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add extra analysis when revising manuscript; code for generating new figures added;
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experimental_data_analysis/Toolbox_CSC/FDP_paper_figures.m
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| % This is the main function to generate all the figures in the paper: | ||
| % Lévy walk dynamics of gamma burst patterns in primate cerebral cortex | ||
| % submitted to Communication Biology | ||
| % | ||
| % Author: Xian Long; [email protected] | ||
| % | ||
| addpath(genpath([pwd,'/Toolbox_CSC'])) % add sub-functions | ||
| addpath(genpath([pwd,'/ToolOthers/nanconv'])) % to interpolate missing chans | ||
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| %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% | ||
| %% fig 1. schematic diagram of Levy flight | ||
| schematicLF | ||
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| %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% | ||
| %% fig 2. gamma bursts | ||
| p1f1 | ||
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| %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% | ||
| %% fig 3A. pattern trajectories | ||
| % flagDetectPatt = 1 ; % 1 run the pattern detection, 0 load directly | ||
| % if flagDetectPatt | ||
| % dataFileName = 'ma027_032' ; | ||
| % stdPara = 2.5 ; | ||
| % [Duration,patternScale,centInterval,WCentroids] = | ||
| % else | ||
| % | ||
| % end | ||
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| %% fig 3B. pattern statistics | ||
| DurationFull = [] ; | ||
| flagDetectPatt = 0 ; % 1 run the pattern detection, 0 load directly | ||
| if flagDetectPatt | ||
| Project1(1) | ||
| Project1(2) | ||
| Project1(3) | ||
| Project1(4) | ||
| else | ||
| load([pwd,'/Results_data/Project1/Project1_submit/',... | ||
| '00.6SmRes2_2.5SD_my147_53_Band30HzMay11_22:53.mat_v4.mat']) | ||
| DurationFull = [DurationFull,Duration] ; | ||
| load([pwd,'/Results_data/Project1/Project1_submit/',... | ||
| '00.6SmRes2_2.5SD_ma025_03_Band30HzMay11_22:49.mat_v4.mat']) | ||
| DurationFull = [DurationFull,Duration] ; | ||
| load([pwd,'/Results_data/Project1/Project1_submit/',... | ||
| '00.6SmRes2_2.5SD_my144_101_Band30HzMay11_12:01.mat_v4.mat']) | ||
| DurationFull = [DurationFull,Duration] ; | ||
| load([pwd,'/Results_data/Project1/Project1_submit/',... | ||
| '00.6SmRes2_2.5SD_ma027_032_Band30HzMay11_22:37.mat_v4.mat']) | ||
| DurationFull = [DurationFull,Duration] ; | ||
| sigDist = DurationFull ; | ||
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| figure; | ||
| subplot(2,2,1) | ||
| stableFit(sigDist,numPts,1) | ||
| subplot(2,2,2) | ||
| stableFitOne(sigDist,numPts,1) | ||
| subplot(2,2,3) | ||
| stableFitCDFTwo(sigDist,numPts,1) | ||
| subplot(2,2,4) | ||
| stableFitCDFOne(sigDist,numPts,1) | ||
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| pf_power = @(x,alpha,xmin) x.^-alpha*(alpha-1)*xmin^(alpha-1); | ||
| cdf_power = @(x,alpha,xmin) (x/xmin).^(-alpha+1) ; | ||
| [lambdaHat1,lambdaCI] = mle(sigDist, 'pdf',pf_power, 'start',[1,30], 'lowerbound',[1,30], 'upperbound', [5,200]) | ||
| [x,n] = histcounts(sigDist,100,'normalization','cdf') ; | ||
