-15,35,'Random walk of \pi digits','Color',[1,1,1],'FontName','Cambria',...
'HorizontalAlignment','center','FontSize',25,'FontAngle','italic')
9 grid chart
Pi=[3,getPi(399)];
% 配色数据
CM=[248,65,69;246,152,36;249,198,81;67,170,139;87,118,146]./255;
% 绘制圆圈
hold on
t=linspace(0,2*pi,100);
x=cos(t).*.8.*.5;
y=sin(t).*.8.*.5;
for i=1:400
[col,row]=ind2sub([20,20],i);
if mod(Pi(i),2)==0
fill(x+col,y+row,CM(round((Pi(i)+1)/2),:),'LineWidth',1,'EdgeAlpha',.8)
else
fill(x+col,y+row,[0,0,0],'EdgeColor',CM(round((Pi(i)+1)/2),:),'LineWidth',1,'EdgeAlpha',.7)
end
end
text(10.5,-.4,'\pi on a grid — 400 digits','Color',[1,1,1],'FontName','Cambria',...
'HorizontalAlignment','center','FontSize',25,'FontAngle','italic')
% 图窗和坐标区域修饰
set(gcf,'Position',[200,100,820,820]);
ax=gca;
ax.YDir='reverse';
ax.XLim=[.5,20.5];
ax.YLim=[-1,20.5];
ax.XTick=[];
ax.YTick=[];
ax.Color=[0,0,0];
ax.DataAspectRatio=[1,1,1];
10 scale grid diagram
Let's still put the numbers in the form of circles, but the difference is that six numbers are grouped together, and the pure purple circle at the end is the six 9s that we are familiar with decimal places 762-767
Pi=[3,getPi(767)];
% 762-767
% 配色数据
CM=[239,32,120;239,60,52;247,98,32;255,182,60;247,235,44;
142,199,57;55,180,70;0,170,239;40,56,146;147,37,139]./255;
% 绘制圆圈
hold on
t=linspace(0,2*pi,100);
x=cos(t).*.9.*.5;
y=sin(t).*.9.*.5;
for i=1:6:length(Pi)
n=round((i-1)/6+1);
[col,row]=ind2sub([10,13],n);
tNum=Pi(i:i+5);
numNum=find([diff(sort(tNum)),1]);
numNum=[numNum(1),diff(numNum)];
cumNum=cumsum(numNum);
uniNum=unique(tNum);
for j=length(cumNum):-1:1
fill(x./6.*cumNum(j)+col,y./6.*cumNum(j)+row,CM(uniNum(j)+1,:),'EdgeColor','none')
end
end
% 绘制图例
for i=1:10
fill(x./4+5.5+(i-5.5)*.32,y./4+14.5,CM(i,:),'EdgeColor','none')
text(5.5+(i-5.5)*.32,14.9,num2str(i-1),'Color',[1,1,1],'FontSize',...
9,'FontName','Cambria','HorizontalAlignment','center')
end
text(5.5,-.2,'FEYNMAN POINT of \pi','Color',[1,1,1],'FontName','Cambria',...
