Added representative traces for simulation channel distance figure, edited nonStatNoiseAnalysis to output individual sweeps

Author: sammykatta

Analysis/SK/AnnotatedScripts/AntVsPost_VoltageAttenuation_180803.m

@@ -66,7 +66,7 @@
 
 sortSweeps = {'magnitude','magnitude','magnitude','magnitude'};
 
-anteriorMRCs = IdAnalysis(ephysData,protList,anteriorDistCells,'num','matchType',matchType, ...
+[anteriorMRCs, antStim] = IdAnalysis(ephysData,protList,anteriorDistCells,'num','matchType',matchType, ...
     'tauType','thalfmax', 'sortSweepsBy', sortSweeps, 'integrateCurrent',1 , ...
     'recParameters', ephysMetaData,'sepByStimDistance',1);
 
@@ -339,7 +339,7 @@
 xlswrite(fname,postNorm,'postNorm','A2');
 
 
-%% Plot representative traces for spatial figure
+%% Plot representative traces for spatial dynamics figure
 
 % check distance and nReps for each recording
 antDists = cell2mat(cellfun(@(x) mean(x(:,12:13)),anteriorMRCs(:,3),'un',0));
@@ -359,126 +359,17 @@
 
 plotfixer
 
+%% Separate and write representative traces for channel-sim-distance figure
+
+% anterior trace FAT 105 at 1, 5, 10um mean traces separated by on/off
+% stimulus, from [stimStart-250, stimEnd+250]ms.
+onStim = 751;
+offStim = 2251;
+sf = 5; %kHz
+boxTime = 150*sf; %ms
+tVec = (-150*sf:150*sf)'/sf/1000; %s
+
+reps(:,1:3) = anteriorMRCs{4,2}([2 5 9],onStim-boxTime:onStim+boxTime)';
+reps(:,4:6) = anteriorMRCs{4,2}([2 5 9],offStim-boxTime:offStim+boxTime)';
+
 
-%% Old code 
-
-% %% Pull out and combine relevant data for plotting single size
-% 
-% % Voltage attenuation data comes from the length constant fitting done in
-% % Igor, which gives a voltage attenuation factor at the location of the
-% % stimulus site for each recording, based on the calculated length
-% % constant.
-% 
-% % Grab the current at the selected step size (e.g., 10um) for each
-% % recording, grab the cell-stimulus distance for that recording, and match
-% % the recording name against the voltage attenuation table to find the
-% % attenuation factor for that recording.
-% whichMRCs = anteriorMRCs;
-% thisAtt = attenuationData(:,[2 8 10]);
-% distCol = 12;
-% peakCol = 6; % 6 for peak current, 11 for integrated current/charge
-% distVPeak = [];
-% stepSize = 10;
-% 
-% for iCell = 1:size(whichMRCs,1)
-%     thisCell = whichMRCs{iCell,3};
-%     whichStep = round(thisCell(:,1)) == stepSize;
-%     if any(whichStep)
-%         thisName = whichMRCs{iCell,1};
-%         hasAtt = strcmp(thisName,thisAtt(:,1));
-%         
-%         if any(hasAtt) && thisAtt{hasAtt,2}
-%             distVPeak(iCell,:) = [thisCell(whichStep,[distCol peakCol]) thisAtt{hasAtt,3}];
-%         else
-%             distVPeak(iCell,:) = [thisCell(whichStep,[distCol peakCol]) nan];
-%         end
-%         
-%     end
-%     
-% end
-% 
-% distVPeak_Ant = distVPeak;
-% 
-% whichMRCs = posteriorMRCs;
-% distVPeak = [];
-% 
-% 
-% for iCell = 1:size(whichMRCs,1)
-%     thisCell = whichMRCs{iCell,3};
-%     whichStep = round(thisCell(:,1)) == stepSize;
-%     if any(whichStep)
-%         thisName = whichMRCs{iCell,1};
-%         hasAtt = strcmp(thisName,thisAtt(:,1));
-%         
-%         if any(hasAtt)
-%             distVPeak(iCell,:) = [thisCell(whichStep,[distCol peakCol]) thisAtt{hasAtt,2}];
-%         else
-%             distVPeak(iCell,:) = [thisCell(whichStep,[distCol peakCol]) nan];
-%         end
-%         
-%     end
-%     
-% end
-% 
-% distVPeak_Post = distVPeak;
-% 
-% clear a iCell thisCell whichMRCs whichStep thisName hasAtt distVPeak
-% 
-% %% Make correction to I for space clamp error
-% % (Note: this is an approximation, assuming that the majority of the
-% % current is happening at the stimulus site, which we know is not entirely
-% % true, and channels at different points along the neurite will experience
-% % different voltages.
-% 
-% % Now calculate what the actual voltage was at the stimulus site based on
-% % the voltage attenuation factor. In this case, command voltage was -60mV
-% % for all steps. 
-% 
-% % attenuation factor = Vm'/Vc so Vm' = Vc * attenuation factor
-%  
-% % Then calculate what current would've been based on sodium reversal
-% % potential. 
-% % For IC2 solution used here, Ena = +94mV.
-%  
-% % Im' = Im * ((Vc-Ena)/(Vm'-Ena))
-%  
-% Vc = -0.06; %in V
-% Ena = 0.094; % in V
-% Im = distVPeak_Ant(:,2);
-% Vatt = distVPeak_Ant(:,3);
-% 
-% Vm = Vc * Vatt;
-% distVPeak_Ant(:,4) = (Im * (Vc-Ena)) ./ (Vm-Ena);
-% 
-% %% Plot anterior and posterior single size on separate plots
-% 
-% figure(); axh(1) = subplot(2,1,1);
-% scatter(distVPeak_Ant(:,1),distVPeak_Ant(:,4));
-% xlabel('Distance from cell body (um)');
-% ylabel(sprintf('Current @%dum (pA)',stepSize))
-% text(100,200,'Anterior');
-% axh(2) = subplot(2,1,2);
-% scatter(distVPeak_Post(:,1),distVPeak_Post(:,2));
-% xlabel('Distance from cell body (um)');
-% ylabel(sprintf('Current @%dum (pA)',stepSize))
-% text(100,200,'Posterior');
-% 
-% for i = 1:length(axh)
-%     xlim(axh(i),[0 200]);
-%     ylim(axh(i),[0 200]);
-% end
-% 
-% %% Plot on one plot
-% 
-% figure();
-% scatter(distVPeak_Ant(:,1),distVPeak_Ant(:,4));
-% hold on;
-% scatter(-distVPeak_Post(:,1),distVPeak_Post(:,2));
-% text(distVPeak_Ant(:,1)+1,distVPeak_Ant(:,4)+1,anteriorMRCs(:,1));
-% text(-distVPeak_Post(:,1)+1,distVPeak_Post(:,2)+1,posteriorMRCs(:,1));
-% xlabel('Distance from cell body (um)');
-% ylabel(sprintf('Current @%dum (pA)',stepSize))
-% xlim([-100 200]);ylim([0 200]);
-% vline(0,'k:');
-% 
-% 

