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Help Document of Chord Chart

Zhaoxu Liu / slandarer on 6 Mar 2024 (Edited on 14 Mar 2024)

Latest activity Reply by Han Geerligs on 16 Jul 2024 at 13:33

Chord diagrams are very common in Python and R, but there are no related functions in MATLAB before. It is not easy to draw chord diagrams of the same quality as R language, But I created a MATLAB tool that could almost do it.

↓ ↓ ↓ ↓ ↓ ↓ ↓ ↓ ↓ ↓

https://www.mathworks.com/matlabcentral/fileexchange/116550-chord-chart

↑ ↑ ↑ ↑ ↑ ↑ ↑ ↑ ↑ ↑

Here is the help document:

1 Data Format

The data requirement is a numerical matrix with all values greater than or equal to 0, or a table array, or a numerical matrix and cell array for names. First, give an example of a numerical matrix:

1.1 Numerical Matrix

dataMat=randi([0,5],[5,4]); 
% 绘图(draw)
CC=chordChart(dataMat);
CC=CC.draw();

Since each object is not named, it will be automatically named Rn and Cn

1.2 Numerical Matrix and Cell Array for Names

dataMat=[2 0 1 2 5 1 2;
         3 5 1 4 2 0 1;
         4 0 5 5 2 4 3];
colName={'G1','G2','G3','G4','G5','G6','G7'};
rowName={'S1','S2','S3'};
CC=chordChart(dataMat,'rowName',rowName,'colName',colName);
CC=CC.draw();

RowName should be the same size as the rows of the matrix

ColName should be the same size as the columns of the matrix

For this example, if the value in the second row and third column is 1, it indicates that there is an energy flow from S2 to G3, and a chord with a width of 1 is needed between these two.

1.3 Table Array

A table array in the following format is required:

2 Decorate Chord

2.1 Batch modification of chords

Batch modification of chords can be done using the setChordProp function, and all properties of the Patch object can be modified. For example, modifying the color of the string, edge color, edge line sstyle, etc.:

CC.setChordProp('EdgeColor',[.3,.3,.3],'LineStyle','--',...
    'LineWidth',.1,'FaceColor',[.3,.3,.3])

2.2 Individual Modification of Chord

The individual modification of chord can be done using the setChordMN function, where the values of m and n correspond exactly to the rows and columns of the original numerical matrix. For example, changing the color of the strings flowing from S2 to G4 to red:

CC.setChordMN(2,4,'FaceColor',[1,0,0])

2.3 Color Mapping of Chords

Just use function colormap to do so:

% version 1.7.0更新
% 可使用colormap函数直接修改颜色
% Colors can be adjusted directly using the function colormap(demo4)
colormap(flipud(pink))

3 Arc Shaped Block Decoration

3.1 Batch Decoration of Arc-Shaped Blocks

use:

setSquareT_Prop
setSquareF_Prop

to modify the upper and lower blocks separately, and all attributes of the Patch object can be modified. For example, batch modify the upper blocks (change to black):

CC.setSquareT_Prop('FaceColor',[0,0,0])

3.2 Arc-Shaped Blocks Individually Decoration

use:

setSquareT_N
setSquareF_N

to modify the upper and lower blocks separately. For example, modify the second block above separately (changed to red):

CC.setSquareT_N(2,'FaceColor',[.8,0,0])

4 Font Adjustment

Use the setFont function to adjust the font, and all properties of the text object can be modified. For example, changing the font size, font, and color of the text:

CC.setFont('FontSize',25,'FontName','Cambria','Color',[0,0,.8])

5 Show and Hide Ticks

Usage:

CC.tickState('on')
% CC.tickState('off')

6 Attribute 'Sep' with Adjustable Square Spacing

If the matrix size is large, the drawing will be out of scale:

dataMat=randi([0,1],[20,10]); 
CC=chordChart(dataMat);
CC=CC.draw();
% CC.tickState('on')

We can modify its Sep attribute:

dataMat=randi([0,1],[20,10]); 
% use Sep to decrease space (separation)
% 使用 sep 减小空隙
CC=chordChart(dataMat,'Sep',1/120);
CC=CC.draw();

7 Modify Text Direction

dataMat=randi([0,1],[20,10]); 
% use Sep to decrease space (separation)
% 使用 sep 减小空隙
CC=chordChart(dataMat,'Sep',1/120);
CC=CC.draw();
CC.tickState('on')
% version 1.7.0更新
% 函数labelRatato用来旋转标签
% The function labelRatato is used to rotate the label
CC.labelRotate('on')

8 Add Tick Labels

dataMat=[2 0 1 2 5 1 2;
         3 5 1 4 2 0 1;
         4 0 5 5 2 4 3];
colName={'G1','G2','G3','G4','G5','G6','G7'};
rowName={'S1','S2','S3'};
CC=chordChart(dataMat,'rowName',rowName,'colName',colName);
CC=CC.draw();
CC.setFont('FontSize',17,'FontName','Cambria')
% 显示刻度和数值
% Displays scales and numeric values
CC.tickState('on')
CC.tickLabelState('on')
% 调节标签半径
% Adjustable Label radius
CC.setLabelRadius(1.3);
% figure()
% dataMat=[2 0 1 2 5 1 2;
%          3 5 1 4 2 0 1;
%          4 0 5 5 2 4 3];
% dataMat=dataMat+rand(3,7);
% dataMat(dataMat<1)=0;
% 
% CC=chordChart(dataMat,'rowName',rowName,'colName',colName);
% CC=CC.draw();
% CC.setFont('FontSize',17,'FontName','Cambria')
% 
% % 显示刻度和数值
% % Displays scales and numeric values
% CC.tickState('on')
% CC.tickLabelState('on')
% 
% % 调节标签半径
% % Adjustable Label radius
% CC.setLabelRadius(1.4);

9 Custom Tick Label Format

A function handle is required to input numeric output strings. The format can be set through the setTickLabelFormat function, such as Scientific notation:

dataMat=[2 0 1 2 5 1 2;
         3 5 1 4 2 0 1;
         4 0 5 5 2 4 3];
dataMat=dataMat+rand(3,7);
dataMat(dataMat<1)=0;
dataMat=dataMat.*1000;
CC=chordChart(dataMat);
CC=CC.draw();
CC.setFont('FontSize',17,'FontName','Cambria')
% 显示刻度和数值
% Displays scales and numeric values
CC.tickState('on')
CC.tickLabelState('on')
% 调节标签半径
% Adjustable Label radius
CC.setLabelRadius(1.4);
% 调整数值字符串格式
% Adjust numeric string format
CC.setTickLabelFormat(@(x)sprintf('%0.1e',x))

10 A Demo

rng(2)
dataMat=randi([1,7],[11,5]);
colName={'Fly','Beetle','Leaf','Soil','Waxberry'};
rowName={'Bartomella','Bradyrhizobium','Dysgomonas','Enterococcus',...
         'Lactococcus','norank','others','Pseudomonas','uncultured',...
         'Vibrionimonas','Wolbachia'};
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=1:5
    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=1:11
    CC.setSquareF_N(i,'FaceColor',CListF(i,:))
end
% 修改弦颜色(Modify chord color)
for i=1:5
    for j=1:11
        CC.setChordMN(j,i,'FaceColor',CListT(i,:),'FaceAlpha',.5)
    end
end
CC.tickState('on')
CC.labelRotate('on')
CC.setFont('FontSize',17,'FontName','Cambria')