wo eye speed kernel

Author: dshimaoka

mainScript.m

@@ -1,6 +1,6 @@
 [saveServer, rootFolder] = getReady();
-animal =  'hugo'; %'ollie';% %'andy';%
-for yy = 1:3
+animal =  'ollie';% %'andy';%
+for yy = 3
     switch yy
         case 1
             year = '2021';
@@ -66,7 +66,7 @@
         clear mFiringRate
     end
 
-    save(fullfile(saveFolder, 'assembly20241212.mat'),...
+    save(fullfile(saveFolder, 'assembly20250128.mat'),...
         'id_pop','expval_tgt_pop','corr_tgt_pop','corr_tgt_rel_pop',...
         'latency_r_pop','avgAmp_hm_pop','p_hm_pop','spkOk_th_pop',...
         'spkOkTrials_pop','spkOkUCueTrials_pop','mFiringRate_pop',...

mainScript_assembly.m

@@ -1,10 +1,10 @@
 %16/12/24 created from fitPSTH_pop.m
 [saveServer, rootFolder] = getReady();
 
-saveSuffix_p = ['20241212'];
+saveSuffix_p = ['20250128'];
 animals = {'hugo', 'ollie'};
 
-n=load(fullfile(saveServer,'param20241223.mat'),'param');
+n=load(fullfile(saveServer,'param20250128.mat'),'param');
 param =n.param;
 
 %% load result of mainscript_assemble.m
@@ -85,9 +85,6 @@
 
 
 %% apply inclusion critetia
-% param.corr_tgtTh = 0.05;
-param.ptonsetRespTh=.2; %.1;
-% param.nLatencyTr_pref_th = 5;
 [okunits, corr_tgtOK, ntargetTrOK, ptonsetRespOK] ...
     = inclusionCriteria(corr_tgt_pop(1,:), ntargetTrials_pop, PtonsetResp_pop, param);
 
@@ -117,9 +114,12 @@
 
 %% selected units
 theseIDs = {'hugo/2021/08August/25/27',... %vision
-    'hugo/2022/07July/26/19',... %eye speed
+    'hugo/2021/03March/22/8',... %eye position
+    'hugo/2022/08August/17/3',... %eye speed+position
     'hugo/2022/08August/15/4'}; %integrator new 2025 
 [~, selectedIDs] = intersect(id_pop, theseIDs);
+
+%    'hugo/2022/07July/26/19',... %eye speed
 %integrator candidates
 % 'hugo/2022/08August/05/2' 2023 JNS
 % 'hugo/2022/08August/23/7'
@@ -160,13 +160,13 @@
 
 %% kernel avg across units (FIG2)
 %average kernel before centering
-[f, kernel_avg] = showKernel3(kernel_pop, tlags, param.cardinalDir, 0);
+[f, kernel_avg] = showKernel_pop(kernel_pop, tlags, param.cardinalDir, 0);
 savePaperFigure(f,fullfile(saveServer,saveSuffix_p,['avgKernel_' animals{:}]));
 close(f);
 
 %centerring by preferred direction
 tgtRange = [0.05 0.15; 0.03 0.25; -0.1 0.1];
-[f, kernel_centered_avg] = showKernel3(kernel_pop, tlags, param.cardinalDir, 1, tgtRange);
+[f, kernel_centered_avg] = showKernel_pop(kernel_pop, tlags, param.cardinalDir, 1, tgtRange);
 savePaperFigure(f, fullfile(saveServer,saveSuffix_p,['avgKernel_centered_' animals{:}]));
 close(f);
 
@@ -177,7 +177,6 @@
 
 
 %% cell type distibution (FIG3)
-
 % correlation during target presentation
 fig_abs = showScatterTriplets(corr_tgt_pop, ...
     param.predictorNames, [-.2 1], selectedIDs,'linear',animalid_pop);
@@ -202,3 +201,6 @@
 %% hit v miss (FIG 5)
 f = showHMScatter(corr_tgt_rel_pop, p_hm_pop, selectedIDs_hm, animalid_pop);
 screen2png(fullfile(saveServer,saveSuffix_p,['p_hm' animals{:}]));close;
+disp(['The number of significant units before regression: '  num2str(sum(p_hm_pop_before<0.05))]);
+disp(['The number of significant units after regression: '  num2str(sum(p_hm_pop_after<0.05))]);
+

populationAnalysis.m

@@ -43,7 +43,9 @@
 xlabel('time from eye movement [s]');
 mcolorbar(a3,.5);
 
-if size(kernelInfo.kernel{3},2)>1
+if numel(kernelInfo.kernel)==2
+    return;
+elseif size(kernelInfo.kernel{3},2)>1
     a4=subplot(4,2,6);
     thisIm = kernelInfo.kernel{3}';
     crange = prctile(abs(thisIm(:)),99);

showKernel.m

@@ -11,7 +11,7 @@
 %tuned = amp>param.ampTh;
 %tuned = 1:numel(okunits);
 
