STree (special dendrogram plot)

Rich and diverse dendrogram plot drawing.

Basic usage

Data = rand(75,3);
N = 5;

% 创建聚类树状图对象 -- create tree(dendrogram) object
Z = linkage(Data, 'average');
ST = STree(Z, 'MaxClust', N);


ST.ClustGap = 'on';        % 每个类之间加入间隙   -- insert gap between each clust
ST.BranchColor = 'on';     % 为不同类树枝添加颜色 -- set the branch's color of each clust
ST.BranchHighlight = 'on'; % 增添树枝高亮         -- add highlight for each clust's branches
ST.ClassHighlight = 'on';  % 分类高亮            -- add class highlight
ST.ClassLabel = 'on';      % 分类文本信息         -- add class-label

ST.draw()
axis off

All kinds of branch

Orientation and TLim

Dendrogram plot with heatmap

Demo1

% 随便捏造了点数据 -- made up some data casually
X1 = randn(20,20) + [(linspace(-1,2.5,20)').*ones(1,8),(linspace(.5,-.7,20)').*ones(1,5),(linspace(.9,-.2,20)').*ones(1,7)];
X2 = randn(20,25) + [(linspace(-1,2.5,20)').*ones(1,10),(linspace(.5,-.7,20)').*ones(1,8),(linspace(.9,-.2,20)').*ones(1,7)];
% 求相关系数矩阵 -- get the correlation matrix
Data = corr(X1,X2);
% rowName and colName
rowName = {'FREM2','ALDH9A1','RBL1','AP2A2','HNRNPK','ATP1A1','ARPC3','SMG5','RPS27A',...
          'RAB8A','SPARC','DDX3X','EEF1D','EEF1B2','RPS11','RPL13','RPL34','GCN1','FGG','CCT3'};
colName = compose('slan%d', 1:25);

% 分类配色 -- Color schemes for each clust
CList = [0.1490    0.4039    0.4980
    0.3882    0.3608    0.4471
    0.5373    0.2157    0.3098
    0.7686    0.4353    0.2431];


fig1 = figure('Units', 'normalized', 'Position', [.05,.1,.6,.8], 'Color', 'w');

% 创建聚类树状图对象 -- create tree(dendrogram) object
% 左侧聚类树状图 -- left Cluster Tree
Z1 = linkage(Data, 'average');
ST1 = STree(Z1, 'MaxClust', 3);
ST1.Orientation = 'left';
ST1.XLim = [-.25,-.05];
ST1.YLim = [0,1.2];
ST1.Label = 'off';
ST1.BranchColor = 'on';
ST1.BranchHighlight = 'on';
ST1.ClassHighlight = 'on';
ST1.RTick = [0,1,1.2,0];
ST1.CData = CList;
ST1.draw()
% 右侧聚类树状图 -- right Cluster Tree
Z2 = linkage(Data.', 'average');
ST2 = STree(Z2, 'MaxClust', 3);
ST2.Orientation = 'top';
ST2.XLim = [0,1];
ST2.YLim = [1.25,1.45];
ST2.Label = 'off';
ST2.BranchColor = 'on';
ST2.BranchHighlight = 'on';
ST2.ClassHighlight = 'on';
ST2.RTick = [0,1,1.2,0];
ST2.CData = CList;
ST2.draw() 

% -------------------------------------------------------------------------
% 创建热图对象 -- create heatmap object
SM = SMatrix(Data);

% 添加分组信息 -- Add grouping information
SM.RowName = rowName;
SM.ColName = colName;
SM.RowOrder = ST1.order;
SM.RowClass = ST1.class;
SM.ColOrder = ST2.order;
SM.ColClass = ST2.class;

% 设置文本和字体 -- Set Text and Font
SM.LeftLabel = 'off';
SM.RightLabel = 'on';
SM.BottomLabelFont = {'FontSize', 12, 'FontName', 'Times New Roman'};
SM.RightLabelFont = {'FontSize', 12, 'FontName', 'Times New Roman'};

% 设置位置 -- set position
SM.XLim = [0,1];
SM.YLim = [0,1.2];
SM.draw()

% 修饰坐标区域 -- Decorate axes
set(gca, 'XColor', 'none', 'YColor', 'none',...
    'DataAspectRatio', [1,1,1], 'XLim', [-.5,1.3]);
CB = colorbar;
CB.Position(4) = CB.Position(4).*0.75;
CB.Position(4) = CB.Position(4).*0.75;
% exportgraphics(fig1, '.\gallery\STree_SMatrix_demo1_1.png')