Analysis/SK/AnnotatedScripts/Velocity_VoltageAtt_180913.m

@@ -180,6 +180,25 @@
 linkaxes(axh,'y');
 plotfixer;
 
+%% Separate and write representative traces for channel-sim-distance figure
+
+% FAT218 mean traces at 106um/s, 320, 3790 separated by on/off
+% stimulus, from [stimStart-250, stimEnd+250]ms.
+onStimStart = 1503; onStimEnd = 2250;
+offStimStart = [5253; 4752; 4521]; offStimEnd = offStimStart + 747;
+sf = 10; %kHz
+boxTime = 150*sf; %ms
+onBox = [onStimStart-boxTime onStimEnd+boxTime];
+offBox = [offStimStart-boxTime offStimEnd+boxTime];
+
+
+reps(:,1:3) = velocityMRCs{4,2}([3 4 8],onBox(1):onBox(2))';
+reps(:,4) = velocityMRCs{4,2}(3,offBox(1,1):offBox(1,2))';
+reps(:,5) = velocityMRCs{4,2}(4,offBox(2,1):offBox(2,2))';
+reps(:,6) = velocityMRCs{4,2}(8,offBox(3,1):offBox(3,2))';
+
+tVec = ((1:length(reps))-boxTime-1)'./(sf*1000);
+
 %% Pull out and combine data to plot one particular velocity vs. distance
 
 % Voltage attenuation data comes from the length constant fitting done in

Analysis/SK/Scripts-in-progress/NonStatNoiseAnalysis.m

@@ -236,6 +236,7 @@
             nonStatOutput.(cellName)(whichRow).sweepsPerWindow = averagingWindow;
             nonStatOutput.(cellName)(whichRow).totalMean = totalMean;
             nonStatOutput.(cellName)(whichRow).totalVar = totalVar;
+            nonStatOutput.(cellName)(whichRow).traces = leakSubtract(responseTime,:);
             nonStatOutput.(cellName)(whichRow).distance = thisDist;
 
 

Analysis/SK/Scripts-in-progress/PreIndentNoiseAnalysis.m

@@ -3,7 +3,7 @@
 
 strainList = {'TU2769'};
 internalList = {'IC6'};
-stimPosition = {'anterior'};
+stimPosition = {'posterior'};
 
 wormPrep = {'dissected'};
 cellDist = [40 100];
@@ -20,6 +20,7 @@
 
 %% Exclusion 
 protList ={'NoisePre','WC_Probe8','WC_Probe4','WC_Probe3','WC_Probe12'};
+% protList ={'WC_Probe8','WC_Probe4','WC_Probe3','WC_Probe12'};
 
 matchType = 'first';
 

Analysis/SK/Scripts-in-progress/QuickPlot.m

@@ -0,0 +1,31 @@
+% calculate
+
+% theseCells = {'FAT186','FAT190','FAT241'};
+% protList ={'WC_Probe';'NoPre'};
+protList ={'NoPre'};
+% protList ={'WC_Probe'};
+matchType = 'first';
+sortSweeps = {'magnitude','magnitude','magnitude','magnitude'};
+
+% use allSteps(190124).xls
+[postSweeps, postStim] = IdAnalysis(ephysData,protList,posteriorDistCells,'num','matchType',matchType, ...
+'tauType','thalfmax', 'sortSweepsBy', sortSweeps, 'integrateCurrent',1 , ...
+'recParameters', ephysMetaData,'sepByStimDistance',1,'saveSweeps',1);
+
+clear protList sortSweeps matchType
+
+%% plot
+figure('Position',[500 100 800 600]);
+stepSize = 10;
+
+for i = 1:size(postSweeps,1)
+    subplot(2,4,i)
+    try
+        plot(postSweeps{i,3}{abs(postSweeps{i,4}(:,1)-stepSize)<0.4}')
+    catch
+        continue
+    end
+    
+end
+
+suptitle('Posterior 250ms step');