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及文章作者：slandarer
hey 真的好久不见了，本期既是一期绘图复刻教程，也是我写的工具函数的版本更新，本期复刻的图片来自《Nature》：
Elmarakeby, H.A., Hwang, J., Arafeh, R. et al. Biologically informed deep neural network for prostate cancer discovery. Nature 598, 348–352 (2021). https://doi.org/10.1038/s41586-021-03922-4
绘图复刻效果如下：
本文所用工具函数的基本使用教程可参见以下文章：MATLAB | 如何使用MATLAB绘制高度自定义的桑基图(sankey)
该文章仅展示工具函数基本使用方法，本文需要用到文末2.0.0版本工具函数
该文章仅展示工具函数基本使用方法，本文需要用到文末2.0.0版本工具函数
绘图复刻教程部分
0 数据
本文所使用的数据大概长这样，存储在.mat文件中：
load('natureRandData.mat')
该文件依旧可以在文末所示仓库获取，当然这组数据是通过以下方式随机生成的，直接复制以下代码也是可以的：
% rng(5)
% SourceValue=[60,40,30];
% LayerNum=[3,10,10,10,10,10,6,1];
% links{1,3}='';
% for k=1
% TargetValue=zeros(1,LayerNum(k+1));
% for i=1:LayerNum(k)
% tValue=randi([1,13],[1,LayerNum(k+1)]);
% tValue=tValue./sum(tValue).*SourceValue(i);
% for j=1:LayerNum(k+1)
% TargetValue(j)=TargetValue(j)+tValue(j);
% if tValue(j)>eps
% tLen=size(links,1);
% links{tLen+1,1}=[char(64+k),num2str(i)];
% links{tLen+1,2}=[char(64+k+1),num2str(j)];
% links{tLen+1,3}=tValue(j);
% end
% end
% end
% SourceValue=TargetValue;
% end
% links(1,:)=[];
% tResidual=0;
% for k=2:5
% [~,tindex]=sort(rand([1,10]));
% for i=1:10
% tLen=size(links,1);
% TargetValue(tindex(i))=SourceValue(i);
% links{tLen+1,1}=[char(64+k),num2str(i)];
% links{tLen+1,2}=[char(64+k+1),num2str(tindex(i))];
% links{tLen+1,3}=SourceValue(i);
% end
% for i=1:10
% tLen=size(links,1);
% links{tLen+1,1}=['Residual-',char(64+k)];
% links{tLen+1,2}=[char(64+k+1),num2str(tindex(i))];
% tValue=rand([1,1])*20./(k.^1);
% links{tLen+1,3}=tValue;
% if k==2,tResidual=tResidual+tValue;end
% if k==5,TargetValue(i)=TargetValue(i)+tValue;end
% end
% SourceValue=TargetValue;
% end
% k=1;tValue=randi([1,13],[1,3]);
% for i=1:3
% tLen=size(links,1);
% links{tLen+1,1}=[char(64+k),num2str(i)];
% links{tLen+1,2}=['Residual-',char(64+k+1)];
% links{tLen+1,3}=tValue(i)./sum(tValue).*tResidual;
% end
% for k=6
% TargetValue=zeros(1,LayerNum(k+1));
% for i=1:LayerNum(k)
% tValue=randi([1,13],[1,LayerNum(k+1)]);
% tValue=tValue./sum(tValue).*SourceValue(i);
% for j=1:LayerNum(k+1)
% TargetValue(j)=TargetValue(j)+tValue(j);
% if tValue(j)>eps
% tLen=size(links,1);
% links{tLen+1,1}=[char(64+k),num2str(i)];
% links{tLen+1,2}=[char(64+k+1),num2str(j)];
% links{tLen+1,3}=tValue(j);
% end
% end
% end
% SourceValue=TargetValue;
% end
% k=7;
% for i=1:LayerNum(end-1)
% tLen=size(links,1);
% links{tLen+1,1}=[char(64+k),num2str(i)];
% links{tLen+1,2}=' ';
% links{tLen+1,3}=SourceValue(i);
% end
% save natureRandData.mat links
1 配色
配色数据就是随便找个颜色提取器提取的论文原图：
