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Plot_DotComps2_Kr.m
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Plot_DotComps2_Kr.m
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%% Plot_DotComps2_Kr.m %%
%
% Analyzing New Shadow data
%
%
% Alistair Boettiger Date Begun: 03/05/10
% Levine Lab Functional Since: 09/13/10
% Last Modified: 03/07/11
%% Description
% comparison
%
%
%% Updates
% Modified 10/18 to also count ectopic nuclei
% Modified 02/28/11 to use cityscape and cumulative sum.
% Modified 03/07/11 to compare total reporter cells to total endogneous.
% Modified 03/16/11 to compute fraction of region activated for both
% endogenous and each reporter (relative to endogenous region).
%% Source Code
clear all;
folder = '/Volumes/Data/Lab Data/Shadow_data/Processed';
emb_roots = {'kr2enh_22C_LacZ_kr';
'krCD1_22C_LacZ_kr';
'krCD2_22C_LacZ_kr'
};
names = {'Kr 2 enhancers, 22C'; %
'Kr distal, 22C'; % CD1
'Kr proximal, 22C' % CD2
};
N = 40;
K = length(emb_roots);
G= length(names);
age_table = cell(1,K);
miss_cnt = cell(1,K);
miss_rate = cell(1,K);
nd = cell(1,K);
lowon = cell(1,K);
cell_var = cell(1,K);
ectop_cnt = cell(1,K);
ectop_rate = cell(1,K);
endog_cnt = cell(1,K);
rept_cnt = cell(1,K);
endog_frac = cell(1,K);
rept_frac = cell(1,K);
for z=1:K
miss_cnt{z} = zeros(N,1);
miss_rate{z} = zeros(N,1);
lowon{z} = zeros(N,1);
nd{z} = zeros(N,1);
age_table{z} = cell(N,2);
ectop_cnt{z} = zeros(N,1);
ectop_rate{z} = zeros(N,1);
endog_cnt{z} = zeros(N,1);
rept_cnt{z} = zeros(N,1);
endog_frac{z} = zeros(N,1);
rept_frac{z} = zeros(N,1);
end
xmin = .2; xmax = .9; ymin = .15; ymax = .4;
% as fractions of the original image dimensions.
for z=1:K % k=2;
for n= 1:N
if n<10
emb = ['0',num2str(n)];
else
emb = num2str(n);
end
try
load([folder,'/',emb_roots{z},emb,'_data.mat']);
% get the indices of all nuclei in green that are not also red.
% require these nuclei also fall in the 'region' for red nuclei.
miss_cnt{z}(n) = length(setdiff(pts2,pts1));
% miss_cnt{z}(n) = length(intersect(setdiff(pts2,pts1), ptr_nucin2));
% miss_cnt{z}(n) = anlz_major_reg(folder,emb_roots{z},emb );
endog_cnt{z}(n) = length(pts2);
rept_cnt{z}(n) = length(pts1);
miss_rate{z}(n) = miss_cnt{z}(n)/length(pts2);
% [lowon{z}(n),cell_var{z}(n)] = lowon_fxn(H,handles,nin2,ptr_nucin2,[emb_roots{z},emb],0);
ectop_cnt{z}(n) = length(intersect(setdiff(pts1,pts2),setdiff(ptr_nucin1,ptr_nucin2)'));
endog_frac{z}(n) = length(intersect(ptr_nucin2,pts2))/length(ptr_nucin2);
rept_frac{z}(n) = length(intersect(ptr_nucin1,pts1))/length(ptr_nucin2);
if length(H) > 2000
im_dim = 2048;
else
im_dim = 1024;
end
lims = round([xmin,xmax,ymin,ymax]*im_dim);
nd{z}(n) = NucDensity(cent,lims,0);
age_table{z}{n,1} = [folder,'/',emb_roots{z},emb,'_data.mat']; %
age_table{z}{n,2} = nd{z}(n);
ectop_rate{z}(n) = ectop_cnt{z}(n)/nd{z}(n);
catch ME
disp(ME.message);
end
end
end
close all;
data_folder = '/Users/alistair/Documents/Berkeley/Levine_Lab/Projects/Shadow Enhancers/Code_Data/';
save([data_folder,'kr_LacZ_data_031611']);
%save([data_folder,'kr_LacZ_data_030711']);
% save kr_LacZ_data2;