'HorizontalAlignment','center','FontSize',25,'FontAngle','italic')
% 图窗和坐标区域修饰
set(gcf,'Position',[200,100,600,820]);
ax=gca;
ax.YDir='reverse';
ax.Position=[0,0,1,1];
ax.XLim=[.3,10.7];
ax.YLim=[-1,15.5];
ax.XTick=[];
ax.YTick=[];
ax.Color=[0,0,0];
ax.DataAspectRatio=[1,1,1];
11 text chart
First, write a code to generate an image of each letter:
function getLogo
if ~exist('image','dir')
mkdir('image\')
end
logoSet=['.',char(65:90)];
for i=1:27
figure();
ax=gca;
ax.XLim=[-1,1];
ax.YLim=[-1,1];
ax.XColor='none';
ax.YColor='none';
ax.DataAspectRatio=[1,1,1];
logo=logoSet(i);
hold on
text(0,0,logo,'HorizontalAlignment','center','FontSize',320,'FontName','Segoe UI Black')
exportgraphics(ax,['image\',logo,'.png'])
close
end
dotPic=imread('image\..png');
newDotPic=uint8(ones([400,size(dotPic,2),3]).*255);
newDotPic(end-size(dotPic,1)+1:end,:,1)=dotPic(:,:,1);
newDotPic(end-size(dotPic,1)+1:end,:,2)=dotPic(:,:,2);
newDotPic(end-size(dotPic,1)+1:end,:,3)=dotPic(:,:,3);
imwrite(newDotPic,'image\..png')
S=20;
for i=1:27
logo=logoSet(i);
tPic=imread(['image\',logo,'.png']);
sz=size(tPic,[1,2]);
sz=round(sz./sz(1).*400);
tPic=imresize(tPic,sz);
tBox=uint8(255.*ones(size(tPic,[1,2])+S));
tBox(S+1:S+size(tPic,1),S+1:S+size(tPic,2))=tPic(:,:,1);
imwrite(cat(3,tBox,tBox,tBox),['image\',logo,'.png'])
end
end
Pi=[3,-1,getPi(150)];
CM=[109,110,113;224,25,33;244,126,26;253,207,2;154,203,57;111,150,124;
121,192,235;6,109,183;190,168,209;151,118,181;233,93,163]./255;
ST={'.','ZERO','ONE','TWO','THREE','FOUR','FIVE','SIX','SEVEN','EIGHT','NINE'};
n=1;
hold on
% 循环绘制字母
for i=1:20%:10
STList='';
NMList=[];
PicListR=uint8(zeros(400,0));
PicListG=uint8(zeros(400,0));
PicListB=uint8(zeros(400,0));
% PicListA=uint8(zeros(400,0));
for j=1:6
STList=[STList,ST{Pi(n)+2}];
NMList=[NMList,ones(size(ST{Pi(n)+2})).*(Pi(n)+2)];
n=n+1;
if length(STList)>15&&length(STList)+length(ST{Pi(n)+2})>20
break;
end
end
for k=1:length(STList)
tPic=imread(['image\',STList(k),'.png']);
% PicListA=[PicListA,tPic(:,:,1)];
PicListR=[PicListR,(255-tPic(:,:,1)).*CM(NMList(k),1)];
PicListG=[PicListG,(255-tPic(:,:,2)).*CM(NMList(k),2)];
PicListB=[PicListB,(255-tPic(:,:,3)).*CM(NMList(k),3)];
end
PicList=cat(3,PicListR,PicListG,PicListB);
image([-1200,1200],[0,150]-(i-1)*150,flipud(PicList))
end
% 图窗及坐标区域修饰
set(gcf,'Position',[200,100,600,820]);
ax=gca;
ax.DataAspectRatio=[1,1,1];
ax.XLim=[-1300,1300];
ax.Position=[0,0,1,1];
ax.XTick=[];
ax.YTick=[];
ax.Color=[0,0,0];
ax.YLim=[-19*150-80,230];
12 spiral chart
Pi=getPi(600);
% 配色列表
CM=[78,121,167;242,142,43;225,87,89;118,183,178;89,161,79;
237,201,72;176,122,161;255,157,167;156,117,95;186,176,172]./255;
% 绘制圆圈
hold on
t=linspace(0,2*pi,100);
x=cos(t).*.8;
y=sin(t).*.8;
for i=1:600
X=i.*cos(i./10)./10;
Y=i.*sin(i./10)./10;
fill(X+x,Y+y,CM(Pi(i)+1,:),'EdgeColor','none','FaceAlpha',.9)
end
text(0,65,'The Circle of \pi','Color',[1,1,1],'FontName','Cambria',...