CList1=[233,163,117; 150,209,224; 78 ,115,180]./255;
CList2=[149, 77, 85; 182, 85, 90; 208, 91, 94;
208, 91, 94; 245,124,112; 252,150,128;
252,173,151; 253,196,176; 253,217,203;
254,236,228; 230,230,230]./255;
2 基础绘图
% 创建桑基图对象(Create a Sankey diagram object)
SK=SSankey(links(:,1),links(:,2),links(:,3));
% % 类似于向右侧对齐
% SK.LayerOrder='reverse';
% 修改链接颜色渲染方式(Set link color rendering method)
% 'left'/'right'/'interp'(default)/'map'/'simple'
SK.RenderingMethod='left';
% 修改对齐方式(Set alignment)
% 'up'/'down'/'center'(default)
SK.Align='center';
% 修改文本位置(Set Text Location)
% 'left'(default)/'right'/'top'/'center'/'bottom'
SK.LabelLocation='right';
% 设置缝隙占比(Separation distance proportion)
SK.Sep=0.02;
% SK.Sep=[.08,.04,.02,.05,.05,.06,.07];
% 设置方块占比(Set the scale of blocks)
% BlockScale>0 & BlockScale<1
SK.BlockScale=.16;
% 设置颜色(Set color)
SK.ColorList=[
CList1;
CList2(1:11,:)
CList2(1:11,:)
CList2(1:11,:)
CList2(1:11,:)
CList2(1:10,:)
CList2(1:6,:)
CList2(1,:)
];
% 开始绘图(Start drawing)
SK.draw()
3 右侧对齐
我们发现此时有的Residual方块由于左侧没有方块会被排列在最左侧，这样会比较混乱，此时选择将LayerOrder设置为反方向(此操作要在SK.draw()之前)：
% 类似于向右侧对齐
SK.LayerOrder='reverse';
4 自定义缝隙比例
我们发现由于流入流出数据不相等，越往右侧整体会越窄，而原图基本上是两端对齐的，因此我们可以调整每一层的缝隙占比，比如(此操作要在SK.draw()之前)：
% 设置缝隙占比(Separation distance proportion)
% SK.Sep=0.02;
SK.Sep=[.08,.04,.02,.05,.05,.06,.07];
5 节点方块修饰
加个白框：
for i=1:SK.BN
SK.setBlock(i,'EdgeColor',[1,1,1],'LineWidth',1)
end
6 添加标签
就直接用text硬画，第i层的横坐标就是i，而宽度是SK.BlockScale，因此比较容易找到每层的X方向中点：
FontCell={'FontSize',22,'FontName','Times New Roman','HorizontalAlignment','center','VerticalAlignment','bottom'};
for i=2:SK.LN-1
text(i+SK.BlockScale/2,min(min(SK.LayerPos(:,3:4))),['H',num2str(i-1)],FontCell{:})
end
text(1+SK.BlockScale/2,min(min(SK.LayerPos(:,3:4))),'Input',FontCell{:})
text(8+SK.BlockScale/2,min(min(SK.LayerPos(:,3:4))),'OutCome',FontCell{:})
绘图复刻完整代码
% -----------------------------------------------------+
% @author | slandarer |
% 公众号 | slandarer随笔 |
% 知乎 | slandarer |
% -----------------------------------------------------+
% 复刻自 | www.nature.com/articles/s41586-021-03922-4 |
% -----------------------------------------------------+
figure('Name','nature sankey demo','Units','normalized','Position',[.05,.2,.9,.56])
clc;clear;
%% 配色 ===================================================================
CList1=[233,163,117; 150,209,224; 78 ,115,180]./255;
CList2=[149, 77, 85; 182, 85, 90; 208, 91, 94;
208, 91, 94; 245,124,112; 252,150,128;
252,173,151; 253,196,176; 253,217,203;
254,236,228; 230,230,230]./255;
%% 随意构造数据 ============================================================
