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1、function[npos,handle]=SeqLogoFig(SEQ,varargin)%SeqLogoFig%AfunctionwhichwrapsaroundthebioinformaticsSeqLogocommand%andcreatesafigurewhichisactuallyaMATLABfigure.All%agruementsforSEQLOGOarepassedalongtotheseqlogocalculation.%Italsosupportsextraarguementsforplotting
2、.%%[npos,handle]=SeqLogoFig(SEQ);%%SEQAmultialignedsetofsequencesthatisacceptable%toSEQLOGO.%nposThepositionsthatwereactuallyplotted%handleAnaxishandletotheobjectthatwasplotted.%%ExtraArguements:%%'CUTOFF'Abit-cutofftousefordecidingwhichcolumnsto%plot.Anycolumnsth
3、athaveaMAXvaluewhichis%greaterthanCUTOFFwillbeprovided.Defaultsto%1.25forNTand2.25forAA.%%'TOP-N'PlotsonlythetopNcolumnsasrankedbythierMAX%bitconservation.%%'AXES_HANDLE'Anaxishandletoplottheseqlogointo.%%'INDS'Asetofindicestotoplot.Thisoverridesany%CUTOFForTOP-Nt
4、hatwereprovided%%%%%%ParsetheinputarguementsALPHA='nt';MAX_BITS=2.5;RES=[20080];CUTOFF=[];TOPN=[];rm_inds=[];colors=[];handle=[];npos=[];fori=1:2:length(varargin)ifstrcmpi(varargin{i},'alphabet')ALPHA=varargin{i+1};elseifstrcmpi(varargin{i},'cutoff')CUTOFF=varargi
5、n{i+1};%weneedtoremovethesesoseqlogodoesn'tgetconfusedrm_inds=[rm_indsi,i+1];%#ok<*AGROW>elseifstrcmpi(varargin{i},'colors')colors=varargin{i+1};rm_inds=[rm_indsi,i+1];elseifstrcmpi(varargin{i},'axes_handle')handle=varargin{i+1};rm_inds=[rm_indsi,i+1];elseifstrcmp
6、i(varargin{i},'top-n')TOPN=varargin{i+1};rm_inds=[rm_indsi,i+1];elseifstrcmpi(varargin{i},'inds')npos=varargin{i+1};rm_inds=[rm_indsi,i+1];endendif~isempty(rm_inds)varargin(rm_inds)=[];endifisempty(colors)colors=GetColors(ALPHA);endifstrcmpi(ALPHA,'nt')MAX_BITS=2.
7、5;elseifstrcmpi(ALPHA,'aa')MAX_BITS=4.5;endifisempty(CUTOFF)CUTOFF=0.5*MAX_BITS;end%%Calculatetheactualseqlogo.wm=seqlogo(SEQ,varargin{:},'displaylogo',false);%%Generatethelettersletters=wm{1};letter_wins=cell(size(letters));[~,loc]=ismember(letters,colors(:,1));l
8、oc(loc==0)=size(colors,1);clr=cell2mat(colors(loc,2));%correspondingcolorsfort=1:numel(letters)hf=figure('position',[200200100110],'color','w');ha=axes(