'HorizontalAlignment','center','FontSize',25,'FontAngle','italic')
% 图窗和坐标区域修饰
set(gcf,'Position',[200,100,820,820]);
ax=gca;
ax.XLim=[-60,60];
ax.YLim=[-60,70];
ax.XTick=[];
ax.YTick=[];
ax.Color=[0,0,0];
ax.DataAspectRatio=[1,1,1];
13 Archimedean spiral diagram
a=1;b=.227;
Pi=getPi(500);
% 配色列表
CM=[78,121,167;242,142,43;225,87,89;118,183,178;89,161,79;
237,201,72;176,122,161;255,157,167;156,117,95;186,176,172]./255;
% 绘制圆圈
hold on
T=0;R=1;
t=linspace(0,2*pi,100);
x=cos(t).*.7;
y=sin(t).*.7;
for i=1:500
X=R.*cos(T);Y=R.*sin(T);
fill(X+x,Y+y,CM(Pi(i)+1,:),'EdgeColor','none','FaceAlpha',.9)
T=T+1./R.*1.4;
R=a+b*T;
end
text(17.25,22,{'The Archimedes spiral of \pi';'—— 500 digits'},...
'Color',[1,1,1],'FontName','Cambria',...
'HorizontalAlignment','right','FontSize',25,'FontAngle','italic')
% 图窗和坐标区域修饰
set(gcf,'Position',[200,100,820,820]);
ax=gca;
ax.XLim=[-19,18.5];
ax.YLim=[-20,25];
ax.XTick=[];
ax.YTick=[];
ax.Color=[0,0,0];
ax.DataAspectRatio=[1,1,1];
14 proportional Archimedean spiral diagram
Pi=[3,getPi(1199)];
% 配色数据
CM=[239,32,120;239,60,52;247,98,32;255,182,60;247,235,44;
142,199,57;55,180,70;0,170,239;40,56,146;147,37,139]./255;
% CM=slanCM(184,10);
% 绘制圆圈
hold on
T=0;R=1;
t=linspace(0,2*pi,100);
x=cos(t).*.7;
y=sin(t).*.7;
for i=1:4:length(Pi)
X=R.*cos(T);Y=R.*sin(T);
tNum=Pi(i:i+3);
numNum=find([diff(sort(tNum)),1]);
numNum=[numNum(1),diff(numNum)];
cumNum=cumsum(numNum);
uniNum=unique(tNum);
for j=length(cumNum):-1:1
fill(x./4.*cumNum(j)+X,y./4.*cumNum(j)+Y,CM(uniNum(j)+1,:),'EdgeColor','none')
end
T=T+1./R.*1.4;
R=a+b*T;
end
text(14,16.5,{'The ratio of four numbers from \pi';'—— 1200 digits'},...
'Color',[1,1,1],'FontName','Cambria',...
'HorizontalAlignment','right','FontSize',23,'FontAngle','italic')
% 图窗和坐标区域修饰
set(gcf,'Position',[200,100,820,820]);
ax=gca;
ax.XLim=[-15,15.5];
ax.YLim=[-15,19];
ax.XTick=[];
ax.YTick=[];
ax.Color=[0,0,0];
ax.DataAspectRatio=[1,1,1];
15 graph
% 构建连接矩阵
corrMat=zeros(10,10);
Pi=getPi(401);
for i=1:400
corrMat(Pi(i)+1,Pi(i+1)+1)=corrMat(Pi(i)+1,Pi(i+1)+1)+1;
end
% 配色列表
colorList=[0.3725 0.2745 0.5647
0.1137 0.4118 0.5882
0.2196 0.6510 0.6471
0.0588 0.5216 0.3294
0.4510 0.6863 0.2824
0.9294 0.6784 0.0314
0.8824 0.4863 0.0196
0.8000 0.3137 0.2431
0.5804 0.2039 0.4314
0.4353 0.2510 0.4392];
t=linspace(0,2*pi,11);t=t(1:10)';
posXY=[cos(t),sin(t)];
maxWidth=max(corrMat(corrMat>0));
minWidth=min(corrMat(corrMat>0));
ttList=linspace(0,1,3)';
% 循环绘图
hold on
for i=1:size(corrMat,1)
for j=i+1:size(corrMat,2)
if corrMat(i,j)>0
tW=(corrMat(i,j)-minWidth)./(maxWidth-minWidth);
colorData=(1-ttList).*colorList(i,:)+ttList.*colorList(j,:);
CData(:,:,1)=colorData(:,1);
CData(:,:,2)=colorData(:,2);
CData(:,:,3)=colorData(:,3);
% 绘制连线
fill(linspace(posXY(i,1),posXY(j,1),3),...
linspace(posXY(i,2),posXY(j,2),3),[0,0,0],'LineWidth',tW.*12+1,...