load('natureRandData.mat')
%% 绘图主要代码 ============================================================
% 创建桑基图对象(Create a Sankey diagram object)
SK=SSankey(links(:,1),links(:,2),links(:,3));
% 类似于向右侧对齐
SK.LayerOrder='reverse';
% 修改链接颜色渲染方式(Set link color rendering method)
% 'left'/'right'/'interp'(default)/'map'/'simple'
SK.RenderingMethod='left';
% 修改对齐方式(Set alignment)
% 'up'/'down'/'center'(default)
SK.Align='center';
% 修改文本位置(Set Text Location)
% 'left'(default)/'right'/'top'/'center'/'bottom'
SK.LabelLocation='right';
% 设置缝隙占比(Separation distance proportion)
% SK.Sep=0.02;
SK.Sep=[.08,.04,.02,.05,.05,.06,.07];
% 设置方块占比(Set the scale of blocks)
% BlockScale>0 & BlockScale<1
SK.BlockScale=.16;
% 设置颜色(Set color)
SK.ColorList=[
CList1;
CList2(1:11,:)
CList2(1:11,:)
CList2(1:11,:)
CList2(1:11,:)
CList2(1:10,:)
CList2(1:6,:)
CList2(1,:)
];
% 开始绘图(Start drawing)
SK.draw()
%% 修饰 ===================================================================
for i=1:SK.BN
SK.setBlock(i,'EdgeColor',[1,1,1],'LineWidth',1)
end
FontCell={'FontSize',22,'FontName','Times New Roman','HorizontalAlignment','center','VerticalAlignment','bottom'};
for i=2:SK.LN-1
text(i+SK.BlockScale/2,min(min(SK.LayerPos(:,3:4))),['H',num2str(i-1)],FontCell{:})
end
text(1+SK.BlockScale/2,min(min(SK.LayerPos(:,3:4))),'Input',FontCell{:})
text(8+SK.BlockScale/2,min(min(SK.LayerPos(:,3:4))),'OutCome',FontCell{:})
工具函数完整代码
classdef SSankey < handle
% Copyright (c) 2023, Zhaoxu Liu / slandarer
% =========================================================================
% @author : slandarer
% 公众号 : slandarer随笔
% 知乎 : slandarer
% =========================================================================
% # update 2.0.0(2024-02-04)
% see natureSankeyDemo1.m
%
% + 层向右对齐(Align layers to the right)
% try : obj.LayerOrder='reverse';
%
% + 单独调整每层间隙大小(Adjust the Sep size of each layer separately)
% try : obj..Sep=[.2,.06,.05,.07,.07,.08,.15];
%
properties
Source;Target;Value;
SourceInd;TargetInd;
Layer;LayerPos;LayerOrder='normal';
AdjMat;BoolMat;
RenderingMethod='interp' % 'left'/'right'/'interp'/'map'/'simple'
LabelLocation='left' % 'left'/'right'/'top'/'center'/'bottom'
Align='center' % 'up'/'down'/'center'
BlockScale=0.05; % BlockScale>0 ! !
Sep=0.05; % Sep>=0 ! !
NodeList={};
ColorList=[[65,140,240;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;
[127,91,93;187,128,110;197,173,143;59,71,111;104,95,126;76,103,86;112,112,124;
72,39,24;197,119,106;160,126,88;238,208,146]./255];
BlockHdl;LinkHdl;LabelHdl;ax;Parent;
BN;LN;VN;TotalLen;SepLen;
arginList={'RenderingMethod','LabelLocation','BlockScale',...