%% ========================================================================
fig2 = figure('Units', 'normalized', 'Position', [.05,.1,.6,.8], 'Color', 'w');
ST1.ax = gca;
ST2.ax = gca;
SM.ax = gca;

% SM.Colormap = slanCM(141, 64);

% 每个类之间加入间隙 -- insert gap between each clust
ST1.ClustGap = 'on';
ST2.ClustGap = 'on';
SM.ClustGap = 'on';

ST1.draw() 
ST2.draw() 
SM.draw()


% 修饰坐标区域 -- Decorate axes
set(gca, 'XColor', 'none', 'YColor', 'none',...
    'DataAspectRatio', [1,1,1], 'XLim', [-.5,1.3]);
CB = colorbar;
CB.Position(4) = CB.Position(4).*0.75;
CB.Position(4) = CB.Position(4).*0.75;

Demo2

% 随便捏造了点数据 -- made up some data casually
rng(5)
X = randn(100,80) + [(linspace(-1,2.5,100)').*ones(1,15),(linspace(.5,-.7,100)').*ones(1,15),...
                  (linspace(.1,-.7,100)').*ones(1,15),(linspace(.9,-.2,100)').*ones(1,15),...
                  (linspace(-.1,.7,100)').*ones(1,10),(linspace(-.9,-.2,100)').*ones(1,10)];
Y = randn(100,8) + [(linspace(-1,2.5,100)').*ones(1,2),(linspace(.5,-.7,100)').*ones(1,3),(linspace(-1,-2.5,100)').*ones(1,3)];
% 求相关系数矩阵 -- get the correlation matrix
Data = corr(X,Y);
% rowName and colName
rowName = compose('slan%d', 1:80);
colName = compose('var%d', 1:8);
% 分类配色 -- Color schemes for each clust
CList = [0.1490    0.4039    0.4980
    0.3882    0.3608    0.4471
    0.5373    0.2157    0.3098
    0.7686    0.4353    0.2431];

fig1 = figure('Units', 'normalized', 'Position', [.05,.1,.6,.8], 'Color', 'w');

% 创建聚类树状图对象 -- create tree(dendrogram) object
% 内侧聚类树状图 -- inner Cluster Tree
Z1 = linkage(Data, 'average');
ST1 = STree(Z1, 'MaxClust', 4);
ST1.Orientation = 'left';
ST1.XLim = [0,1];
ST1.TLim = [pi/2,2*pi+pi/4];
ST1.Label = 'off';
ST1.BranchColor = 'on';
ST1.CData = CList;
ST1.draw()
% 径向聚类树状图 -- radial Cluster Tree
Z2 = linkage(Data.', 'average');
ST2 = STree(Z2, 'MaxClust', 2);
ST2.Orientation = 'top';
ST2.XLim = [1,2];
ST2.TLim = [pi/4,pi/4];
ST2.YLim = [0,0.3];
ST2.Label = 'off';
ST2.BranchColor = 'on';
ST2.RTick = [0,1,1.2,0];
ST2.CData = CList;
ST2.draw() 

% -------------------------------------------------------------------------
% 创建热图对象 -- create heatmap object
SM = SMatrix(Data);

% 添加分组信息 -- Add grouping information
SM.RowName = rowName;
SM.ColName = colName;
SM.RowOrder = ST1.order;
SM.RowClass = ST1.class;
SM.ColOrder = ST2.order;
SM.ColClass = ST2.class;

% 设置文本和字体 -- Set Text and Font
SM.LeftLabel = 'off';
SM.RightLabel = 'on';
SM.BottomLabelFont = {'FontSize', 12, 'FontName', 'Times New Roman'};
SM.RightLabelFont = {'FontSize', 12, 'FontName', 'Times New Roman'};

% 设置位置 -- set position
SM.XLim = [1,2];
SM.TLim = [pi/2,2*pi+pi/4];
SM.draw()

% 修饰坐标区域 -- Decorate axes
set(gca, 'XColor', 'none', 'YColor', 'none',...
    'DataAspectRatio', [1,1,1], 'XLim', [-2.2,2.3]);

% exportgraphics(fig1, '.\gallery\STree_SMatrix_demo2_1.png')

%% ========================================================================
fig2 = figure('Units', 'normalized', 'Position', [.05,.1,.6,.8], 'Color', 'w');
ST1.ax = gca;
ST2.ax = gca;
SM.ax = gca;

% SM.Colormap = slanCM(141, 64);

% 每个类之间加入间隙 -- insert gap between each clust
ST1.ClustGap = 'on';
ST2.ClustGap = 'on';
SM.ClustGap = 'on';