'CData',CData,'EdgeColor','interp','EdgeAlpha',.7,'FaceAlpha',.7)
end
end
% 绘制圆点
scatter(posXY(i,1),posXY(i,2),200,'filled','LineWidth',1.2,...
'MarkerFaceColor',colorList(i,:),'MarkerEdgeColor',[.7,.7,.7]);
text(posXY(i,1).*1.13,posXY(i,2).*1.13,num2str(i-1),'Color',[1,1,1].*.7,...
'FontSize',30,'FontWeight','bold','FontName','Cambria','HorizontalAlignment','center')
end
text(0,1.3,'Numerical adjacency of \pi — 400 digits','Color',[1,1,1],'FontName','Cambria',...
'HorizontalAlignment','center','FontSize',25,'FontAngle','italic')
% 图窗和坐标区域修饰
set(gcf,'Position',[200,100,820,820]);
ax=gca;
ax.XLim=[-1.2,1.2];
ax.YLim=[-1.21,1.5];
ax.XTick=[];
ax.YTick=[];
ax.Color=[0,0,0];
ax.DataAspectRatio=[1,1,1];
16 circos chart
Need to use this tool:
https://www.mathworks.com/matlabcentral/fileexchange/118655-circos-plot
Class=getPi(1001)+1;
Data=diag(ones(1,1000),-1);
className={'0','1','2','3','4','5','6','7','8','9'};
colorOrder=[239,65,75;230,115,48;229,158,57;232,136,85;239,199,97;
144,180,116;78,166,136;81,140,136;90,118,142;43,121,159]./255;
CC=circosChart(Data,Class,'ClassName',className,'ColorOrder',colorOrder);
CC=CC.draw();
ax=gca;
ax.Color=[0,0,0];
CC.setClassLabel('Color',[1,1,1],'FontSize',25,'FontName','Cambria')
CC.setLine('LineWidth',.7)
YOU CAN GET ALL CODE HERE:
https://www.mathworks.com/matlabcentral/fileexchange/126210-happy-pi-day
Mathworks has always had quality documentation but in 2023, the documentation quality fell. Will this improve in 2024?
Hi
I have Matlab 2015b installed and if I try:
ones(2,3,4)+ones(2,3)
of course I get an error. But my student has R2023b installed and she gets a 2x3x4 matrix as a result, with all elements = 2.
How is it possible?
Thanks
A
This study explores the demographic patterns and disease outcomes during the cholera outbreak in London in 1849. Utilizing historical records and scholarly accounts, the research investigates the impact of the outbreak on the city' s population. While specific data for the 1849 cholera outbreak is limited, trends from similar 19th - century outbreaks suggest a high infection rate, potentially ranging from 30% to 50% of the population, owing to poor sanitation and overcrowded living conditions . Additionally, the birth rate in London during this period was estimated at 0.037 births per person per year . Although the exact reproduction number (R₀) for cholera in 1849 remains elusive, historical evidence implies a high R₀ due to the prevalent unsanitary conditions . This study sheds light on the challenges of estimating disease parameters from historical data, emphasizing the critical role of sanitation and public health measures in mitigating the impact of infectious diseases.
Introduction
The cholera outbreak of 1849 was a significant event in the history of cholera, a deadly waterborne disease caused by the bacterium Vibrio cholera. Cholera had several major outbreaks during the 19th century, and the one in 1849 was particularly devastating.
During this outbreak, cholera spread rapidly across Europe, including countries like England, France, and Germany . The disease also affected North America, with outbreaks reported in cities like New York and Montreal. The exact number of casualties from the 1849 cholera outbreak is difficult to determine due to limited record - keeping at that time. However, it is estimated that tens of thousands of people died as a result of the disease during this outbreak.
