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Figure7.m
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%% PD-1 & PD-L1 interaction (all slides)
k=10;
minD = 15;
tic;
for i = 1:length(slideName)
disp(strcat('Processing:',slideName{i}));
data1 = eval(strcat('data',slideName{i}));
% ---- Calculate interaction----
[idx,d]=knnsearch(data1{:,{'Xt','Yt'}},data1{data1.PD_1p,{'Xt','Yt'}},'k',k+1);
idx = idx(:,2:k+1);
d = d(:,2:k+1);
idx1 = idx(d<=minD);
idx1 = unique(idx1);
data1.PD1nb = false(size(data1,1),1);
data1.PD1nb(idx1) = true;
toc;
[idx,d]=knnsearch(data1{:,{'Xt','Yt'}},data1{data1.PD_L1p,{'Xt','Yt'}},'k',k+1);
idx = idx(:,2:k+1);
d = d(:,2:k+1);
idx1 = idx(d<=minD);
idx1 = unique(idx1);
data1.PDL1nb = false(size(data1,1),1);
data1.PDL1nb(idx1) = true;
toc;
data1.PD1intPDL1 = false(size(data1,1),1);
data1.PD1intPDL1(data1.PD_1p & data1.PDL1nb) = true;
data1.PD1intPDL1(data1.PD_L1p & data1.PD1nb) = true;
eval(strcat('data',slideName{i},'=data1;'));
end
%% assign allPD1/PDL1
allPD1i = alldata(alldata.PD_1p & alldata.PD1intPDL1,:);
allPDL1i = alldata(alldata.PD_L1p & alldata.PD1intPDL1,:);
sumPD1i = varfun(@mean,allPD1i,'GroupingVariables','slideName');
sumPDL1i = varfun(@mean,allPDL1i,'GroupingVariables','slideName');
allPD1ni = alldata(alldata.PD_1p & ~alldata.PD1intPDL1,:);
allPDL1ni = alldata(alldata.PD_L1p & ~alldata.PD1intPDL1,:);
sumPD1ni = varfun(@mean,allPD1ni,'GroupingVariables','slideName');
sumPDL1ni = varfun(@mean,allPDL1ni,'GroupingVariables','slideName');
%% plot PD-1 PD-L1 cells composition (in all PD1-PDL1 pairs)
figure('units','normalized','outerposition',[0 0 1 1]);
subplot(2,2,1);
violinplot(sumPDL1i{:,strcat('mean_',labelp2)});
set(gca,'xticklabels',labelp3);
set(gca,'xticklabelrotation',90);
xlim([0 length(labelp3)+1]);
title('PD-L1+(in PD1-PDL1) cells');
subplot(2,2,2);
violinplot(sumPDL1ni{:,strcat('mean_',labelp2)});
set(gca,'xticklabels',labelp3);
set(gca,'xticklabelrotation',90);
xlim([0 length(labelp3)+1]);
title('PD-L1+(not in PD1-PDL1) cells');
subplot(2,2,3);
violinplot(sumPD1i{:,strcat('mean_',labelp2)});
set(gca,'xticklabels',labelp3);
set(gca,'xticklabelrotation',90);
xlim([0 length(labelp3)+1]);
title('PD-1+(in PD1-PDL1) cells');
subplot(2,2,4);
violinplot(sumPD1ni{:,strcat('mean_',labelp2)});
set(gca,'xticklabels',labelp3);
set(gca,'xticklabelrotation',90);
xlim([0 length(labelp3)+1]);
title('PD-1+(not in PD1-PDL1) cells');
%% Pair-wise violinplot for interactor and non-interactors (PD1+ and PDL1+);
figure('units','normalized','outerposition',[0 0 1 1]);
for i = 1:length(labelp2)
marker1 = strcat('mean_',labelp2{i});
list1 = sumPD1ni{:,marker1};
list2 = sumPDL1ni{:,marker1};
subplot(5,6,i)
myviolin2(list1,list2,'PD-1+(n)','PD-L1+(n)');
title(labelp3{i},'fontsize',12);
end
%% display cell type (CD45+) & ROI (New 2022) ==> Fig7A
name1 = 'TNP097';
