-
Notifications
You must be signed in to change notification settings - Fork 10
/
Copy pathsc_scattermarker.m
314 lines (276 loc) · 9.87 KB
/
sc_scattermarker.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
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
function [h1, h2] = sc_scattermarker(X, genelist, ...
s, targetg, methodid, ...
sz, showcam)
% SC_SCATTERMARKER(X,genelist,g,s,methodid)
%
% USAGE:
% s=sc_tsne(X,3);
% g=["AGER","SFTPC","SCGB3A2","TPPP3"];
% sc_scattermarker(X,genelist,s,genelist(1));
%
% INPUTS:
% X: Numeric matrix of gene expression data (genes x cells).
% genelist: Cell array or string array of gene names (length = rows of X).
% s: Matrix of 2D or 3D coordinates for cells (cells x 2 or cells x 3).
% targetg: Gene(s) to visualize (string, char, or cell array).
% methodid: (Optional) Visualization method (1 to 5).
% sz: (Optional) Marker size for scatter plots (default = 5).
% showcam: (Optional) Enable/disable camera controls (default = true).
%
% OUTPUTS:
% h1: Handle to the primary axes.
% h2: Handle to the secondary axes (if applicable).
import gui.*
h1 = [];
h2 = [];
if nargin < 4
error('sc_scattermarker(X, genelist, s, g)');
end
if ~isnumeric(X) || ~ismatrix(X)
error('Input X must be a numeric matrix.');
end
if size(X, 1) ~= length(genelist)
error('The number of rows in X must match the length of genelist.');
end
if isvector(s) || isscalar(s)
error('S should be a matrix.');
end
if nargin < 7, showcam = true; end
if nargin < 6 || isempty(sz), sz = 5; end
if nargin < 5, methodid = 1; end
if iscell(targetg)
for k = 1:length(targetg)
figure;
sc_scattermarker(X, genelist, s, targetg{k}, methodid, sz);
end
elseif isstring(targetg) && ~isStringScalar(targetg)
for k = 1:length(targetg)
figure;
sc_scattermarker(X, genelist, s, targetg(k), methodid, sz);
end
elseif isStringScalar(targetg) || ischar(targetg)
if ismember(targetg, genelist)
x = s(:, 1);
y = s(:, 2);
if min(size(s)) == 2
z = [];
else
z = s(:, 3);
end
% c=log2(1+X(genelist==targetg,:));
% c = X(genelist == targetg, :);
idx = strcmp(genelist, targetg);
c = full(X(idx, :));
titxt = '';
switch methodid
case 1
% within_stemscatter(x, y, c);
% assignin("base","x",x)
% assignin("base","y",y)
% assignin("base","c",c)
gui.i_stemscatter([x, y], c);
h1 = gca;
grid on
title(targetg)
titxt = gui.i_getsubtitle(c);
subtitle(titxt);
case 2
if isempty(z)
scatter(x, y, sz, c, 'filled');
else
scatter3(x, y, z, sz, c, 'filled');
end
h1 = gca;
set(h1, 'XTickLabel', []);
set(h1, 'YTickLabel', []);
set(h1, 'ZTickLabel', []);
grid on
title(targetg)
titxt = gui.i_getsubtitle(c);
subtitle(titxt);
case 3
case 4
h1 = subplot(1, 2, 1);
sc_scattermarker(X, genelist, s, targetg, 2, sz, false);
h2 = subplot(1, 2, 2);
sc_scattermarker(X, genelist, s, targetg, 1, sz, false);
hFig = gcf;
hFig.Position(3) = hFig.Position(3) * 2;
case 5 % ============ 5
if size(s, 2) >= 3
x = s(:, 1);
y = s(:, 2);
z = s(:, 3);
is2d = false;
else
x = s(:, 1);
y = s(:, 2);
z = zeros(size(x));
is2d = true;
end
% explorer2IDX = y;
% assignin('base', 'explorer2IDX', explorer2IDX);
% c=log2(1+X(genelist==g,:));
h1 = subplot(1, 2, 1);
s1 = scatter3(x, y, z, sz, c, 'filled');
set(h1, 'XTickLabel', []);
set(h1, 'YTickLabel', []);
set(h1, 'ZTickLabel', []);
grid on
% h1.YDataSource='explorer2IDX';
title(targetg)
titxt = gui.i_getsubtitle(c);
subtitle(titxt);
h2 = subplot(1, 2, 2);
s2 = stem3(x, y, c, 'marker', 'none', 'color', 'm');
hold on;
scatter3(x, y, zeros(size(y)), 5, c, 'filled');
%[ayy,byy]=view(h2);
% h2.YDataSource='explorer2IDX';
% hLD = linkdata('on');
set(h2, 'XTickLabel', []);
set(h2, 'YTickLabel', []);
%set(h2,'ZTickLabel',[]);
grid on
if ~is2d
% evalin('base', 'h=findobj(gcf,''type'',''axes'');');
evalin('base', 'linkprop(findobj(gcf,''type'',''axes''), {''CameraPosition'',''CameraUpVector''});');
evalin('base', 'rotate3d on');
end
hFig = gcf;
hFig.Position(3) = hFig.Position(3) * 1.8;
if ~is2d
view(h1, 3);
else
view(h2, 3);
end
end % end of switch of methodid
a = getpref('scgeatoolbox', 'prefcolormapname', 'autumn');
gui.i_setautumncolor(c, a, true, any(c==0));
ori_c = c;
title(targetg);
subtitle(titxt);
% subtitle(sprintf('(%s/%s = %.2f%% nonzero)', ...