'Sep','Align','ColorList','Parent','NameList'}
end
% 构造函数 =================================================================
methods
function obj=SSankey(varargin)
% 获取基本数据 -------------------------------------------------
if isa(varargin{1},'matlab.graphics.axis.Axes')
obj.ax=varargin{1};varargin(1)=[];
else
end
obj.Source=varargin{1};
obj.Target=varargin{2};
obj.Value=varargin{3};
varargin(1:3)=[];
% 获取其他信息 -------------------------------------------------
for i=1:2:(length(varargin)-1)
tid=ismember(obj.arginList,varargin{i});
if any(tid)
obj.(obj.arginList{tid})=varargin{i+1};
end
end
if isempty(obj.ax)&&(~isempty(obj.Parent)),obj.ax=obj.Parent;end
if isempty(obj.ax),obj.ax=gca;end
obj.ax.NextPlot='add';
% 基本数据预处理 -----------------------------------------------
if isempty(obj.NodeList)
obj.NodeList=[obj.Source;obj.Target];
obj.NodeList=unique(obj.NodeList,'stable');
end
obj.BN=length(obj.NodeList);
if length(obj.NodeList)>size(obj.ColorList,1)
obj.ColorList=[obj.ColorList;rand(length(obj.NodeList),3).*.7];
end
obj.VN=length(obj.Value);
% 坐标区域基础设置 ---------------------------------------------
obj.ax.YDir='reverse';
obj.ax.XColor='none';
obj.ax.YColor='none';
end
% 绘图函数 =================================================================
function draw(obj)
% 生成整体邻接矩阵 ---------------------------------------------
obj.AdjMat=zeros(obj.BN,obj.BN);
for i=1:length(obj.Source)
obj.SourceInd(i)=find(strcmp(obj.Source{i},obj.NodeList));
obj.TargetInd(i)=find(strcmp(obj.Target{i},obj.NodeList));
obj.AdjMat(obj.SourceInd(i),obj.TargetInd(i))=obj.Value{i};
end
obj.BoolMat=abs(obj.AdjMat)>0;
% 计算每个对象位于的层、每层方块长度、每个方块位置 ----------------
if strcmp(obj.LayerOrder,'normal')
obj.Layer=zeros(obj.BN,1);
obj.Layer(sum(obj.BoolMat,1)==0)=1;
startMat=diag(obj.Layer);
for i=1:(obj.BN-1)
tLayer=(sum(startMat*obj.BoolMat^i,1)>0).*(i+1);
obj.Layer=max([obj.Layer,tLayer'],[],2);
end
else
obj.Layer=zeros(obj.BN,1);
obj.Layer(sum(obj.BoolMat,2)==0)=-1;
startMat=diag(obj.Layer);
for i=1:(obj.BN-1)
tLayer=(sum(startMat*(obj.BoolMat.')^i,1)<0).*(-i-1);
obj.Layer=min([obj.Layer,tLayer'],[],2);
end
obj.Layer=obj.Layer-min(obj.Layer)+1;
end
obj.LN=max(obj.Layer);
obj.TotalLen=max([sum(obj.AdjMat,1).',sum(obj.AdjMat,2)],[],2);
obj.SepLen=max(obj.TotalLen).*obj.Sep;
obj.LayerPos=zeros(obj.BN,4);
for i=1:obj.LN
tBlockInd=find(obj.Layer==i);
tBlockLen=[0;cumsum(obj.TotalLen(tBlockInd))];
tY1=tBlockLen(1:end-1)+(0:length(tBlockInd)-1).'.*obj.SepLen(min(i,length(obj.Sep)));
tY2=tBlockLen(2:end)+(0:length(tBlockInd)-1).'.*obj.SepLen(min(i,length(obj.Sep)));
obj.LayerPos(tBlockInd,3)=tY1;
obj.LayerPos(tBlockInd,4)=tY2;
% for j=1:length(tY2)
% plot([i,i],[tY1(j),tY2(j)],'LineWidth',2)
% end
end
obj.LayerPos(:,1)=obj.Layer;
obj.LayerPos(:,2)=obj.Layer+obj.BlockScale;
% 根据对齐方式调整Y坐标 -----------------------------------------
tMinY=min(obj.LayerPos(:,3));
tMaxY=max(obj.LayerPos(:,4));
for i=1:obj.LN
tBlockInd=find(obj.Layer==i);
tBlockPos3=obj.LayerPos(tBlockInd,3);
tBlockPos4=obj.LayerPos(tBlockInd,4);
switch obj.Align
case 'up'
case 'down'
obj.LayerPos(tBlockInd,3)=obj.LayerPos(tBlockInd,3)+tMaxY-max(tBlockPos4);
obj.LayerPos(tBlockInd,4)=obj.LayerPos(tBlockInd,4)+tMaxY-max(tBlockPos4);
case 'center'
obj.LayerPos(tBlockInd,3)=obj.LayerPos(tBlockInd,3)+...
min(tBlockPos3)/2-max(tBlockPos4)/2+tMinY/2-tMaxY/2;
obj.LayerPos(tBlockInd,4)=obj.LayerPos(tBlockInd,4)+...