-f = figure('position',[ 680         485        1181         493]);
+f = figure('position',[ 680         485        800 1200]);
 for aa = 1:numel(unique(animalid_pop))
     if aa==1
         asymbol = 'o';
@@ -29,7 +29,9 @@
                 v = [2 3];
         end
         %doubleTuned = find(tuned(:,v(1))+tuned(:,v(2))==2);
-        subplot(2,3,ii);
+        
+        %% scatter plot
+        subplot(3,2,2*ii-1);
         plot(prefDir(animalid_pop==aa,v(1)), prefDir(animalid_pop==aa,v(2)), asymbol);hold on
         %plot(prefDir(doubleTuned,v(1)), prefDir(doubleTuned,v(2)), 'b.');
         squareplot;
@@ -40,7 +42,8 @@
         ylabel(param.predictorNames{v(2)});
         set(gca,'tickdir','out');
 
-        subplot(2,3,ii+3)
+        %% histogram
+        subplot(3,2,2*ii)
         histogram(prefDir(animalid_pop==aa,v(1)) - prefDir(animalid_pop==aa,v(2)),-180:5:180); hold on;
         %histogram(prefDir(doubleTuned,v(1)) - prefDir(doubleTuned,v(2)), -180:5:180,  'facecolor', 'b');
         if aa == numel(unique(animalid_pop))

showKernelPrefDirScatter.m

@@ -1,6 +1,8 @@
-function [fig, kernel_avg,prefdir, prefdirPval] = showKernel3(kernel_pop, ...
+function [fig, kernel_avg,prefdir, prefdirPval] = showKernel_pop(kernel_pop, ...
     tlags, cardinalDir, centering, tgtRange)
-% fig = showKernel3(kernel_pop, tlags, cardinalDir, centering)
+% fig = showKernel_pop(kernel_pop, tlags, cardinalDir, centering)
+
+useSameYrange = true;
 
 prefDirOption = 0;%
 %very slow in option=1
@@ -35,18 +37,25 @@
     end
 end
 
+if useSameYrange
+    absMax = max(cellfun(@(x)abs(max(x(:))), kernel_avg));
+end
+
 % created rom showKernel
 fig = figure('position',[1          41        1440         783]);
 a2=subplot(3,2,1);
 thisIm = kernel_avg{1}';
 crange = prctile(abs(thisIm(:)),99);
-%crange = prctile(thisIm(:),[1 99]);
+if useSameYrange
+    crange = absMax;
+end
+
 imagesc(tlags{1}(:,1), directions, thisIm);
 vline(0);
 if centering
     hline(0);
 end
-caxis([-crange crange]);
+clim([-crange crange]);
 set(gca,'ytick',directions);
 xlabel('time from targetOnset [s]');
 mcolorbar(a2,.5);
@@ -57,12 +66,15 @@
 thisIm = kernel_avg{2}';
 crange = prctile(abs(thisIm(:)),99);
 %crange = prctile(thisIm(:),[1 99]);
+if useSameYrange
+    crange = absMax;
+end
 imagesc(tlags{2}(:,1),directions, thisIm);
 vline(0);
 if centering
     hline(0);
 end
-caxis([-crange crange]);
+clim([-crange crange]);
 set(gca,'ytick',directions);
 xlabel('time from eye movement [s]');
 mcolorbar(a3,.5);
@@ -73,6 +85,10 @@
     thisIm = kernel_avg{3}';
     crange = prctile(abs(thisIm(:)),99);
     %crange = prctile(thisIm(:),[1 99]);
+    if useSameYrange
+        crange = absMax;
+    end
+    
     imagesc(tlags{3}(:,1),directions, thisIm);
     vline(0);
     if centering