data1 = eval(strcat('data',name1));
marker1 = 'CD45p';
markname1 = 'CD45+ cells';
figure('units','normalized','outerposition',[0.5 0 0.5 1]);
%-----plot all cells--------
data4 = datasample(data1,50000);
colors = repmat([0.8 0.8 0.8],size(data4,1),1);
scatter(data4.Xt,data4.Yt,6,colors,'fill');
%xlims = xlim;
%ylimx = ylim;
hold on;
%----Plot ROI & labels----
data2 = data1(data1.ROI>0,:);
data2 = datasample(data2,10000,'replace',false);
colors = repmat([0.65 0.65 0.65],size(data2,1),1);
scatter(data2.Xt,data2.Yt,8,colors,'fill');
% for i = 1:6
% x1 = mean(data1{data1.ROI==i,'Xt'});
% y1 = mean(data1{data1.ROI==i,'Yt'});
% text(x1,y1,num2str(i),'FontSize',20,'Color','k');
% end
set(gca,'XAxisLocation','bottom','YAxisLocation','left','ydir','reverse');
%---Plot budding & labels---
data2 = data1(data1.budding>0,:);
colors = repmat([0.5 0.5 0.5],size(data2,1),1);
scatter(data2.Xt,data2.Yt,8,colors,'fill');
%text(mean(data2.Xt),mean(data2.Yt),'TB','FontSize',25,'Color','k');
%---Plot marker -----
data3 = data1(data1{:,marker1},:);
data3 = datasample(data3,20000,'replace',false);
scatter(data3.Xt,data3.Yt,3,'m','fill');
dscatter(data3.Xt,data3.Yt,'PLOTTYPE','CONTOUR');
legend off;
daspect([1 1 1]);
for i = 1:6
x1 = mean(data1{data1.ROI==i,'Xt'});
y1 = mean(data1{data1.ROI==i,'Yt'});
text(x1,y1,num2str(i),'FontSize',20,'Color','k');
end
xlim([50 16000]);
ylim([0 18000]);
text(mean(data2.Xt),mean(data2.Yt),'TB','FontSize',25,'Color','k');
legend('All','ROIs','Budding','CD45+','Density');
set(gca,'xticklabel',[]);
set(gca,'yticklabel',[]);
%% display cell type (CD8+ & CD4+FOXP3+) & ROI (New 2022) ==> Fig7B
name1 = 'TNP097';
data1 = eval(strcat('data',name1));
figure('units','normalized','outerposition',[0.5 0 0.5 1]);
%-----plot all cells--------
data4 = datasample(data1,50000);
colors = repmat([0.8 0.8 0.8],size(data4,1),1);
scatter(data4.Xt,data4.Yt,6,colors,'fill');
%xlims = xlim;
%ylimx = ylim;
hold on;
%----Plot ROI & labels----
data2 = data1(data1.ROI>0,:);
data2 = datasample(data2,10000,'replace',false);
colors = repmat([0.65 0.65 0.65],size(data2,1),1);
scatter(data2.Xt,data2.Yt,8,colors,'fill');
set(gca,'XAxisLocation','bottom','YAxisLocation','left','ydir','reverse');
%---Plot budding & labels---
data2 = data1(data1.budding>0,:);
colors = repmat([0.5 0.5 0.5],size(data2,1),1);
scatter(data2.Xt,data2.Yt,8,colors,'fill');
%text(mean(data2.Xt),mean(data2.Yt),'TB','FontSize',25,'Color','k');
%---Plot marker 1-----
data3 = data1(data1.Celltype==29,:);
%data3 = datasample(data3,20000);
scatter(data3.Xt,data3.Yt,3,'c','fill');
%---Plot marker 1-----
data3 = data1(data1.Celltype==21,:);
%data3 = datasample(data3,20000,'replace',false);
scatter(data3.Xt,data3.Yt,3,'m','fill');
dscatter(data3.Xt,data3.Yt,'PLOTTYPE','CONTOUR');
daspect([1 1 1]);
for i = 1:6
x1 = mean(data1{data1.ROI==i,'Xt'});
