MATLAB | 绘图复刻 | 热图+差异气泡图
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前言
发现基迪奥生物复刻了nature communications 中期刊 Qie, J., Liu, Y., Wang, Y. et al. Integrated proteomic and transcriptomic landscape of macrophages in mouse tissues. Nat Commun 13, 7389 (2022).这篇文章中的分组热图与差异气泡图的组合型图表：
很帅啊，咱也来画！绘制效果如下：
教程部分
0 数据准备
数据在test.csv中，来源为https://www.omicshare.com/forum/thread-8159-1-1.html
文末所示的gitee仓库中也能下载，若是懒得下载可以直接使用下半部分代码：
% 数据导入
% 若下载了test.csv数据则可如下方式读取
DataTable=readtable('test.csv');
rowName=DataTable.gene;
colName=DataTable.Properties.VariableNames(2:end);
DataTable(:,1)=[];
Data=DataTable.Variables;
Data=Data(:,1:6);
pValue=DataTable.pvalue;
log2fc=DataTable.log2fc;
negLog10pValue=-log(pValue)./log(10);
% 若未下载则直接如下方式输入数据
% Data=[1.5864 0.6541 0.2134 -0.8593 -0.8017 -0.7929
% 0.3845 1.0750 1.1756 NaN NaN NaN
% 1.1575 0.1645 1.2177 NaN NaN NaN
% 1.3135 0.7609 0.5834 -0.8976 -0.8639 -0.8963
% 0.0842 1.7035 0.5355 -0.8321 -0.7396 -0.7514
% 1.2165 0.4733 0.9692 -0.8847 NaN -0.8803
% 0.4412 1.2686 0.9186 -0.9177 -0.7025 -1.0082
% 0.6485 1.2007 0.8095 -1.0422 -0.5964 -1.0201
% 0.1135 0.9586 1.4159 NaN NaN NaN
% 1.1576 -1.0688 0.1170 -1.2459 0.9733 0.0668
% 0.6961 1.1603 0.6978 -1.4045 -0.7309 -0.4188
% 1.1161 0.9638 0.6186 -0.9938 -0.8178 -0.8869
% 0.9603 0.8072 0.7459 -1.4862 -0.2553 -0.7719
% -0.8845 1.8258 -0.1787 0.3954 -0.6913 -0.4667
% 1.3863 0.7003 0.5386 -0.8950 -0.8591 -0.8710
% 0.2966 0.3935 1.6926 -0.7993 -0.8023 -0.7809
% 1.1849 1.1460 0.2237 -0.9502 -0.6559 -0.9484];
% colName='KC_1','KC_2','KC_3','Liver_rec_1','Liver_rec_2','Liver_rec_3';
% rowName='Hmox1','Hrg','Tfr2','Tfrc','Trf','Atp13a2','Atp6ap1','Hpx','Slc11a1','Slc11a2','Slc40a1','Lrp1','Hmox2','Fth1','Cd163','Abcb6','Hscb';
% pValue=[0.0558,0.0195,0.0384,0.0149,0.0843,0.0148,0.0104,0.0013,0.0490,0.8875,0.0135,0.0032,0.0389,0.6076,0.0212,0.0717,0.0241];
% log2fc=[1.3481,4.4350,4.9859,1.6607,1.0708,2.3686,0.9994,0.8831,4.6713,0.0449,0.5541,0.8657,0.3719,0.1013,1.3980,1.1047,0.8352];
% negLog10pValue=-log(pValue)./log(10);
1 配色
论文中的配色看起来像是RdYlBu和Reds配色截取一部分，这些配色MATLAB不自带，但我写过相关工具包：https://slandarer.blog.csdn.net/article/details/127719784
若是下载了工具包或者gitee提供的文件则可直接用前半部分设置颜色，否则使用后半部分代码设置颜色：
% 配色
% 不同类型颜色
type=[1,1,1,2,2,2];
typeColor=[105,143,45;157,191,61]./255;
% 以下是colormap配色
% 若下载了slanCM配色工具包
% 该工具函数使用详见：https://mp.weixin.qq.com/s/6Fr2pYMrA5_EStF9UudvsQ
% 引用：Zhaoxu Liu / slandarer (2023). 200 colormap
% (https://www.mathworks.com/matlabcentral/fileexchange/120088-200-colormap),
% MATLAB Central File Exchange. 检索来源 2023/2/6.
