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[×ÊÔ´] Matlab ʵÏÖDGGEµçӾͼÆ×µÄ Ó¾µÀ¶àÑùÐÔÖ¸Êý£¬ÏàËÆÐÔÖ¸Êý£¬Ó¾µÀ¾ÛÀà·ÖÎö

ǰ¶Îʱ¼äдÁËÒ»µãMatlabµÄʹÓÃÐĵ㬴ó¼ÒÌÖÂÛºÜÈÈÁÒ£¬ÀïÃæ¹ØÓÚDGGE·ÖÎöµÄ²¿·Ö£¬ºÜ¶à³æÓÑÓÐÐËȤ£¬ÎÒÔÚÕâÀïÍêÕûÌù³öÀ´£¬¹©´ó¼Òѧϰ²Î¿¼¡£ÓÐʲô²»¶ÔµÄµØ·½»¶Ó­´ó¼ÒÅúÆÀÖ¸Õý¡£
http://muchong.com/bbs/viewthread.php?tid=4340045
http://www.dxy.cn/bbs/topic/13125577
1£¬Ê×ÏÈ Gel Pro Analyzer»òÕ߯äËûµçӾͼƬ·ÖÎöÈí¼þ¶ÔDGGEͼÆ×Êý¾Ý»¯
2£¬Gel Pro Analyzer½«DGGEͼÆ×Êý¾Ýµ¼Èëexcel
3£¬matlab¶ÁÈ¡excelµÄÊý¾Ý£¬ÓÃmatlab³ÌÐò·ÖÎö¡£
¸½¼þÖÐÓÐmatlab³ÌÐòÎļþºÍÓÃÓÚ¼ÆËãµÄÊý¾Ýamout.xls
CODE:
function DGGEdataanalysis(data)
%ÊäÈëµÄÊý¾ÝΪGel pro plus»òÕ߯äËûÄý½º·ÖÎö
%Èí¼þµÃµ½µÄ¹ØÓÚÓ¾µÀ±ÈÒÆÖµ»òÕ߸÷¸öÓ¾µÀÁÁ¶ÈÊý¾Ý
%ΪÁ˺óÐøËùÓзÖÎöÄܼÌÐø£¬½¨ÒéÓø÷¸öÓ¾µÀÁÁ¶ÈÊý¾Ý
%Shannon-Wiener¶àÑùÐÔÖ¸ÊýH=-¡ÆPln(P)
%ÏàËÆÐÔÖ¸ÊýS=2Lab/(La+Lb) LabΪa,bÓ¾µÀ¶¼´æÔÚµÄÌõ´øÊý
%example
%x1=xlsread('amout.xls')
%DGGEdataanalysis(x1)
%×÷Õߣºdbb627
%dbb627[at=923817]163.com[/at]
%2012 .6.1
%=========Ó¾µÀµÄ¶àÑùÐÔÖ¸Êý=====
X=data;
[m,n]=size(X);
S=cell(1,n);
for i=1:n
S{1,i}=['Lane',num2str(i)];
end

y1=DGGEdivsityindex(X)
figure;
lane=1:n;
bar(lane,y1)
set(gca,  'XTickLabel',S, 'XTick',lane);
title('¸÷Ó¾µÀµÄShannon-Wiener¶àÑùÐÔÖ¸Êý')
%========Ó¾µÀ¼äµÄÏàËÆÐÔÖ¸Êý====
y2=DGGEsimilaritymatrix(data)
%=====Ó¾µÀ¼äµÄ¾ÛÀà·ÖÎö=====
Z=linkage(y2,'average');
figure;
dendrogram(Z,n,'ORIENTATION','left','LABELS',S)
title('Ó¾µÀ¼äµÄ¾ÛÀà·ÖÎö')