%save kr_LacZ_data_ect;
%%
%%
% clear all;
% data_folder = '/Users/alistair/Documents/Berkeley/Levine_Lab/Projects/Shadow Enhancers/Code_Data/';
% load([data_folder,'kr_LacZ_data_ect']);
%%
% load kr_LacZ_data_ect;
ND = cell2mat(nd);
emb_cycle = 4.8 + log2( nonzeros( sort(ND(:)) ) );
figure(10); clf; plot( emb_cycle ,'r.');
T_embs = length(nonzeros(ND(:))) ;
title(['kr embryos, N = ',num2str(T_embs) ],'FontSize',15);
set(gca,'FontSize',15); grid on;
set(gcf,'color','w'); ylabel('log_2(nuc density)'); xlabel('embryo number');
ylim([10,14.99]); xlim([0,T_embs + 10]);
%%
cc14 =cell(1,G); cc13 = cell(1,G); cc12 = cell(1,G); cc11 = cell(1,G); cc10 = cell(1,G); cc9 = cell(1,G);
for z=1:G
logage = 4.8 + log2( ND(:,z) );
cc14{z} = logage >14;
cc13{z} = logage <14 & logage> 13;
cc12{z} = logage <13 & logage > 12;
cc11{z} = logage <12 ;
end
%% Fraction of missing nuclei
F = 14;
xlab = 'fraction of missed nuclei';
names = {'Kr 2 enhancers, 22C'; %
'Kr distal, 22C'; % CD1
'Kr proximal, 22C' % CD2
};
colordef white;
plot_miss = cell(1,G);
for k=1:G; plot_miss{k} = miss_rate{k}(cc14{k}); end
data = plot_miss;
Ts = length(data);% number of tracks
pW = zeros(Ts);
pA = zeros(Ts);
for i=1:Ts
for j = 1:Ts
pW(i,j) = ranksum(data{i},data{j}); % Wilcox Rank Sum
pA(i,j)=anovan([data{i}',data{j}'],{[zeros(1,length(data{i})),ones(1,length(data{j}))]},'display','off'); % 2-way ANOVA
end
end
Wpvals = ['p_{CA} = ',num2str(pW(1,2),2), ' p_{CB} = ',num2str(pW(1,3),2) , ' p_{AB} = ',num2str(pW(2,3),2) ];
Apvals = ['p_{12} = ',num2str(pA(1,2),2), ' p_{13} = ',num2str(pA(1,3),2) , ' p_{23} = ',num2str(pA(2,3),2) ];
disp(['pairwise Wilcoxon rank sum: ', Wpvals]);
disp(['2-way ANOVA: ',Apvals]);
figure(1); clf;
cityscape(data,names,xlab,F);
figure(3); clf;
cumhist(data,names,xlab,F);
title(['pairwise Wilcoxon: ' Wpvals]);
set(gcf,'color','w');
disp([names{1}, ': ' ,num2str(median([data{1}])),'+/-',num2str(std([data{1}])), ' missing']);
disp([names{2}, ': ' ,num2str(median([data{2}])),'+/-',num2str(std([data{2}])), ' missing']);
disp([names{3}, ': ' ,num2str(median([data{3}])),'+/-',num2str(std([data{3}])), ' missing']);
%% Compare endog vs rept
F = 14;
xlab = 'expressing nuclei';
names = {'Kr 2 enhancers, Kr';
'Kr CD1, Kr'; % CD1
'Kr CD2, Kr' % CD2
'Kr 2 enhancers, LacZ';
'Kr CD1, LacZ'; % CD1
'Kr CD2, LacZ' % CD2
};
colordef white;
endog = cell(1,G);
rept = cell(1,G);
for k=1:G; endog{k} = endog_cnt{k}(cc14{k})./ND(cc14{k},k)/5; end
for k=1:G; rept{k} = rept_cnt{k}(cc14{k})./ND(cc14{k},k)/5; end
data = cat(2,endog,rept);
Ts = length(data);% number of tracks
pW = zeros(Ts);
pA = zeros(Ts);
for i=1:Ts
for j = 1:Ts
pW(i,j) = ranksum(data{i},data{j}); % Wilcox Rank Sum
pA(i,j)=anovan([data{i}',data{j}'],{[zeros(1,length(data{i})),ones(1,length(data{j}))]},'display','off'); % 2-way ANOVA
end
end
Wpvals = ['p_{14} = ',num2str(pW(1,4),2), ' p_{25} = ',num2str(pW(2,5),2) , ' p_{36} = ',num2str(pW(3,6),2) ];
Apvals = ['p_{14} = ',num2str(pA(1,4),2), ' p_{25} = ',num2str(pA(2,5),2) , ' p_{36} = ',num2str(pA(3,6),2) ];
disp(['pairwise Wilcoxon rank sum: ', Wpvals]);
disp(['2-way ANOVA: ',Apvals]);