| n0 = 10.^(0.5*(log10(n(2:end))+log10(n(1:end-1)))) ; | ||
| sigDist(sigDist<58) = [] ; | ||
| xmin = min(sigDist) ; | ||
| xmax = max(sigDist) ; | ||
| pf_TP = @(x,alpha) (alpha+1)*(xmax.^(alpha+1)-xmin.^(alpha+1)).^(-1).*x.^(alpha) ; | ||
| cdf_TP = @(x,alpha) (x.^(alpha+1)-xmin.^(alpha+1))./(xmax.^(alpha+1)-xmin.^(alpha+1)) ; | ||
| [lambdaHat1,lambdaCI] = mle(sigDist, 'pdf',pf_TP, 'start',[-4], 'lowerbound',[-5], 'upperbound', [-1]) | ||
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| % pf_powerC = @(x,alpha,lambda,xmin) x.^-alpha.*exp(-lambda*x)*... | ||
| % lambda^(1-alpha)/gamma_incomplete(lambda*xmin,1-alpha) ; | ||
| % [lambdaHat2,lambdaCI] = mle(sigDist, 'pdf',pf_powerC, 'start',[1,0,30], 'lowerbound',[1,0,30], 'upperbound', [5,10,1000]) ; | ||
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| % [x,n] = histcounts(sigDist,100,'normalization','pdf') ; | ||
| % n0 = 10.^(0.5*(log10(n(2:end))+log10(n(1:end-1)))) ; | ||
| % figure; | ||
| % loglog(n0,x,'b.','MarkerSize',12) | ||
| % hold on | ||
| % loglog(n0,pf_powerC(n0,lambdaHat2(1),lambdaHat2(2),lambdaHat2(3)),'lineWidth',2) | ||
| % | ||
| % figure; | ||
| % [x,n] = histcounts(sigDist,500,'normalization','pdf') ; | ||
| % n0 = 0.5*((n(2:end))+(n(1:end-1))) ; | ||
| % loglog(n0,x,'b.','MarkerSize',12) | ||
| % hold on | ||
| % loglog(n0,pf_TP(n0,lambdaHat1(1)),'lineWidth',2) | ||
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| figure; | ||
| [x,n] = histcounts(sigDist,1000,'normalization','cdf') ; | ||
| % n0 = 10.^(0.5*(log10(n(2:end))+log10(n(1:end-1)))) ; | ||
| n0 = 0.5*((n(2:end))+(n(1:end-1))) ; | ||
| loglog(n0,1-x,'b.','MarkerSize',12) | ||
| hold on | ||
| loglog(n0,1-cdf_TP(n0,lambdaHat1(1)),'r','lineWidth',2) | ||
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| [lambdaHat1,lambdaCI] = mle(sigDist, 'pdf',pf_TP, 'start',[-4], 'lowerbound',[-5], 'upperbound', [-1]) | ||
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| paraDist2 = fitdist(sigDist','normal') ; | ||
| y02 = cdf(paraDist2,n0) ; | ||
| hold on | ||
| loglog(n0,1-y02,'k','lineWidth',2) | ||
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| % load([pwd,'/Results/Project1/project1_results_recent/final_2.5SD/',... | ||
| % 'v4_00.6Sm_2.5SD_ma027_032_Band30HzSeptember23_11:07.mat']) | ||
| % figure; | ||
| % subplot(2,2,1) | ||
| % sigDist = Duration ; | ||
| % stableFit(sigDist,numPts,1) | ||
| % subplot(2,2,2) | ||
| % stableFitOne(sigDist,numPts,1) | ||
| % subplot(2,2,3) | ||
| % stableFitCDFTwo(sigDist,numPts,1) | ||
| % subplot(2,2,4) | ||
| % stableFitCDFOne(sigDist,numPts,1) | ||
| end | ||
|
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| %% fig 3CDE. MSD | ||
| close all | ||
| superFull = []; | ||
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| sdPara = 2; | ||
| tic | ||
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| load([pwd,'/Results_data/Project1/Project1_submit/',... | ||
| '00.6SmRes2_2.5SD_my147_53_Band30HzMay11_22:53.mat_v4.mat'],'WCentroids','centInterval') | ||
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| % step length fitting 1D | ||
| % figure; | ||
| superFull = [] ; | ||
| minDisp = 0.1 ; | ||