% see slanCMdisplay
% and Zhaoxu Liu / slandarer (2024). 200 colormaps, MATLAB Central File Exchange.
% https://www.mathworks.com/matlabcentral/fileexchange/120088-200-colormap
SM.Colormap = slanCM(136, 64);

ST1.draw() 
ST2.draw() 
SM.draw()


% 修饰坐标区域 -- Decorate axes
set(gca, 'XColor', 'none', 'YColor', 'none',...
    'DataAspectRatio', [1,1,1], 'XLim', [-2.2,2.3]);

Demo3

% STree_SMatrix_demo3

% 随机生成数据
X=randn(20,20)+[(linspace(-1,2.5,20)').*ones(1,8),(linspace(.5,-.7,20)').*ones(1,5),(linspace(.9,-.2,20)').*ones(1,7)];
Data = corr(X);
% 变量名列表
NameList=compose('Sl-%d',1:20);
% 分类配色 -- Color schemes for each clust
CList = [0.1490    0.4039    0.4980
    0.3882    0.3608    0.4471
    0.5373    0.2157    0.3098
    0.7686    0.4353    0.2431];


fig1 = figure('Units', 'normalized', 'Position', [.05,.1,.6,.8], 'Color', 'w');

% 创建聚类树状图对象 -- create tree(dendrogram) object
% 左侧聚类树状图 -- left Cluster Tree
Z1 = linkage(Data, 'average');
ST1 = STree(Z1, 'MaxClust', 3);
ST1.Orientation = 'left';
ST1.XLim = [-.25,-.05];
ST1.YLim = [0,1];
ST1.TLim = [-pi/4,-pi/4];
ST1.Label = 'off';
ST1.BranchColor = 'on';
ST1.BranchHighlight = 'on';
ST1.ClassHighlight = 'on';
ST1.RTick = [0,1,1.2,0];
ST1.CData = CList;
ST1.draw()

% 创建热图对象 -- create heatmap object
SM = SMatrix(Data);

% 添加分组信息 -- Add grouping information
SM.ColName = NameList;
SM.RowOrder = ST1.order;
SM.RowClass = ST1.class;
SM.ColOrder = ST1.order;
SM.ColClass = ST1.class;

% 设置文本和字体 -- Set Text and Font
SM.LeftLabel = 'off';
SM.BottomLabel = 'off';
SM.TopLabel = 'on';
SM.TopLabelFont = {'FontSize', 12, 'FontName', 'Times New Roman', 'Rotation', 45};

% 设置位置 -- set position
SM.XLim = [0,1];
SM.YLim = [0,1];
SM.TLim = [-pi/4,-pi/4];
SM.draw()

% 修饰句柄 -- decorate handles
% 清除热图下半部分 -- Clear the bottom half of the heatmap
tData = triu(ones(size(Data)),1);
tInd = find(tData(:) == 1);
for i = 1:length(tInd)
    set(SM.heatmapHdl{tInd(i)}, 'Visible', 'off')
end

% 修饰坐标区域 -- decorate axes
set(gca, 'XColor', 'none', 'YColor', 'none',...
    'DataAspectRatio', [1,1,1],'XLim', [-.15,1.45]);
CB = colorbar();
CB.Location = 'southoutside';

%% ========================================================================
fig2 = figure('Units', 'normalized', 'Position', [.05,.1,.6,.8], 'Color', 'w');
ST1.ax = gca;
SM.ax = gca;

% SM.Colormap = slanCM(141, 64);

% 每个类之间加入间隙 -- insert gap between each clust
ST1.ClustGap = 'on';
SM.ClustGap = 'on';

% see slanCMdisplay
% and Zhaoxu Liu / slandarer (2024). 200 colormaps, MATLAB Central File Exchange.
% https://www.mathworks.com/matlabcentral/fileexchange/120088-200-colormap
SM.Colormap = slanCM(141, 64);

ST1.draw() 
SM.draw()

% 修饰句柄 -- decorate handles
% 清除热图下半部分 -- Clear the bottom half of the heatmap
tData = triu(ones(size(Data)),1);
tInd = find(tData(:) == 1);
for i = 1:length(tInd)
    set(SM.heatmapHdl{tInd(i)}, 'Visible', 'off')
end


% 修饰坐标区域 -- decorate axes
set(gca, 'XColor', 'none', 'YColor', 'none',...
    'DataAspectRatio', [1,1,1],'XLim', [-.15,1.45]);
CB = colorbar();
CB.Location = 'southoutside';