forked from labsyspharm/CRC_atlas_2022
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Figure6.m
219 lines (172 loc) · 5.49 KB
/
Figure6.m
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
%% Plot 2D TLS with 3D outlines (#097 only) ==> Fig6A
data1 = dataTNP097;
figure('units','normalized','outerposition',[0.5 0 0.5 1]);
data2 = datasample(data1,50000,'replace',false);
scatter(data2.Xt,data2.Yt,5,repmat([0.8 0.8 0.8],50000,1),'fill');
xlims = xlim;
ylims = ylim;
hold on;
data4 = data1(data1.ROI>0,:);
data4 = datasample(data4,20000,'replace',false);
scatter(data4.Xt,data4.Yt,6,repmat([0.65 0.65 0.65],20000,1),'fill');
data3 = data1(data1.TLS>0,:);
CycIF_tumorview(data3,'TLS',12);
daspect([1 1 1]);
xlim(xlims);
ylim(ylims);
grid off;
title('2D TLS in #097');
%% Plot 3D network ==> Fig6B
figure('units','normalized','outerposition',[0.5 0 0.5 1]);
%---Plot all cells---
data1 = allsample_re;
data1 = datasample(data1,50000,'replace',false);
scatter(data1.Xtt,data1.Ytt,5,repmat([0.8 0.8 0.8],50000,1),'fill');
xlims = xlim;
ylims = ylim;
hold on;
data1 = allsample_re(allsample_re.ROI>0,:);
data1 = datasample(data1,20000,'replace',false);
scatter(data1.Xtt,data1.Ytt,5,repmat([0.65 0.65 0.65],20000,1),'fill');
xlim(xlims);
ylim(ylims);
%----Plot TLS, colored by clusters----
data2 = allTLS;
CycIF_tumorviewTTX(data2,'label1',9,50000);
xlim(xlims);
ylim(ylims);
grid off;
daspect([1 1 1]);
title('3D Networks (2D projected)');
set(gcf,'color','w');
list1 = [5,7,11,13,14,62,71];
name1 = {'A','B','C','D','E','F','G'};
for i = 1:length(list1)
data3 = allTLS(allTLS.label1==list1(i),:);
%k = boundary(data3.Xtt,data3.Ytt);
%plot(data3.Xtt(k),data3.Ytt(k),'k','LineWidth',1);
text(mean(data3.Xtt),mean(data3.Ytt),name1{i},'FontSize',18);
end
%% TLS cluster heatmap (CRC1) ==> Fig6D
sum1 = sumAllTLS4;
sum1{:,strcat('mean_',labelp2)} = zscore(sum1{:,strcat('mean_',labelp2)});
sum2 = varfun(@mean,sum1,'GroupingVariables','idx1');
figure('units','normalized','outerposition',[0.4 0.4 0.6 0.6]);
subplot(1,10,1:8.5);
imagesc(sum2{:,strcat('mean_mean_',labelp2)});
colormap(redbluecmap);
set(gca,'xtick',1:length(labelp2));
set(gca,'xticklabels',labelp3);
set(gca,'xticklabelrotation',90);
ylabel('TLS cluster');
caxis([-1.5 1.5]);
subplot(1,10,9:10);
barh(sum2.GroupCount);
set(gca,'ytick',[]);
%set(get(h,'Parent'),'xdir','r')
ylim([0.5 7.5]);
xlabel('TLS count');
text(sum2.GroupCount,1:7,num2str(sum2.GroupCount));
set(gca, 'YDir','reverse')
%% Plot 3D network (outline big clusters) ==> Fig6E (new version)
figure('units','normalized','outerposition',[0.5 0 0.5 1]);
%---Plot all cells---
data1 = allsample_re;
data1 = datasample(data1,50000,'replace',false);
scatter(data1.Xtt,data1.Ytt,5,repmat([0.8 0.8 0.8],50000,1),'fill');
xlims = xlim;
ylims = ylim;
%----Plot TLS, colored by clusters----
hold on;
data2 = allTLS;