function  y=DGGEsimilaritymatrix(X)
%¼ÆËãDGGEͼÆ×¸÷Ó¾µÀ¼äµÄÏàËÆÐÔÖ¸Êý×é³ÉÏàËÆ¾ØÕó
%ÊäÈë²ÎÊýxΪͼÆ×µÄÓ¾µÀµÄÁÁ¶È£¨»Ò¶È£©»òÕß±ÈÒÆÖµ¾ØÕó
[M,N]=size(X);
Xc=zeros(1,N);
Same=zeros(N,N);
similaritymatrix=zeros(N,N);
for i=1:N
    for j=1:M
        if X(j,i)>0
            Xc(1,i)=Xc(1,i)+1;
        end
    end
end
Xc;
for i=1:N
    for k=1:N
        for j=1:M
            if (X(j,i)>0)&(X(j,k)>0)
                Same(i,k)= Same(i,k)+1;
            end
        end
    end
end
Same;
for i=1:N
    for k=1:N
        similaritymatrix(i,k)=2*Same(i,k)/(Xc(1,i)+Xc(1,k));
    end
end
y=similaritymatrix;

function y=DGGEdivsityindex(x)
%¼ÆËãDGGEͼÆ×¸÷Ó¾µÀµÄ¶àÑùÐÔÖ¸Êý
%ÊäÈë²ÎÊýxΪͼÆ×µÄÓ¾µÀµÄÁÁ¶È£¨»Ò¶È£©¾ØÕó
[M,N]=size(x);
divsityindex=zeros(1,N);
for i=1:N
    P=x(:,i);
Sumc(i)=sum(P(P>0));
end
for i=1:N
    for j=1:M-1
        if x(j,i)>0
            divsityindex(1,i)=divsityindex(1,i)-x(j,i)/Sumc(i)*log(x(j,i)/Sumc(i));
        else
         divsityindex(1,i)=divsityindex(1,i)+0;
        end
    end
end
y=divsityindex;

[ À´×Ô¿ÆÑмÒ×å ²©Ê¿ÀÖÔ° ][ Last edited by dbb627 on 2012-6-1 at 17:27 ]
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  • ¸½¼þ 1 : amout.xls
  • 2012-06-01 16:24:29, 23.5 K
  • ¸½¼þ 2 : DGGEdataanalysis.m
  • 2012-06-01 17:27:04, 1.88 K

» ÊÕ¼±¾ÌûµÄÌÔÌûר¼­ÍƼö

dgge ѧϰ

» ²ÂÄãϲ»¶

» ±¾Ö÷ÌâÏà¹Ø¼ÛÖµÌùÍÆ¼ö£¬¶ÔÄúͬÑùÓаïÖú:

ÒÑÔÄ   »Ø¸´´ËÂ¥   ¹Ø×¢TA ¸øTA·¢ÏûÏ¢ ËÍTAºì»¨ TAµÄ»ØÌû
»ØÌûÖö¥ ( ¹²ÓÐ4¸ö )
¼ÆËãµÄ½á¹ûÈçÏÂ
y1 =

    2.4855    2.9451    2.8280    2.9727


y2 =

    1.0000    0.6341    0.7179    0.6341
    0.6341    1.0000    0.7391    0.7917
    0.7179    0.7391    1.0000    0.7826
    0.6341    0.7917    0.7826    1.0000

¸÷Ó¾µÀµÄShannon-Wiener¶àÑùÐÔÖ¸Êý



Ó¾µÀ¼äµÄ¾ÛÀà·ÖÎö

2Â¥2012-06-01 16:29:51
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ÒýÓûØÌû:
4Â¥: Originally posted by ÔÚÓêÖÐ at 2012-06-04 09:55:29
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26Â¥2015-01-26 20:50:26
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ÒýÓûØÌû:
2Â¥: Originally posted by dbb627 at 2012-06-01 16:29:51
¼ÆËãµÄ½á¹ûÈçÏÂ
y1 =

    2.4855    2.9451    2.8280    2.9727


y2 =

    1.0000    0.6341    0.7179    0.6341
    0.6341    1.0000    0.7391    0.7917
    0.7179    0.7391    1.0000    0.7 ...

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