CM1=slanCM(98);
CM1=flipud(CM1(37:220,:));
CM2=slanCM(12);
CM2=CM2(30:200,:);
% 若没下载slanCM配色工具包
% CM1=[0.6471 0 0.1490
% 0.7503 0.0991 0.1511
% 0.8491 0.2008 0.1587
% 0.9090 0.3267 0.2165
% 0.9606 0.4543 0.2751
% 0.9792 0.5884 0.3370
% 0.9928 0.7133 0.4095
% 0.9948 0.8165 0.5065
% 0.9969 0.9040 0.6035
% 0.9990 0.9680 0.7005
% 0.9680 0.9876 0.8078
% 0.9040 0.9628 0.9255
% 0.8128 0.9207 0.9540
% 0.7034 0.8671 0.9230
% 0.5911 0.7874 0.8791
% 0.4776 0.6966 0.8295
% 0.3773 0.5860 0.7717
% 0.2803 0.4704 0.7119
% 0.2334 0.3418 0.6483
% 0.1922 0.2118 0.5843];
% CM2=[1.0000 0.9608 0.9412
% 0.9983 0.9261 0.8916
% 0.9967 0.8914 0.8421
% 0.9940 0.8402 0.7730
% 0.9907 0.7792 0.6921
% 0.9882 0.7164 0.6120
% 0.9882 0.6487 0.5344
% 0.9882 0.5810 0.4568
% 0.9868 0.5148 0.3893
% 0.9851 0.4487 0.3232
% 0.9744 0.3769 0.2654
% 0.9546 0.2993 0.2159
% 0.9298 0.2241 0.1695
% 0.8704 0.1664 0.1447
% 0.8109 0.1086 0.1199
% 0.7490 0.0830 0.1038
% 0.6863 0.0681 0.0906
% 0.6087 0.0495 0.0774
% 0.5063 0.0248 0.0642
% 0.4039 0 0.0510];
% CMX1=linspace(0,1,size(CM1,1))';
% CMX2=linspace(0,1,size(CM2,1))';
% CMXX256=linspace(0,1,256)';
% CM1=[interp1(CMX1,CM1(:,1),CMXX256,'pchip'),interp1(CMX1,CM1(:,2),CMXX256,'pchip'),interp1(CMX1,CM1(:,3),CMXX256,'pchip')];
% CM2=[interp1(CMX2,CM2(:,1),CMXX256,'pchip'),interp1(CMX2,CM2(:,2),CMXX256,'pchip'),interp1(CMX2,CM2(:,3),CMXX256,'pchip')];
%
% CM1=flipud(CM1(37:220,:));
% CM2=CM2(30:200,:);
2 坐标区域创建
% figure窗口及axes坐标区域创建
fig=figure('Units','normalized','Position',[.3,.2,.39,.63],'Color',[1,1,1]);
ax1=axes(fig);hold on
ax1.Position=[.02,.1,.37,.88];
ax1.XLim=[0,size(Data,2)]+.5;
ax1.YLim=[-1.25,size(Data,1)]+.5;
ax1.XTick=[];
ax1.YDir='reverse';
ax1.YTick=1:size(Data,1);
ax1.YTickLabel=rowName;
ax1.YAxisLocation='right';
ax1.FontName='Cambria';
ax1.FontSize=13;
ax1.Box='on';
ax1.LineWidth=.01;
ax2=axes(fig);hold on
ax2.Position=[.55,.1,.2,.88./(size(Data,1)+1.25).*size(Data,1)];
ax2.YLim=[0,size(Data,1)]+.5;
ax2.XLim=[-1,1];
ax2.XTick=0;
ax2.XTickLabel='';
ax2.Box='off';
ax2.LineWidth=2;
ax2.TickDir='out';
ax2.YDir='reverse';
ax2.YTick=1:size(Data,1);
ax2.YTickLabel='';
ax2.XGrid='on';
ax2.YGrid='on';
ax2.FontName='Cambria';
ax2.FontSize=13;
fill(ax2,ax2.XLim([1,1,2,2]),ax2.YLim([1,2,2,1]),'w','LineWidth',2,'FaceColor','none')
热图绘制
由于HeatmapChart 不能是 Axes 的子级, 直接硬画，当然这段代码单独自己画一些数据图也可以，调调坐标区域位置就行：
% 热图绘制
% 由于HeatmapChart 不能是 Axes 的子级, 直接硬画
CLim1=[min(min(Data)),max(max(Data))];
% 生成颜色映射函数
CMX1=linspace(CLim1(1),CLim1(2),size(CM1,1))';
colorFunc1=@(X)[interp1(CMX1,CM1(:,1),X,'pchip'),interp1(CMX1,CM1(:,2),X,'pchip'),interp1(CMX1,CM1(:,3),X,'pchip')];
% 循环绘制分类
fill(ax1,[0,0,size(Data,2),size(Data,2)]+.5,[.5,0,0,.5],[1,1,1],'EdgeColor',[1,1,1])
for j=1:size(Data,2)