y1 = mean(data1{data1.ROI==i,'Yt'});
text(x1,y1,num2str(i),'FontSize',20,'Color','k');
end
xlim([50 16000]);
ylim([0 18000]);
text(mean(data2.Xt),mean(data2.Yt),'TB','FontSize',25,'Color','k');
legend('All','ROIs','Budding','CD8+','CD4+FOXP3+','Density');
set(gca,'xticklabel',[]);
set(gca,'yticklabel',[]);
set(gcf,'color','w');
%% display cell type (PD-L1+) & ROI (New 2022) ==> Fig7C
name1 = 'TNP097';
data1 = eval(strcat('data',name1));
figure('units','normalized','outerposition',[0.5 0 0.5 1]);
%-----plot all cells--------
data4 = datasample(data1,50000);
colors = repmat([0.8 0.8 0.8],size(data4,1),1);
scatter(data4.Xt,data4.Yt,6,colors,'fill');
%xlims = xlim;
%ylimx = ylim;
hold on;
%----Plot ROI & labels----
data2 = data1(data1.ROI>0,:);
data2 = datasample(data2,10000,'replace',false);
colors = repmat([0.65 0.65 0.65],size(data2,1),1);
scatter(data2.Xt,data2.Yt,8,colors,'fill');
set(gca,'XAxisLocation','bottom','YAxisLocation','left','ydir','reverse');
%---Plot budding & labels---
data2 = data1(data1.budding>0,:);
colors = repmat([0.5 0.5 0.5],size(data2,1),1);
scatter(data2.Xt,data2.Yt,8,colors,'fill');
%text(mean(data2.Xt),mean(data2.Yt),'TB','FontSize',25,'Color','k');
%---Plot marker -----
data3 = data1(data1.PDL1p,:);
data3 = datasample(data3,20000,'replace',false);
scatter(data3.Xt,data3.Yt,3,'m','fill');
dscatter(data3.Xt,data3.Yt,'PLOTTYPE','CONTOUR');
legend off;
daspect([1 1 1]);
for i = 1:6
x1 = mean(data1{data1.ROI==i,'Xt'});
y1 = mean(data1{data1.ROI==i,'Yt'});
text(x1,y1,num2str(i),'FontSize',20,'Color','k');
end
xlim([50 16000]);
ylim([0 18000]);
text(mean(data2.Xt),mean(data2.Yt),'TB','FontSize',25,'Color','k');
legend('All','ROIs','Budding','PD-L1+','Density');
set(gca,'xticklabel',[]);
set(gca,'yticklabel',[]);
%% display PD-1::PD-L1 interaction & ROI (New 2022) ==> Fig7D
name1 = 'TNP097';
data1 = eval(strcat('data',name1));
figure('units','normalized','outerposition',[0.5 0 0.5 1]);
%-----plot all cells--------
data4 = datasample(data1,50000);
colors = repmat([0.8 0.8 0.8],size(data4,1),1);
scatter(data4.Xt,data4.Yt,6,colors,'fill');
%xlims = xlim;
%ylimx = ylim;
hold on;
%----Plot ROI & labels----
data2 = data1(data1.ROI>0,:);
data2 = datasample(data2,10000,'replace',false);
colors = repmat([0.65 0.65 0.65],size(data2,1),1);
scatter(data2.Xt,data2.Yt,8,colors,'fill');
set(gca,'XAxisLocation','bottom','YAxisLocation','left','ydir','reverse');
%---Plot budding & labels---
data2 = data1(data1.budding>0,:);
colors = repmat([0.5 0.5 0.5],size(data2,1),1);
scatter(data2.Xt,data2.Yt,8,colors,'fill');
%text(mean(data2.Xt),mean(data2.Yt),'TB','FontSize',25,'Color','k');
%---Plot marker 2(PD-L1+)-----
data3 = data1(data1.PDL1p,:);
%data3 = datasample(data3,20000,'replace',false);
scatter(data3.Xt,data3.Yt,3,'m','fill');
%---Plot marker 1(PD-1+)-----
data3 = data1(data1.PD1p,:);
