chordChart (chord diagram | 弦图)

Plot beautiful chord chart/chord diagram (好看的弦图/和弦图绘制)

Plot beautiful chord chart (好看的弦图绘制), see demos for detail (详细使用请看demo).

含有自连接的弦图请见 https://www.mathworks.com/matlabcentral/fileexchange/121043-bichordchart-bidirectional-chord-diagram

For self-loop chord diagram, see https://www.mathworks.com/matlabcentral/fileexchange/121043-bichordchart-bidirectional-chord-diagram

Basic usage

dataMat=[2 0 1 2 5 1 2;
         3 5 1 4 2 0 1;
         4 0 5 5 2 4 3];
colName={'B1','G2','G3','G4','G5','G6','G7'};
rowName={'S1','S2','S3'};

% 创建弦图对象并绘图(Create chord diagram object and draw)
CC=chordChart(dataMat,'RowName',rowName,'ColName',colName);
CC=CC.draw();

% 调整字体并显示刻度(Set Font for labels and show ticks)
CC.setFont('FontSize',17,'FontName','Cambria')
CC.tickState('on')
CC.tickLabelState('on')

Set color for top split blocks/squares for chord ends

+ 单独设置每一个弦末端方块(Set individual end blocks for each chord)

Use obj.setEachSquareT_Prop

or obj.setEachSquareF_Prop

F means from (blocks below)

T means to (blocks above)

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, 'SSqRatio',1);
CC = CC.draw();
CC.labelRotate('on')

% 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;
CC.setSquareColorF(CListF)
% 修改弦颜色(Modify chord color)
CC.setChordColorBySquareF()

% 单独设置每一个弦末端方块(Set individual end blocks for each chord)
% Use obj.setEachSquareF_Prop | F means from (blocks below)
% or  obj.setEachSquareT_Prop | T means to   (blocks above)
CListT = [173,70,65; 79,135,136]./255;
% Upregulated:1 | Downregulated:2
Regulated = (rand([7, 22]) < .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', 'Box','off', 'FontSize',13);
lgdHdl.ItemTokenSize = [12,12];

Square ratio

+ 可使用`SSqRatio`属性调整弦末端弧形块占比

The 'SSqRatio' attribute can be used to adjust

the ratio of arc-shaped blocks at the end of the chord

+ 新增辅助属性`OSqRatio`用来调整原本弧形块占比

The 'OSqRatio' attribute can be used to adjust

the ratio of original arc-shaped blocks

dataMat = round(10.*rand([11,4]).*((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, 'OSqRatio',80/100);
CC.RowName = repmat({' '}, [1, length(rowName)]);
CC = CC.draw();

% 修改上方方块颜色(Modify the color of the blocks above)
CListT = [.93,.60,.62; .55,.80,.99; .95,.82,.18; 1.0,.81,.91];
CC.setSquareColorT(CListT)
% 修改下方方块颜色(Modify the color of the blocks below)
CListF = [.75,.73,.86; .56,.83,.78; .00,.60,.20; 1.0,.49,.02; .78,.77,.95; .59,.24,.36; 
          .98,.51,.45; .96,.55,.75; .47,.71,.84; .65,.35,.16; .40,.00,.64];
CC.setSquareColorF(CListF)
% 修改弦颜色(Modify chord color)
CC.setChordColorBySquareT()

% 添加刻度
CC.tickState('on')
% 修改字体，字号及颜色
CC.setFont('FontName','Cambria', 'FontSize',17)


% 绘制图例(Draw legend)
lgdHdl = legend(CC.squareFHdl, rowName, 'Location','eastoutside', ...
    'FontSize',16, 'FontName','Cambria', 'Box','off');
lgdHdl.ItemTokenSize = [18,8];

Rotation

+ 新增辅助属性`Rotation`用来整体旋转图形

The 'Rotation' attribute is used to rotate the entire shape

clc;clear
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, 'Rotation',3*pi/2);
CC = CC.draw();

% 修改上方方块颜色(Modify the color of the blocks above)
CListT = [0.47 0.58 0.75; 0.48 0.54 0.58; 0.65 0.72 0.65; 0.94 0.92 0.90; 0.98 0.76 0.68];
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
% 一个红白蓝配色 colorbar
CMap = interp1([0,.5,1].', [0,0,1;1,1,1;1,0,0], linspace(0,1,50).');
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];


% Draw legend
text(1.25,-.15, 'LogFC', 'FontSize',16)
text(1.25,1, 'Terms', 'FontSize',16)

lgdHdl = legend(CC.squareTHdl, colName, 'Location','best', 'FontSize',14, 'Box','off');
lgdHdl.Position = [.735,.53,.167,.27];
lgdHdl.ItemTokenSize = [18,8];

Square, tick, label radius

More convenient radius control:

Add highlight arrow

dataMat = [2 0 1 2 5 1 2;
           3 5 1 4 2 0 1;
           4 0 5 5 2 4 3];

CC = chordChart(dataMat);
CC = CC.draw();

CC.addHighlightArrow(3, 4)
CC.addHighlightArrow(2, 2)