| xmax = 12.8*200 ; | ||
| noiseThre = 20 ; | ||
| grid2Micro = 200 ; | ||
| DisplaceNorm = p1f2_stepLength_TP(WCentroids,superFull,0,minDisp,xmax,noiseThre,grid2Micro) ; | ||
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| ylim([10^-3 10^0]) | ||
| set(gcf,'Position',[534 721 293 245]) | ||
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| %% | ||
| load([pwd,'/Results_data/Project1/Project1_submit/',... | ||
| '00.6SmRes2_2.5SD_ma025_03_Band30HzMay11_22:49.mat_v4.mat'],'WCentroids','centInterval') | ||
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| % step length fitting 1D | ||
| % figure; | ||
| superFull = [] ; | ||
| xmax = 12.4*200 ; | ||
| DisplaceNorm = p1f2_stepLength_TP(WCentroids,superFull,0,minDisp,xmax,noiseThre,grid2Micro) ; | ||
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| ylim([10^-3 10^0]) | ||
| set(gcf,'Position',[534 721 293 245]) | ||
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| %% | ||
| load([pwd,'/Results_data/Project1/Project1_submit/',... | ||
| '00.6SmRes2_2.5SD_my144_101_Band30HzMay11_12:01.mat_v4.mat'],'WCentroids','centInterval') | ||
| WCenFull = [WCenFull,WCentroids] ; | ||
| InterFull = [InterFull,centInterval] ; | ||
| % step length fitting 1D | ||
| % figure; | ||
| superFull = [] ; | ||
| xmax = 12.0*200 ; | ||
| DisplaceNorm = p1f2_stepLength_TP(WCentroids,superFull,0,minDisp,xmax,noiseThre,grid2Micro) ; | ||
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| ylim([10^-3 10^0]) | ||
| set(gcf,'Position',[534 721 293 245]) | ||
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| %% | ||
| load([pwd,'/Results_data/Project1/Project1_submit/',... | ||
| '00.6SmRes2_2.5SD_ma027_032_Band30HzMay11_22:37.mat_v4.mat'],'WCentroids','centInterval') | ||
| WCenFull = [WCenFull,WCentroids] ; | ||
| InterFull = [InterFull,centInterval] ; | ||
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| % step length fitting 1D | ||
| % figure; | ||
| superFull = [] ; | ||
| xmax = 10.0*200 ; | ||
| DisplaceNorm = p1f2_stepLength_TP(WCentroids,superFull,0,minDisp,xmax,noiseThre,grid2Micro) ; | ||
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| ylim([10^-3 10^0]) | ||
| set(gcf,'Position',[534 721 293 245]) | ||
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| % [superIdx,meanSlope,stdSlope] = p1f2_msdDist(WCentroids) ; | ||
| % superFull = [superFull,superIdx] ; | ||
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| toc | ||
| clearvars WCentroids | ||
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| %% angle model | ||
| load([pwd,'/Results_data/Project1/Project1_submit/',... | ||
| '00.6SmRes2_2.5SD_ma025_03_Band30HzMay11_22:49.mat_v4.mat'],'WCentroids','centInterval') | ||
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| % step length fitting 1D | ||
| % figure; | ||
| superFull = [] ; | ||
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| iFig = 1 ; | ||
| turnAngle = 20 ; | ||
| subplot(2,3,iFig) | ||
| % figure; | ||
| superIdx = [] ; | ||
| flagUseBetween = 1 ; | ||
| maxOffset = 200*8 ; %10 8 for 120 | ||
| minDisp = 200*0.12 ; | ||
| flagPlotPart = 1; | ||