min(tBlockPos3)/2-max(tBlockPos4)/2+tMinY/2-tMaxY/2;
end
end
% 绘制连接 -----------------------------------------------------
for i=1:obj.VN
tSource=obj.SourceInd(i);
tTarget=obj.TargetInd(i);
tS1=sum(obj.AdjMat(tSource,1:(tTarget-1)))+obj.LayerPos(tSource,3);
tS2=sum(obj.AdjMat(tSource,1:tTarget))+obj.LayerPos(tSource,3);
tT1=sum(obj.AdjMat(1:(tSource-1),tTarget))+obj.LayerPos(tTarget,3);
tT2=sum(obj.AdjMat(1:tSource,tTarget))+obj.LayerPos(tTarget,3);
if isempty(tS1),tS1=0;end
if isempty(tT1),tT1=0;end
tX=[obj.LayerPos(tSource,1),obj.LayerPos(tSource,2),obj.LayerPos(tTarget,1),obj.LayerPos(tTarget,2)];
qX=linspace(obj.LayerPos(tSource,1),obj.LayerPos(tTarget,2),200);qT=linspace(0,1,50);
qY1=interp1(tX,[tS1,tS1,tT1,tT1],qX,'pchip');
qY2=interp1(tX,[tS2,tS2,tT2,tT2],qX,'pchip');
XX=repmat(qX,[50,1]);YY=qY1.*(qT'.*0+1)+(qY2-qY1).*(qT');
MeshC=ones(50,200,3);
switch obj.RenderingMethod
case 'left'
MeshC(:,:,1)=MeshC(:,:,1).*obj.ColorList(tSource,1);
MeshC(:,:,2)=MeshC(:,:,2).*obj.ColorList(tSource,2);
MeshC(:,:,3)=MeshC(:,:,3).*obj.ColorList(tSource,3);
case 'right'
MeshC(:,:,1)=MeshC(:,:,1).*obj.ColorList(tTarget,1);
MeshC(:,:,2)=MeshC(:,:,2).*obj.ColorList(tTarget,2);
MeshC(:,:,3)=MeshC(:,:,3).*obj.ColorList(tTarget,3);
case 'interp'
MeshC(:,:,1)=repmat(linspace(obj.ColorList(tSource,1),obj.ColorList(tTarget,1),200),[50,1]);
MeshC(:,:,2)=repmat(linspace(obj.ColorList(tSource,2),obj.ColorList(tTarget,2),200),[50,1]);
MeshC(:,:,3)=repmat(linspace(obj.ColorList(tSource,3),obj.ColorList(tTarget,3),200),[50,1]);
case 'map'
MeshC=MeshC(:,:,1).*obj.Value{i};
case 'simple'
MeshC(:,:,1)=MeshC(:,:,1).*.6;
MeshC(:,:,2)=MeshC(:,:,2).*.6;
MeshC(:,:,3)=MeshC(:,:,3).*.6;
end
obj.LinkHdl(i)=surf(obj.ax,XX,YY,XX.*0,'EdgeColor','none','FaceAlpha',.3,'CData',MeshC);
end
% 绘制方块 -----------------------------------------------------
for i=1:obj.BN
obj.BlockHdl(i)=fill(obj.ax,obj.LayerPos(i,[1,2,2,1]),...
obj.LayerPos(i,[3,3,4,4]),obj.ColorList(i,:),'EdgeColor','none');
end
% 绘制文本 -----------------------------------------------------
for i=1:obj.BN
switch obj.LabelLocation
case 'right'
obj.LabelHdl(i)=text(obj.ax,obj.LayerPos(i,2),mean(obj.LayerPos(i,[3,4])),...
[' ',obj.NodeList{i}],'FontSize',15,'FontName','Times New Roman','HorizontalAlignment','left');
case 'left'
obj.LabelHdl(i)=text(obj.ax,obj.LayerPos(i,1),mean(obj.LayerPos(i,[3,4])),...
