annotate rDiff/src/locfit/m/lfplot.m @ 2:233c30f91d66

updated python based GFF parsing module which will handle GTF/GFF/GFF3 file types
author vipints <vipin@cbio.mskcc.org>
date Tue, 08 Oct 2013 07:15:44 -0400
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children
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1 function lfplot(varargin)
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2
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3 % Plot (for one or two dimensions) a locfit() fit.
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4 %
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5 % Usage:
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6 % fit = locfit(x,y);
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7 % lfplot(fit);
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8 %
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9 % Plot the fitted smooth curve, and add a scatterplot of the data.
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10 %
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11 % Required argument:
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12 % fit (produced by locfit()).
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13 %
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14 % Optional arguments:
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15 % 'nodata' - don't add data to plot.
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16 % 'contour' - for 2-d predictors, use contour instead of surf.
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17 % 'direct' - fit directly, instead of using interpolation
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18 % (see the predict() function).
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19 % 'what' - locfit what argument ('coef', 'infl', 'vari', 'band' etc).
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20 % Any additional arguments are passed to Matlab's plot(), contour()
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21 % or surf() function as appropriate.
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22 %
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23 % To add confidence bands, use the lfband() function.
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24 %
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25 % Author: Catherine Loader.
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26
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27 fit = varargin{1};
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28 data = fit.data;
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29 xdata = data.x;
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30 n = size(xdata,1);
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31 d = size(xdata,2);
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32 fali = fit.fit_points.family_link;
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33 ydata = data.y;
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34 wdata = data.weights;
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35 cdata = data.censor;
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36 if (length(cdata)==1) cdata = zeros(n,1); end;
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37 showdata = (fit.evaluation_structure.derivative==0);
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38 ppargs = {};
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39 plotargs = {};
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40
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41 type = 's';
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42 na = 2;
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43 while na <= length(varargin)
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44 inc = 0;
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45 if (strcmp(varargin{na},'contour'))
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46 type = 'c';
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47 inc = 1;
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48 end;
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49 if (strcmp(varargin{na},'what'))
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50 ppargs = {ppargs{:}, 'what', varargin{na+1}};
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51 showdata = 0;
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52 inc = 2;
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53 end;
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54 if (strcmp(varargin{na},'nodata'))
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55 showdata = 0;
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56 inc = 1;
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57 end;
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58 if (strcmp(varargin{na},'direct'))
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59 ppargs = {ppargs{:} 'direct'};
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60 inc = 1;
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61 end;
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62 if (inc==0)
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63 plotargs = {plotargs{:} varargin{na}};
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64 inc = 1;
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65 end;
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66 na = na+inc;
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67 end;
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68
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69 xfit = lfmarg(fit);
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70 yfit = predict(fit,xfit,ppargs{:});
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71 yfit = invlink(yfit,fali);
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72 fam = mod(fali(1),64);
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73 if (fam>4)
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74 ydata = ydata ./ wdata;
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75 end;
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76
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77 if (d==1)
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78 plot(xfit{1},yfit,plotargs{:});
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79 if (showdata)
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80 hold on;
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81 if (length(ydata)==1) ydata = zeros(n,1); end;
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82 plotbyfactor(xdata,ydata,cdata);
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83 hold off;
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84 end;
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85 end;
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86
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87 if (d==2)
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88 x1 = xfit{1};
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89 x2 = xfit{2};
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90 yfit = reshape(yfit,length(x1),length(x2));
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91 if (type=='c')
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92 [C h] = contour(x1,x2,yfit',plotargs{:});
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93 clabel(C,h);
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94 if (showdata)
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95 hold on;
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96 plotbyfactor(xdata(:,1),xdata(:,2),cdata);
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97 hold off;
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98 end;
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99 else
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100 surf(x1,x2,yfit',plotargs{:});
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101 end;
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102 end;
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103
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104 return;