% num2bankScalar(sum(c > 0)), ...
% num2bankScalar(numel(c)), ...
% 100 * sum(c > 0) ./ numel(c)));
% pt = uipushtool(defaultToolbar);
% tx.ButtonDownFcn=@dispgname;
if showcam
hFig = gcf;
tb = uitoolbar(hFig);
pkg.i_addbutton2fig(tb, 'off', @gui.i_linksubplots, 'keyframes-minus.jpg', 'Link subplots');
pkg.i_addbutton2fig(tb, 'on', {@i_genecards, targetg}, 'www.jpg', 'GeneCards...');
pkg.i_addbutton2fig(tb, 'on', {@i_PickColorMap, c}, 'plotpicker-compass.gif', 'Pick new color map...');
pkg.i_addbutton2fig(tb, 'off', @i_RescaleExpr, 'IMG00074.GIF', 'Rescale expression level [log2(x+1)]');
pkg.i_addbutton2fig(tb, 'off', @i_ResetExpr, 'plotpicker-geobubble2.gif', 'Reset expression level');
pkg.i_addbutton2fig(tb, 'off', {@gui.i_savemainfig, 3}, "powerpoint.gif", 'Save Figure to PowerPoint File...');
end
else
warning('%s no expression', targetg);
end
if showcam
gui.gui_3dcamera(tb, targetg);
end
end
function i_RescaleExpr(~, ~)
c = log2(1+c);
[ax, bx] = view(h2);
delete(s2);
s2 = stem3(h2, x, y, c, 'marker', 'none', 'color', 'm');
view(h2, ax, bx);
%title(h2,titxt);
title(h2, targetg);
subtitle(h2, titxt);
[ax, bx] = view(h1);
delete(s1);
s1 = scatter3(h1, x, y, z, sz, c, 'filled');
view(h1, ax, bx);
colorbar(h1);
%title(h1,titxt);
title(h1, targetg);
subtitle(h1, titxt);
end
function i_ResetExpr(~, ~)
c = ori_c;
delete(s2);
s2 = stem3(h2, x, y, c, 'marker', 'none', 'color', 'm');
%view(h2,ayy,byy);
delete(s1);
s1 = scatter3(h1, x, y, z, sz, c, 'filled');
%view(h1,axx,bxx);
title(h1, targetg);
subtitle(h1, titxt);
title(h2, targetg);
subtitle(h2, titxt);
end
end
function i_genecards(~, ~, g)
web(sprintf('https://www.genecards.org/cgi-bin/carddisp.pl?gene=%s', g));
end
function i_PickColorMap(~, ~, c)
list = {'parula', 'turbo', 'hsv', 'hot', 'cool', 'spring', ...
'summer', 'autumn (default)', ...
'winter', 'jet'};
[indx, tf] = listdlg('ListString', list, 'SelectionMode', 'single', ...
'PromptString', 'Select a colormap:', 'ListSize', [220, 300]);
if tf == 1
a = list{indx};
if strcmp(a, 'autumn (default)')
a = 'autumn';
end
gui.i_setautumncolor(c, a);
setpref('scgeatoolbox', 'prefcolormapname', a);
end
end
% function callback_linksubplots(~,~)
% evalin('base', 'h=findobj(gcf,''type'',''axes'');');
% evalin('base', 'hlink = linkprop(h,{''CameraPosition'',''CameraUpVector''});');
% evalin('base', 'rotate3d on');
% end
% function i_setautumncolor(c)
% a = colormap('autumn');
% a(1, :) = [.8 .8 .8];
% if numel(unique(c)) == 1
% for kk = 1:size(a, 1)
% a(kk, :) = [.8 .8 .8];
% end
% end
% colormap(a);
% end
function selectcolormapeditor(~, ~)
% colormapeditor;
end
% function [str] = num2bankScalar(num)
% % https://www.mathworks.com/matlabcentral/answers/96131-is-there-a-format-in-matlab-to-display-numbers-such-that-commas-are-automatically-inserted-into-the
% num = floor(num*100) / 100;
% str = num2str(num);
% k = find(str == '.', 1);
% if isempty(k)
% % str=[str,'.00'];
% end
% % FIN = min(length(str),find(str == '.')-1);
% FIN = length(str);
% for i = FIN - 2:-3:2
% str(i + 1:end + 1) = str(i:end);
% str(i) = ',';
% end
% end
function within_stemscatter(x, y, z)
if nargin < 3
x = randn(300, 1);
y = randn(300, 1);
z = abs(randn(300, 1));
end
if isempty(z)
warndlg('No expression');
scatter(x, y, '.');
else
stem3(x, y, z, 'marker', 'none', 'color', 'm');
hold on;
scatter(x, y, 10, z, 'filled');
hold off;
end
% [caz,cel]=view;
% view([-45,-45,300]);
end