figure(1); clf;
cityscape(data,names,xlab,F);
figure(3); clf;
cumhist(data,names,xlab,F);
title(['pairwise Wilcoxon: ' Wpvals]);
set(gcf,'color','w');
%% Ectopic expression rate
xlab = 'ectopic expression rate';
names = {'Kr 2 enhancers, 22C';
'Kr distal, 22C';
'Kr proximal, 22C'
};
plot_miss = cell(1,G);
for k=1:G; plot_miss{k} = ectop_rate{k}(cc14{k}); end
data = plot_miss;
Ts = length(data);% number of tracks
pW = zeros(Ts);
pA = zeros(Ts);
for i=1:Ts
for j = 1:Ts
pW(i,j) = ranksum(data{i},data{j}); % Wilcox Rank Sum
pA(i,j)=anovan([data{i}',data{j}'],{[zeros(1,length(data{i})),ones(1,length(data{j}))]},'display','off'); % 2-way ANOVA
end
end
Wpvals = ['p_{KI} = ',num2str(pW(1,2),2), ' p_{KJ} = ',num2str(pW(1,3),2) , ' p_{IJ} = ',num2str(pW(2,3),2) ];
Apvals = ['p_{12} = ',num2str(pA(1,2),2), ' p_{13} = ',num2str(pA(1,3),2) , ' p_{23} = ',num2str(pA(2,3),2) ];
disp(['pairwise Wilcoxon rank sum: ', Wpvals]);
disp(['2-way ANOVA: ',Apvals]);
figure(2); clf;
cityscape(data,names,xlab,F);
figure(4); clf;
cumhist(data,names,xlab,F);
title(['pairwise Wilcoxon: ' Wpvals]);
set(gcf,'color','w');
disp([names{1}, ': ' ,num2str(median([data{1}])),'+/-',num2str(std([data{1}])), ' missing']);
disp([names{2}, ': ' ,num2str(median([data{2}])),'+/-',num2str(std([data{2}])), ' missing']);
disp([names{3}, ': ' ,num2str(median([data{3}])),'+/-',num2str(std([data{3}])), ' missing']);
%% Fraction of Region Activated
F=14;
xlab = 'expressing nuclei';
names = {'Kr 2 enhancers, Kr';
'Kr distal, Kr'; % CD1
'Kr proximal, Kr' % CD2
'Kr 2 enhancers, LacZ';
'Kr distal, LacZ'; % CD1
'Kr proximal, LacZ' % CD2
};
colordef white;
endog = cell(1,G);
rept = cell(1,G);
for k=1:G; endog{k} = endog_frac{k}(cc14{k}); end
for k=1:G; rept{k} = rept_frac{k}(cc14{k}); end
data = cat(2,endog,rept);
Ts = length(data);% number of tracks
pW = zeros(Ts);
pA = zeros(Ts);
for i=1:Ts
for j = 1:Ts
pW(i,j) = ranksum(data{i},data{j}); % Wilcox Rank Sum
% pA(i,j)=anovan([data{i}',data{j}'],{[zeros(1,length(data{i})),ones(1,length(data{j}))]},'display','off'); % 2-way ANOVA
end
end
Wpvals = ['p_{14} = ',num2str(pW(1,4),2), ' p_{25} = ',num2str(pW(2,5),2) , ' p_{36} = ',num2str(pW(3,6),2) ];
Apvals = ['p_{14} = ',num2str(pA(1,4),2), ' p_{25} = ',num2str(pA(2,5),2) , ' p_{36} = ',num2str(pA(3,6),2) ];
disp(['pairwise Wilcoxon rank sum: ', Wpvals]);
disp(['2-way ANOVA: ',Apvals]);
figure(1); clf;
cityscape(data,names,xlab,F);
figure(3); clf;
cumhist(data,names,xlab,F);
title(['pairwise Wilcoxon: ' Wpvals]);
set(gcf,'color','w');
disp([names{1}, ': ' ,num2str(median([data{1}])),'+/-',num2str(std([data{1}])), ' missing']);
disp([names{2}, ': ' ,num2str(median([data{2}])),'+/-',num2str(std([data{2}])), ' missing']);
disp([names{3}, ': ' ,num2str(median([data{3}])),'+/-',num2str(std([data{3}])), ' missing']);
disp([names{4}, ': ' ,num2str(median([data{4}])),'+/-',num2str(std([data{4}])), ' missing']);
disp([names{5}, ': ' ,num2str(median([data{5}])),'+/-',num2str(std([data{5}])), ' missing']);
disp([names{6}, ': ' ,num2str(median([data{6}])),'+/-',num2str(std([data{6}])), ' missing']);