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| [DisplaceNorm,lambdaHat1] = p1f2_stepLength_TP_2D(WCentroids,superIdx,turnAngle,... | ||
| flagUseBetween,maxOffset,minDisp,flagPlotPart) ; | ||
| title(['\theta = ',num2str(turnAngle), char(176) ,' , \lambda = ',num2str(-lambdaHat1,'%0.2f')]) | ||
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| ylim([10^-3 10^0]) | ||
| xlim([10^1 10^4]) | ||
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| % set(gcf,'Position',[534 721 293 245]) | ||
| % exportgraphics(gcf,['S2_angle',num2str(turnAngle),'.pdf'],'ContentType','vector') | ||
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| for turnAngle = 40:20:120 ; | ||
| iFig = iFig+1 ; | ||
| subplot(2,3,iFig) | ||
| % figure; | ||
| superIdx = [] ; | ||
| flagUseBetween = 1 ; | ||
| maxOffset = 200*8 ; %10 8 for 120 | ||
| minDisp = 200*0.1 ; | ||
| flagPlotPart = 1; | ||
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| [DisplaceNorm,lambdaHat1] = p1f2_stepLength_TP_2D(WCentroids,superIdx,turnAngle,... | ||
| flagUseBetween,maxOffset,minDisp,flagPlotPart) ; | ||
| title(['\theta = ',num2str(turnAngle), char(176) ,' , \lambda = ',num2str(-lambdaHat1,'%0.2f')]) | ||
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| ylim([10^-3 10^0]) | ||
| xlim([10^1 10^4]) | ||
| % set(gcf,'Position',[534 721 293 245]) | ||
| % exportgraphics(gcf,['S2_angle',num2str(turnAngle),'.pdf'],'ContentType','vector') | ||
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| end | ||
| annotation(gcf,'textbox',... | ||
| [0.0731343873517787 0.945709281961471 0.0306205533596838 0.0437828371278459],... | ||
| 'String','A',... | ||
| 'LineStyle','none',... | ||
| 'FitBoxToText','off'); | ||
| annotation(gcf,'textbox',... | ||
| [0.359695652173913 0.945709281961471 0.0306205533596838 0.0437828371278459],... | ||
| 'String','B',... | ||
| 'LineStyle','none',... | ||
| 'FitBoxToText','off'); | ||
| annotation(gcf,'textbox',... | ||
| [0.637363636363635 0.945709281961471 0.0306205533596838 0.0437828371278459],... | ||
| 'String','C',... | ||
| 'LineStyle','none',... | ||
| 'FitBoxToText','off'); | ||
| annotation(gcf,'textbox',... | ||
| [0.0731343873517787 0.455341506129597 0.0306205533596838 0.0437828371278459],... | ||
| 'String','D',... | ||
| 'LineStyle','none',... | ||
| 'FitBoxToText','off'); | ||
| annotation(gcf,'textbox',... | ||
| [0.359695652173913 0.455341506129597 0.0306205533596838 0.0437828371278459],... | ||
| 'String','E',... | ||
| 'LineStyle','none',... | ||
| 'FitBoxToText','off'); | ||
| annotation(gcf,'textbox',... | ||
| [0.637363636363635 0.455341506129597 0.0306205533596838 0.0437828371278459],... | ||
| 'String','F',... | ||
| 'LineStyle','none',... | ||
| 'FitBoxToText','off'); | ||
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| %% s.d. | ||
| close all | ||
| load([pwd,'/Project1_preprocessedData/',... | ||
| '00.6SmRes2_1.5SD_ma025_03_Band30HzJanuary16_01:52.mat_v4.mat'],'WCentroids','centInterval') | ||
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| minDisp = 0.2 ; | ||
| xmax = 7.2*200 ; | ||
| noiseThre = 20 ; | ||
| grid2Micro = 200 ; | ||
| subplot(1,3,1) | ||
| DisplaceNorm = p1f2_stepLength_TP(WCentroids,superFull,0,minDisp,xmax,noiseThre,grid2Micro) ; | ||