Cholera is highly contagious and spreads through contaminated water and food . The lack of proper sanitation and hygiene practices in the 19th century contributed to the rapid spread of the disease. It wasn't until the late 19th and early 20th centuries that advancements in public health, sanitation, and clean drinking water significantly reduced the incidence and impact of cholera outbreaks in many parts of the world.
Infection Rate
Based on general patterns observed in 19th - century cholera outbreaks and the conditions of that time, it' s reasonable to assume that the infection rate was quite high. During major cholera outbreaks in densely populated and unsanitary areas, infection rates could be as high as 30 - 50% or even more.
This means that in a densely populated city like London, with an estimated population of around 2.3 million in 1849, tens of thousands of people could have been infected during the outbreak. It' s important to emphasize that this is a rough estimation based on historical patterns and not specific to the 1849 outbreak. The actual infection rate could have varied widely based on the local conditions, public health measures in place, and the effectiveness of efforts to contain the disease.
For precise and localized estimations, detailed historical records specific to the 1849 cholera outbreak in a particular city or region would be required, and such data might not be readily available due to the limitations of historical documentation from that time period
Mortality Rate
It' s challenging to provide an exact death rate for the 1849 cholera outbreak because of the limited and often unreliable historical records from that time period. However, it is widely acknowledged that the death rate was significant, with tens of thousands of people dying as a result of the disease during this outbreak.
Cholera has historically been known for its high mortality rate, particularly in areas with poor sanitation and limited access to clean water. During cholera outbreaks in the 19th century, mortality rates could be extremely high, sometimes reaching 50% or more in affected communities. This high mortality rate was due to the rapid onset of severe dehydration and electrolyte imbalance caused by the cholera toxin, leading to death if not promptly treated.
Studies and historical accounts from various cholera outbreaks suggest that the R₀ for cholera can range from 1.5 to 2.5 or even higher in conditions where sanitation is inadequate and clean water is scarce. This means that one person with cholera could potentially infect 1.5 to 2.5 or more other people in such settings.
Unfortunately, there are no specific and reliable data available regarding the recovery rates from the 1849 cholera outbreak, as detailed and accurate record - keeping during that time period was limited. Cholera outbreaks in the 19th century were often devastating due to the lack of effective medical treatments and poor sanitation conditions. Recovery from cholera largely depended on the individual's ability to rehydrate, which was difficult given the rapid loss of fluids through severe diarrhea and vomiting .
LONDON CASE OF STUDY
In 1849, the estimated population of London was around 2.3 million people. London experienced significant population growth during the 19th century due to urbanization and industrialization. It’s important to note that historical population figures are often estimates, as comprehensive and accurate record-keeping methods were not as advanced as they are today.
% Define parameters
R0 = 2.5;
beta = 0.5;
gamma = 0.2; % Recovery rate
N = 2300000; % Total population
I0 = 1; % Initial number of infected individuals
% Define the SIR model differential equations
sir_eqns = @(t, Y) [-beta * Y(1) * Y(2) / N; % dS/dt
beta * Y(1) * Y(2) / N - gamma * Y(2); % dI/dt
gamma * Y(2)]; % dR/dt
% Initial conditions
Y0 = [N - I0; I0; 0]; % Initial conditions for S, I, R
% Time span
tmax1 = 100; % Define the maximum time (adjust as needed)
tspan = [0 tmax1];
% Solve the SIR model differential equations
[t, Y] = ode45(sir_eqns, tspan, Y0);
% Plot the results
figure;
plot(t, Y(:,1), 'b', t, Y(:,2), 'r', t, Y(:,3), 'g');
legend('Susceptible', 'Infected', 'Recovered');
xlabel('Time');
ylabel('Population');
title('SIR Model');
axis tight;
grid on;
% Assuming t and Y are obtained from the ode45 solver for the SIR model
% Extract the infected population data (second column of Y)
infected = Y(:,2);
% Plot the infected population over time
figure;
plot(t, infected, 'r');
legend('Infected');
xlabel('Time');
ylabel('Population');
title('Infected Population over Time');
grid on;
The code provides a visual representation of how the disease spreads and eventually diminishes within the population over the specified time interval . It can be used to understand the impact of different parameters (such as infection and recovery rates) on the progression of the outbreak .