showKernel3.m showKernel_pop.m

@@ -205,7 +205,9 @@
 hold on;
 boundedline(winSamps, mtOnsetResp(allMdlIdx,:), setOnsetResp(allMdlIdx,:),'b', 'transparency', 0.5);
 boundedline(winSamps, mtOnsetResp(visionIdx,:), setOnsetResp(visionIdx,:),'m', 'transparency', 0.5);
-boundedline(winSamps, mtOnsetResp(eyevelIdx,:), setOnsetResp(eyevelIdx,:),'c', 'transparency', 0.5);
+if ~isempty(eyevelIdx)
+    boundedline(winSamps, mtOnsetResp(eyevelIdx,:), setOnsetResp(eyevelIdx,:),'c', 'transparency', 0.5);
+end
 boundedline(winSamps, mtOnsetResp(eyeposIdx,:), setOnsetResp(eyeposIdx,:),'g', 'transparency', 0.5);
 %boundedline(winSamps, mtOnsetResp(5,:), setOnsetResp(5,:),'g', 'transparency', 0.5);
 %vbox(param.baseWin(1), param.baseWin(2))
@@ -227,7 +229,9 @@
 hold on;
 boundedline(winSamps, mtOnsetResp_v(allMdlIdx,:), setOnsetResp_v(allMdlIdx,:),'b', 'transparency', 0.5);
 boundedline(winSamps, mtOnsetResp_v(visionIdx,:), setOnsetResp_v(visionIdx,:),'m', 'transparency', 0.5);
-boundedline(winSamps, mtOnsetResp_v(eyevelIdx,:), setOnsetResp_v(eyevelIdx,:),'c', 'transparency', 0.5);
+if ~isempty(eyevelIdx)
+    boundedline(winSamps, mtOnsetResp_v(eyevelIdx,:), setOnsetResp_v(eyevelIdx,:),'c', 'transparency', 0.5);
+end
 boundedline(winSamps, mtOnsetResp_v(eyeposIdx,:), setOnsetResp_v(eyeposIdx,:),'g', 'transparency', 0.5);
 %vbox(param.baseWin(1), param.baseWin(2))
 %vbox(param.tOnRespWin(1), param.tOnRespWin(2),[],[.7 1 .7]);
@@ -240,7 +244,9 @@
 hold on;
 boundedline(winSamps, mtOnsetResp_f(allMdlIdx,:), setOnsetResp_f(allMdlIdx,:),'b', 'transparency', 0.5);
 boundedline(winSamps, mtOnsetResp_f(visionIdx,:), setOnsetResp_f(visionIdx,:),'m', 'transparency', 0.5);
-boundedline(winSamps, mtOnsetResp_f(eyevelIdx,:), setOnsetResp_f(eyevelIdx,:),'c', 'transparency', 0.5);
+if ~isempty(eyevelIdx)
+    boundedline(winSamps, mtOnsetResp_f(eyevelIdx,:), setOnsetResp_f(eyevelIdx,:),'c', 'transparency', 0.5);
+end
 boundedline(winSamps, mtOnsetResp_f(eyeposIdx,:), setOnsetResp_f(eyeposIdx,:),'g', 'transparency', 0.5);
 %vbox(param.baseWin(1), param.baseWin(2))
 %vbox(param.tOnRespWin(1), param.tOnRespWin(2),[],[.7 1 .7]);
@@ -255,7 +261,9 @@
 hold on;
 boundedline(winSamps, msaccResp(allMdlIdx,:), sesaccResp(allMdlIdx,:),'b', 'transparency', 0.5);
 boundedline(winSamps, msaccResp(visionIdx,:), sesaccResp(visionIdx,:),'m', 'transparency', 0.5);
-boundedline(winSamps, msaccResp(eyevelIdx,:), sesaccResp(eyevelIdx,:),'c', 'transparency', 0.5);
+if ~isempty(eyevelIdx)
+    boundedline(winSamps, msaccResp(eyevelIdx,:), sesaccResp(eyevelIdx,:),'c', 'transparency', 0.5);
+end
 boundedline(winSamps, msaccResp(eyeposIdx,:), sesaccResp(eyeposIdx,:),'g', 'transparency', 0.5);
 axis tight;
 xlim([figTWin(1)-medianSaccDelay figTWin(end)-medianSaccDelay])
@@ -266,7 +274,9 @@
 hold on;
 boundedline(winSamps, mcOnsetResp(allMdlIdx,:), secOnsetResp(allMdlIdx,:),'b', 'transparency', 0.5);
 boundedline(winSamps, mcOnsetResp(visionIdx,:), secOnsetResp(visionIdx,:),'m', 'transparency', 0.5);
-boundedline(winSamps, mcOnsetResp(eyevelIdx,:), secOnsetResp(eyevelIdx,:),'c', 'transparency', 0.5);
+if ~isempty(eyevelIdx)
+    boundedline(winSamps, mcOnsetResp(eyevelIdx,:), secOnsetResp(eyevelIdx,:),'c', 'transparency', 0.5);
+end
 boundedline(winSamps, mcOnsetResp(eyeposIdx,:), secOnsetResp(eyeposIdx,:),'g', 'transparency', 0.5);
 axis tight;
 xlim([figTWin(1)-medianSaccDelay figTWin(end)-medianSaccDelay])
@@ -286,6 +296,7 @@
 
 ylabel(sprintf('cOnset (success)\nn=%d',numel(theseTrials)));
 legend('observed','all mdl','vision','eye velocity','eye position','location','northwest')
+%legend('observed','all mdl','vision','eye velocity','location','northwest')
 
 end