| ylim([10^-3 10^0]) | ||
| % set(gcf,'Position',[534 721 293 245]) | ||
|
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| load([pwd,'/Project1_preprocessedData/',... | ||
| '00.6SmRes2_2SD_ma025_03_Band30HzJanuary16_01:04.mat_v4.mat'],'WCentroids','centInterval') | ||
| minDisp = 0.2 ; | ||
| xmax = 10.8*200 ; | ||
| noiseThre = 20 ; | ||
| grid2Micro = 200 ; | ||
| subplot(1,3,2) | ||
| DisplaceNorm = p1f2_stepLength_TP(WCentroids,superFull,0,minDisp,xmax,noiseThre,grid2Micro) ; | ||
| ylim([10^-3 10^0]) | ||
| % set(gcf,'Position',[534 721 293 245]) | ||
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| load([pwd,'/Results_data/Project1/Project1_submit/',... | ||
| '00.6SmRes2_2.5SD_ma025_03_Band30HzMay11_22:49.mat_v4.mat'],'WCentroids','centInterval') | ||
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| minDisp = 0.2 ; | ||
| xmax = 12.8*200 ; | ||
| noiseThre = 20 ; | ||
| grid2Micro = 200 ; | ||
| subplot(1,3,3) | ||
| DisplaceNorm = p1f2_stepLength_TP(WCentroids,superFull,0,minDisp,xmax,noiseThre,grid2Micro) ; | ||
| ylim([10^-3 10^0]) | ||
| % set(gcf,'Position',[534 721 293 245]) | ||
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| %% different threshold | ||
| load([pwd,'/Results_data/Project1/Project1_submit/',... | ||
| '00.6SmRes2_2.5SD_ma025_03_Band30HzMay11_22:49.mat_v4.mat'],'WCentroids','centInterval') | ||
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| minDisp = 80 ; | ||
| xmax = 12*200 ; | ||
| noiseThre = 80 ; | ||
| grid2Micro = 200 ; | ||
| DisplaceNorm = p1f2_stepLength_TP(WCentroids,superFull,0,minDisp,xmax,noiseThre,grid2Micro) ; | ||
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| ylim([10^-3 10^0]) | ||
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| figure; | ||
| minDisp = 400 ; | ||
| xmax = 17*200 ; | ||
| noiseThre = 400 ; | ||
| grid2Micro = 200 ; | ||
| DisplaceNorm = p1f2_stepLength_TP(WCentroids,superFull,0,minDisp,xmax,noiseThre,grid2Micro) ; | ||
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| ylim([10^-3 10^0]) | ||
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| %% load the data with no spatial scaling | ||
| WCenFull = [] ; | ||
| sdPara = 1; | ||
| tic | ||
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| figure; | ||
| load([pwd,'/Project1_preprocessedData/',... | ||
| '00.6SmRes1_2.5SD_ma025_03_Band30HzApril06_15:59.mat_v4.mat'],'WCentroids','centInterval') | ||
| WCenFull = [WCenFull,WCentroids] ; | ||
|
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| minDisp = 80 ; | ||
| xmax = 6*400 ; | ||
| noiseThre = 80 ; | ||
| grid2Micro = 400 ; | ||
| DisplaceNorm = p1f2_stepLength_TP(WCentroids,superFull,0,minDisp,xmax,noiseThre,grid2Micro) ; | ||
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| ylim([10^-3 10^0]) | ||
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| figure; | ||
| minDisp = 400 ; | ||
| xmax = 17*400 ; | ||
| noiseThre = 400 ; | ||
| grid2Micro = 400 ; | ||
| DisplaceNorm = p1f2_stepLength_TP(WCentroids,superFull,0,minDisp,xmax,noiseThre,grid2Micro) ; | ||
|
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| ylim([10^-3 10^0]) |
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