data3 = datasample(data3,20000);
%data3 = datasample(data3,20000);
scatter(data3.Xt,data3.Yt,3,'c','fill');
%---Plot interaction-----
data3 = data1(data1.PD1intPDL1,:);
dscatter(data3.Xt,data3.Yt,'PLOTTYPE','CONTOUR');
daspect([1 1 1]);
for i = 1:6
x1 = mean(data1{data1.ROI==i,'Xt'});
y1 = mean(data1{data1.ROI==i,'Yt'});
text(x1,y1,num2str(i),'FontSize',20,'Color','k');
end
xlim([50 16000]);
ylim([0 18000]);
text(mean(data2.Xt),mean(data2.Yt),'TB','FontSize',25,'Color','k');
legend('All','ROIs','Budding','PD-L1+','PD-1+','Interaction');
set(gca,'xticklabel',[]);
set(gca,'yticklabel',[]);
set(gcf,'color','w');
%% display PD-1::PD-L1 interaction & ROI (New 2022) ==> Fig7K
name1 = 'TNP097';
data1 = eval(strcat('data',name1));
figure('units','normalized','outerposition',[0.5 0 0.5 1]);
%-----plot all cells--------
data4 = datasample(data1,50000);
colors = repmat([0.8 0.8 0.8],size(data4,1),1);
scatter(data4.Xt,data4.Yt,6,colors,'fill');
%xlims = xlim;
%ylimx = ylim;
hold on;
%----Plot ROI & labels----
data2 = data1(data1.ROI>0,:);
data2 = datasample(data2,10000,'replace',false);
colors = repmat([0.65 0.65 0.65],size(data2,1),1);
scatter(data2.Xt,data2.Yt,8,colors,'fill');
set(gca,'XAxisLocation','bottom','YAxisLocation','left','ydir','reverse');
%---Plot budding & labels---
data2 = data1(data1.budding>0,:);
colors = repmat([0.5 0.5 0.5],size(data2,1),1);
scatter(data2.Xt,data2.Yt,8,colors,'fill');
%---Plot marker 2(PD-L1+)-----
data3 = data1(data1.Celltype==4,:);
scatter(data3.Xt,data3.Yt,5,'m','fill');
%---Plot marker 1(PD-1+)-----
data3 = data1(data1.Celltype==30,:);
scatter(data3.Xt,data3.Yt,5,'c','fill');
%---Plot interaction-----
data3 = data1(data1.Link_4_30,:);
dscatter(data3.Xt,data3.Yt,'PLOTTYPE','CONTOUR');
daspect([1 1 1]);
for i = 1:6
x1 = mean(data1{data1.ROI==i,'Xt'});
y1 = mean(data1{data1.ROI==i,'Yt'});
text(x1,y1,num2str(i),'FontSize',20,'Color','k');
end
xlim([50 16000]);
ylim([0 18000]);
text(mean(data2.Xt),mean(data2.Yt),'TB','FontSize',25,'Color','k');
legend('All','ROIs','Budding','panCK+PD-L1+','CD8+PD-1+','Interaction');
set(gca,'xticklabel',[]);
set(gca,'yticklabel',[]);
set(gcf,'color','w');
%% Single marker comparison (only PD-L1+ pair)==> Fig7J
figure('units','normalized','outerposition',[0.5 0.5 0.25 0.5]);
name1 = 'HLA_A';
marker1 = strcat('mean_',name1,'p');
list1 = sumPDL1i{:,marker1};
list2 = sumPDL1ni{:,marker1};
myviolin2(list1*100,list2*100,'Int.','non-int.',true);
ytickformat('percentage');
hold on;
line([1,2],[list1(6)*100,list2(6)*100],'Color','r','LineWidth',2);
title(strcat(name1,'+'),'Interpreter','none');
list1 = sumPDL1i{:,marker1};
list2 = sumPDL1ni{:,marker1};
myviolin2(list1*100,list2*100,'Int.','non-int.',true);
ytickformat('percentage');
hold on;
%line([1,2],[list1(5)*100,list2(5)*100],'Color','r','LineWidth',2);
title(strcat(name1,'+'),'Interpreter','none');