The study of nonlinear dynamical systems in lattices is an area of research with continuously growing interest.The first systematic studies of these systems emerged in the late 1930 s,thanks to the work of Frenkel and Kontorova on crystal dislocations.These studies led to the formulation of the discrete Klein-Gordon equation (DKG).Specifically,in 1939,Frenkel and Kontorova proposed a model that describes the structure and dynamics of a crystal lattice in a dislocation core.The FK model has become one of the fundamental models in physics,as it has been proven to reliably describe significant phenomena observed in discrete media.The equation we will examine is a variation of the following form:
The process described involves approximating a nonlinear differential equation through the Taylor method and simplifying it into a linear model.Let's analyze step by step the process from the initial equation to its final form.For small angles, can be approximated through the Taylor series as:
We substitute in the original equation with the Taylor approximation:
To map this equation to a linear model,we consider the angles to correspond to displacements in a mass-spring system.Thus,the equation transforms into:
We recognize that the term expresses the nonlinearity of the system,while β is a coefficient corresponding to this nonlinearity,simplifying the expression.The final form of the equation is:
The exact value of β depends on the mapping of coefficients in the Taylor approximation and its application to the specific physical problem.Our main goal is to derive results regarding stability and convergence in nonlinear lattices under nonlinear conditions.We will examine the basic characteristics of the discrete Klein-Gordon equation:
This model is often used to describe the opening of the DNA double helix during processes such as transcription.The model focuses on the transverse motion of the base pairs,which can be represented by a set of coupled nonlinear differential equations.
% Parameters
numBases = 50; % Number of base pairs
kappa = 0.1; % Elasticity constant
omegaD = 0.2; % Frequency term
beta = 0.05; % Nonlinearity coefficient
% Initial conditions
initialPositions = 0.01 + (0.02 - 0.01) * rand(numBases, 1);
initialVelocities = zeros(numBases, 1);
Time span
tSpan = [0 50];
>> % Differential equations
odeFunc = @(t, y) [y(numBases+1:end); ... % velocities
kappa * ([y(2); y(3:numBases); 0] - 2 * y(1:numBases) + [0; y(1:numBases-1)]) + ...
omegaD^2 * (y(1:numBases) - beta * y(1:numBases).^3)]; % accelerations
% Solve the system
[T, Y] = ode45(odeFunc, tSpan, [initialPositions; initialVelocities]);
% Visualization
plot(T, Y(:, 1:numBases))
legend(arrayfun(@(n) sprintf('Base %d', n), 1:numBases, 'UniformOutput', false))
xlabel('Time')
ylabel('Position')
title('Dynamics of DNA Base Pairs')
% Choose a specific time for the snapshot
snapshotTime = 10;
% Find the index in T that is closest to the snapshot time
[~, snapshotIndex] = min(abs(T - snapshotTime));
% Extract the solution at the snapshot time
snapshotSolution = Y(snapshotIndex, 1:numBases);
% Generate discrete plot for the DNA model at the snapshot time
figure;
stem(1:numBases, snapshotSolution, 'filled')
title(sprintf('DNA Model Displacement at t = %d', snapshotTime))
xlabel('Base Pair Index')
ylabel('Displacement')
% Time vector for detailed sampling
tDetailed = 0:0.5:50;
% Initialize an empty array to hold the data
data = [];
% Generate the data for 3D plotting
for i = 1:numBases
% Interpolate to get detailed solution data for each base pair
detailedSolution = interp1(T, Y(:, i), tDetailed);
% Concatenate the current base pair's data to the main data array
data = [data; repmat(i, length(tDetailed), 1), tDetailed', detailedSolution'];
end
% 3D Plot
figure;
scatter3(data(:,1), data(:,2), data(:,3), 10, data(:,3), 'filled')
xlabel('Base Pair')
ylabel('Time')
zlabel('Displacement')
title('3D Plot of DNA Base Pair Displacements Over Time')
colormap('rainbow')
colorbar