CycIF_tumorviewTTX(data2,'idx1',4,0);
colormap(jet(7));
colorbar off;
xlim(xlims);
ylim(ylims);
grid off;
daspect([1 1 1]);
%----Outline large 3D networks----
list1 = [5,7,11,13,14,62,71];
name1 = {'A','B','C','D','E','F','G'};
for i = 1:length(list1)
data3 = allTLS(allTLS.label1==list1(i),:);
k = boundary(data3.Xtt,data3.Ytt);
plot(data3.Xtt(k),data3.Ytt(k),'k','LineWidth',1);
text(mean(data3.Xtt),mean(data3.Ytt),name1{i},'FontSize',18);
end
set(gcf,'color','w');
title('TLS network (colored by clusters)');
%% Generate color legends ==> Fig 6E
figure,scatter(ones(7,1),1:7,150,1:7,'fill');
colormap(jet(7));
xlim([0.5 1.5]);
ylim([0.5 7.5]);
text(ones(7,1)+0.05,1:7,num2str((1:7)'),'FontSize',20,'HorizontalAlign','left');
box off;
set(gca,'XColor', 'none','YColor','none')
set(gcf,'color','w');
%% 3D view of block 7, with boundary lines ==> Fig6G
data3 = allTLS(allTLS.label1 ==7,:);
figure('units','normalized','outerposition',[0.5 0 0.5 1]);
scatter3(data3.Xtt,data3.Ytt,data3.Ztt,5,data3.idx1,'fill');
set(gca,'XAxisLocation','bottom','YAxisLocation','left','ydir','reverse');
hold on;
colormap(jet(7));
daspect([1 1 0.15]);
%colorbar;
set(gcf,'color','w');
zlim([0 600]);
ylim([10500 15500]);
xlim([5500 13500]);
view(-16,28);
temp1 = tabulate(data3.slice);
temp1 = temp1(temp1(:,2)>0,:);
for i = 1:size(temp1,1)
slice = temp1(i,1);
data4 = data3(data3.slice == slice,:);
temp2 = tabulate(data4.TLS);
temp2 = temp2(temp2(:,2)>0,:);
for j = 1:size(temp2,1)
TLS = temp2(j,1);
data5 = data4(data4.TLS == TLS,:);
k = boundary(data5.Xtt,data5.Ytt);
%plot3(data5.Xtt(k),data5.Ytt(k),repmat(data5.Ztt(1),length(k),1),'k','LineWidth',1.5);
scatter3(data5.Xtt(k),data5.Ytt(k),repmat(data5.Ztt(1),length(k),1),5,'k','fill');
plot3(data5.Xtt(k),data5.Ytt(k),repmat(data5.Ztt(1),length(k),1),'k','LineWidth',1.5);
end
end
%% 3D view of block 7, Shu's PCA version ==> Fig6H
data3 = allTLS(allTLS.label1 ==7,:);
temp1 = sumAllTLS4(:,{'slice','TLS','PCA1','PCA2','PCA3'});
data3 = join(data3,temp1,'keys',{'slice','TLS'});
% --------------
figure('units','normalized','outerposition',[0.5 0 0.5 1]);
scatter3(data3.Xtt,data3.Ytt,data3.Ztt,3,data3.PCA1,'fill');
set(gca,'XAxisLocation','bottom','YAxisLocation','left','ydir','reverse');
colormap(cool);
daspect([1 1 0.15]);
%colorbar;
set(gcf,'color','w');
title('Color by PC1');
caxis([-3 3]);
colorbar;
zlim([0 600]);
ylim([10500 15000]);
xlim([5500 14000]);
view(-16,28);
% ----------------
figure('units','normalized','outerposition',[0.5 0 0.5 1]);
scatter3(data3.Xtt,data3.Ytt,data3.Ztt,3,data3.PCA2,'fill');
set(gca,'XAxisLocation','bottom','YAxisLocation','left','ydir','reverse');
colormap(cool);
daspect([1 1 0.15]);
%colorbar;
set(gcf,'color','w');
title('Color by PC2');
caxis([-2.5 2.5]);
colorbar;
zlim([0 600]);
ylim([10500 15000]);
xlim([5500 14000]);
view(-16,28);