Plot density of transposon over the whole genome

Post date: May 18, 2016 4:18:22 PM

The first common analysis that you may want to do is to plot the transposon density over the whole genome (to find hot- or cold-spot of transposon insertion):

%%%%plot density on chromosome

chrcoord=infobam.SequenceDictionary(1).SequenceLength;

centromerecoord=cell2mat(gff(strmatch('centromere',gff(:,3),'exact'),4));

for ii=2:16

chrcoord(ii)=infobam.SequenceDictionary(ii).SequenceLength+chrcoord(ii-1);

centromerecoord(ii)=centromerecoord(ii)+chrcoord(ii-1)

end

% hist(double(tncoordinates_copy(:,2)),[1:10000:14000000])

% hold on

% plot(chrcoord,[1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1],'.r')

% plot(centromerecoord,300*[1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1],'.g');

            %%%OPTIONAL! to space out the plot

            densityplotccord=tncoordinates_copy;

            densityplotccord(find(densityplotccord(:,1)==2),2)=densityplotccord(find(densityplotccord(:,1)==2),2)+100000;

            densityplotccord(find(densityplotccord(:,1)==3),2)=densityplotccord(find(densityplotccord(:,1)==3),2)+200000;

            densityplotccord(find(densityplotccord(:,1)==4),2)=densityplotccord(find(densityplotccord(:,1)==4),2)+300000;

            densityplotccord(find(densityplotccord(:,1)==5),2)=densityplotccord(find(densityplotccord(:,1)==5),2)+400000;

            densityplotccord(find(densityplotccord(:,1)==6),2)=densityplotccord(find(densityplotccord(:,1)==6),2)+500000;

            densityplotccord(find(densityplotccord(:,1)==7),2)=densityplotccord(find(densityplotccord(:,1)==7),2)+600000;

            densityplotccord(find(densityplotccord(:,1)==8),2)=densityplotccord(find(densityplotccord(:,1)==8),2)+700000;

            densityplotccord(find(densityplotccord(:,1)==9),2)=densityplotccord(find(densityplotccord(:,1)==9),2)+800000;

            densityplotccord(find(densityplotccord(:,1)==10),2)=densityplotccord(find(densityplotccord(:,1)==10),2)+900000;

            densityplotccord(find(densityplotccord(:,1)==11),2)=densityplotccord(find(densityplotccord(:,1)==11),2)+1000000;

            densityplotccord(find(densityplotccord(:,1)==12),2)=densityplotccord(find(densityplotccord(:,1)==12),2)+1100000;

            densityplotccord(find(densityplotccord(:,1)==13),2)=densityplotccord(find(densityplotccord(:,1)==13),2)+1200000;

            densityplotccord(find(densityplotccord(:,1)==14),2)=densityplotccord(find(densityplotccord(:,1)==14),2)+1300000;

            densityplotccord(find(densityplotccord(:,1)==15),2)=densityplotccord(find(densityplotccord(:,1)==15),2)+1400000;

            densityplotccord(find(densityplotccord(:,1)==16),2)=densityplotccord(find(densityplotccord(:,1)==16),2)+1500000;

            densityplotccord(find(densityplotccord(:,1)==17),2)=densityplotccord(find(densityplotccord(:,1)==17),2)+1600000;

            for ii=2:16

                chrcoord(ii)=chrcoord(ii)+(ii-1)*100000

                centromerecoord(ii)=centromerecoord(ii)+(ii-1)*100000;

end

            hist(double(densityplotccord(:,2)),[1:10000:14000000])

            hold on

            plot(chrcoord,[1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1],'.r')

            plot(centromerecoord,300*[1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1],'.g');

            %%%%%%%%%%%%%%%%%%%%%%%%%%%

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