fill(ax1,j+[-.5,-.5,.5,.5],-.5+[-.5,.5,.5,-.5],typeColor(type(j),:),'EdgeColor','none')
end
% 循环绘制热图，nan处绘制x号
for i=1:size(Data,1)
for j=1:size(Data,2)
if ~isnan(Data(i,j))
tColor=colorFunc1(Data(i,j));
else
tColor=[205,205,205]./255;
end
fill(ax1,j+[-.5,-.5,.5,.5],i+[-.5,.5,.5,-.5],tColor,'EdgeColor',[160,160,160]./255,'LineWidth',1.2)
if isnan(Data(i,j))
plot(ax1,j+[-.5,.5,.5,-.5],i+[-.5,.5,-.5,.5],'Color',[160,160,160]./255,'LineWidth',1.2)
end
end
end
% colorbar 绘制
ax1.Colormap=CM1;
ax1.CLim=CLim1;
ax1.Colormap=CM1;
cbHdl1=colorbar(ax1,'north','LineWidth',.8);
cbHdl1.Position=[ax1.Position(1),.05,ax1.Position(3),cbHdl1.Position(4)];
cbHdl1.XAxisLocation='bottom';
% nan 图例绘制
nanFillHdl=fill(ax1,[-.5,-.5,.5,.5]-100,[-.5,.5,.5,-.5],[205,205,205]./255,'EdgeColor',[160,160,160]./255,'LineWidth',1.2);
lgdHdl1=legend(ax1,nanFillHdl,'NaN');
lgdHdl1.Box='off';
lgdHdl1.Position(1)=ax1.Position(1)+ax1.Position(3);
lgdHdl1.Position(2)=cbHdl1.Position(2);
lgdHdl1.Position(4)=cbHdl1.Position(4);
lgdHdl1.ItemTokenSize=lgdHdl1.ItemTokenSize(2).*[1,1];
差异气泡图
使用bubblechart函数和bubblelegend绘制~
% 绘制气泡图
CLim2=[min(min(Data)),max(max(Data))];
% 生成颜色映射函数
CMX2=linspace(CLim2(1),CLim2(2),size(CM2,1))';
colorFunc2=@(X)[interp1(CMX2,CM2(:,1),X,'pchip'),interp1(CMX2,CM2(:,2),X,'pchip'),interp1(CMX2,CM2(:,3),X,'pchip')];
% 绘图
bubblechart(ax2,log2fc(:).*0,1:length(log2fc(:)),log2fc(:),negLog10pValue(:),'LineWidth',1,'MarkerEdgeColor',[0,0,0],'MarkerFaceAlpha',1)
bubblesize([15 40])
% 调整 colormap 范围
CLim2=[min(min(negLog10pValue)),max(max(negLog10pValue))];
ax2.Colormap=CM2;
ax2.CLim=CLim2;
% 绘制 bubblechart legend
bLgdHdl=bubblelegend(ax2);
bLgdHdl.Position(1)=ax2.Position(1)+ax2.Position(3).*1.1;
bLgdHdl.Position(2)=ax2.Position(2)+ax2.Position(4).*.65;
bLgdHdl.Box='off';
bLgdHdl.FontName='Cambria';
bLgdHdl.FontSize=12;
% 绘制 colorbar
cbHdl2=colorbar(ax2,'east','LineWidth',.8);
cbHdl2.Position(1)=bLgdHdl.Position(1)+bLgdHdl.Position(3)/5.5;
cbHdl2.Position(2)=ax2.Position(2);
cbHdl2.Position(4)=ax2.Position(4).*.55;
cbHdl2.YAxisLocation='right';
cbHdl2.Position(3)=.032;
% 绘制 colorbar 及 bubblechart legend 的 title
annotation(gcf,'textbox',[ax2.Position(1)+ax2.Position(3).*1.1,ax2.Position(2)+ax2.Position(4).*.95,.01,.01],...
'String','log2fc','HorizontalAlignment','left','VerticalAlignment','middle','FontSize',16,'FontName','Cambria',...
'FontWeight','bold','LineStyle','none')
annotation(gcf,'textbox',[ax2.Position(1)+ax2.Position(3).*1.05,ax2.Position(2)+ax2.Position(4).*.58,.01,.01],...
'String','-log10(pvalue)','HorizontalAlignment','left','VerticalAlignment','middle','FontSize',16,'FontName','Cambria'MATLAB | 绘图复刻 | 带树状图的环形热图
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