[obj.NodeList{i},' '],'FontSize',15,'FontName','Times New Roman','HorizontalAlignment','right');
case 'top'
obj.LabelHdl(i)=text(obj.ax,mean(obj.LayerPos(i,[1,2])),obj.LayerPos(i,3),...
obj.NodeList{i},'FontSize',15,'FontName','Times New Roman','HorizontalAlignment','center','VerticalAlignment','bottom');
case 'center'
obj.LabelHdl(i)=text(obj.ax,mean(obj.LayerPos(i,[1,2])),mean(obj.LayerPos(i,[3,4])),...
obj.NodeList{i},'FontSize',15,'FontName','Times New Roman','HorizontalAlignment','center');
case 'bottom'
obj.LabelHdl(i)=text(obj.ax,mean(obj.LayerPos(i,[1,2])),obj.LayerPos(i,4),...
obj.NodeList{i},'FontSize',15,'FontName','Times New Roman','HorizontalAlignment','center','VerticalAlignment','top');
end
end
% -------------------------------------------------------------
axis tight;help SSankey
end
% =========================================================================
function setBlock(obj,n,varargin)
set(obj.BlockHdl(n),varargin{:})
end
function setLink(obj,n,varargin)
set(obj.LinkHdl(n),varargin{:})
end
function setLabel(obj,n,varargin)
set(obj.LabelHdl(n),varargin{:})
end
function moveBlockY(obj,n,dy)
obj.LayerPos(n,[3,4])=obj.LayerPos(n,[3,4])-dy;
set(obj.BlockHdl(n),'YData',obj.LayerPos(n,[3,3,4,4]));
switch obj.LabelLocation
case 'right',set(obj.LabelHdl(n),'Position',[obj.LayerPos(n,2),mean(obj.LayerPos(n,[3,4]))]);
case 'left',set(obj.LabelHdl(n),'Position',[obj.LayerPos(n,1),mean(obj.LayerPos(n,[3,4]))]);
case 'top',set(obj.LabelHdl(n),'Position',[mean(obj.LayerPos(n,[1,2])),obj.LayerPos(n,3)]);
case 'center',set(obj.LabelHdl(n),'Position',[mean(obj.LayerPos(n,[1,2])),mean(obj.LayerPos(n,[3,4]))]);
case 'bottom',set(obj.LabelHdl(n),'Position',[mean(obj.LayerPos(n,[1,2])),obj.LayerPos(n,4)]);
end
for i=1:obj.VN
tSource=obj.SourceInd(i);
tTarget=obj.TargetInd(i);
if tSource==n||tTarget==n
tS1=sum(obj.AdjMat(tSource,1:(tTarget-1)))+obj.LayerPos(tSource,3);
tS2=sum(obj.AdjMat(tSource,1:tTarget))+obj.LayerPos(tSource,3);
tT1=sum(obj.AdjMat(1:(tSource-1),tTarget))+obj.LayerPos(tTarget,3);
tT2=sum(obj.AdjMat(1:tSource,tTarget))+obj.LayerPos(tTarget,3);
if isempty(tS1),tS1=0;end
if isempty(tT1),tT1=0;end
tX=[obj.LayerPos(tSource,1),obj.LayerPos(tSource,2),obj.LayerPos(tTarget,1),obj.LayerPos(tTarget,2)];
qX=linspace(obj.LayerPos(tSource,1),obj.LayerPos(tTarget,2),200);qT=linspace(0,1,50);
qY1=interp1(tX,[tS1,tS1,tT1,tT1],qX,'pchip');
qY2=interp1(tX,[tS2,tS2,tT2,tT2],qX,'pchip');
YY=qY1.*(qT'.*0+1)+(qY2-qY1).*(qT');
set(obj.LinkHdl(i),'YData',YY);
end
end
end
end
% Copyright (c) 2023, Zhaoxu Liu / slandarer
% =========================================================================
% @author : slandarer
% 公众号 : slandarer随笔
% 知乎 : slandarer
% -------------------------------------------------------------------------
end
完
以上已经是完整代码，对于工具函数2.0.0更新版，未经允许本代码请勿作商业用途，引用的话可以引用我file exchange上的链接，可使用如下格式：
Zhaoxu Liu / slandarer (2023). sankey plot (https://www.mathworks.com/matlabcentral/fileexchange/128679-sankey-plot), MATLAB Central File Exchange. 检索来源 2023/4/28.
若转载请保留以上file exchange链接及本文链接！！！！!
该工具可通过上述fileexchange链接获取，或者通过以下gitee仓库下载：
https://gitee.com/slandarer/matlab-sankey-diagram
对于绘图复刻以及.mat文件，可以去以下gitee仓库获取全部代码：
https://gitee.com/slandarer/PLTreprint/
