adding Megan's matlab code to SNLC/SpikeAnalysis

Intancode_Megan/Plotting/make_psth_plot.m

@@ -0,0 +1,45 @@
+function make_psth_plot(binsize,spikes,which_trials,prestim,stimtime,totaltime,light_trialtypes,light_start,light_dur)
+
+% binsize = size of bins in which to count spikes (in sec)
+% spikes = cell array of a single unit's spike times with length of number of trials.
+% which_trials = 1xnum_trials vector of 1s and 0s, 1s indicating trials to look
+% prestim = time before visual stimulus onset (in sec)
+% stimtime = duration of visual stimulus (in sec)
+% totaltime = total time of trial(in sec)
+% light_trialtypes = 1xnumtrials vector defining each trial's light
+    % condition
+% light_start = time when the light started (in sec) (if not an opto
+    % experiment, should be [])
+% light_dur = duration of light pulse (in sec) (if not an opto
+    % experiment, should be [])
+
+    color_mat = [0 0 0; 0 .8 1; 0 0 1; 0 0.5 .4; 0 .7 .2]; % for graphing purposes (first is black, last is green)
+
+
+edges = [0:binsize:totaltime-binsize];
+psth = make_psth(binsize,edges,which_trials,spikes,light_trialtypes);
+
+edges_stim = [-prestim:binsize:(totaltime-prestim-binsize)]'; % x signifies the timepoint of the START of the bin
+for c = 1:size(psth,2)
+    plot(edges_stim,psth(:,c),'color',color_mat(c,:),'linewidth',2)
+    hold on
+end
+
+xlim([-prestim totaltime-prestim-binsize])  % because points mark the START of the bin
+set(gca,'XMinorTick','on')
+yax = get(gca,'YLim');
+line([0 0], [0 yax(2)]','Color','r','LineStyle','--')
+line([stimtime stimtime], [0 yax(2)]','Color','r','LineStyle','--')
+xlabel('Time (sec)','fontsize',14)
+ylabel('spikes/sec','Fontsize',14)
+
+% if it's not an opto experiment, draw patch
+if ~isempty(light_start)     
+    x1 = light_start - prestim;     % when the light starts
+    xx = [x1 x1 x1+light_dur x1+light_dur x1];
+    yy = [0 yax(2) yax(2) 0 0];
+    patch(xx, yy, -1 * ones(size(xx)), [0.9 0.9 0.9], 'LineStyle', 'none')
+end
+
+end
+

Intancode_Megan/Plotting/make_raster_plot.asv

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+function make_raster_plot(spikes,Fs,prestim,totaltime,light_trialtypes,light_start,pulse_dur)
+
+% spikes = cell array of a single unit's spike times with length of number of trials.
+% Fs = sampling rate (in sec)
+% prestim = time before visual stimulus onset (in sec)
+% totaltime = total time of trial(in sec)
+% light_trialtypes = 1xnumtrials vector defining each trial's light
+    % condition
+% light_start = time when the light started (in sec)
+% pulse_dur = duration of light pulse (in sec)
+    % pulse_dur in trains experiments)
+
+spike_raster = make_raster(spikes,Fs,totaltime);
+num_trials = length(spikes);
+color_mat = [0 0 0; 0 0 1; 0 .8 1; 0 0.5 .4; 0 .7 .2]; % for graphing purposes (first is black, last is green)
+
+time_vec = linspace(-prestim,totaltime-prestim,size(spike_raster,2));      % for x-axis 
+cond_colors = ones(1,num_trials);      % just in case you have multiple conditions
+
+% if light experiment, add blue shading on raster
+if length(unique(light_trialtypes)) > 1         % it was an opto experiment if there's more than one "light" condition (one condition would be nolight)
+    [cond,idx] = sort(light_trialtypes);    % sort trials by light conditions
+    diff_conds = unique(cond);
+    new_spike_rast = spike_raster(idx,:);             % reordered according to light condition
+    new_spike_rast(find(~new_spike_rast)) = nan;        % so that you don't plot absence of spikes as y=0
+    for c = 1:length(diff_conds)
+        cond_colors(find(cond==diff_conds(c)))=c;
+    end
+    start_patch = find(cond>0,1,'first');     % first trial with light
+    end_patch = num_trials;         % assumes all trials where cond > 0 had light
+    x1 = light_start-prestim;       % when the light starts
+
+    for c = 1:length(diff_conds)
+        start_patch = find(cond==diff_conds(c),1,'first')-1;
+        end_patch = find(cond==diff_conds(c),1,'last')-1;
+        if sum(diff_conds>10)         % if it was a trains experiment
+            for p = 1:(light_trialtypes(idx(end_patch)))
+                space = 1/(light_trialtypes(idx(end_patch)));
+                patch([x1+((p-1)*space) x1+((p-1)*space) x1+pulse_dur+((p-1)*space) x1+pulse_dur+((p-1)*space) x1+((p-1)*space)],[start_patch end_patch end_patch start_patch start_patch], [0.9 0.9 0.9], 'LineStyle', 'none')
+            end
+        elseif diff_conds(c)         % any other light condition
+            patch([x1 x1 x1+pulse_dur x1+pulse_dur x1],[start_patch end_patch end_patch start_patch start_patch], [0.9 0.9 0.9], 'LineStyle', 'none')
+        end
+        line([prestim totaltime-prestim], [end_patch end_patch]','Color','r','LineStyle','--')
+    end
+
+
+%         patch([x1 x1 border border x1],[start_patch end_patch end_patch start_patch start_patch], [0.9 0.9 0.9], 'LineStyle', 'none')
+    hold on
+end
+
+if exist('xrange','var')        
+    rasterrange = [find(time_vec==.4):find(time_vec==.8)];
+else
+    rasterrange = 1:size(new_spike_rast,2);
+end
+
+% draw raster
+for t = 1:num_trials     % for each trial
+    new_spike_rast(t,find(new_spike_rast(t,:))) = new_spike_rast(t,find(new_spike_rast(t,:)))+(t-1);        % plot 'ones' in vector so that y = trial number
+    plot(time_vec(rasterrange),new_spike_rast(t,rasterrange),'.','Color',color_mat(cond_colors(t),:),'MarkerSize',6)    
+    hold on
+end
+ylim([0 num_trials])
+
+xlabel('Time from visual stimulus onset (sec)')
+ylabel('Trial (by condition)')
+
+return

Intancode_Megan/Plotting/make_raster_plot.m

@@ -0,0 +1,70 @@
+function make_raster_plot(spikes,Fs,prestim,totaltime,light_trialtypes,light_start,pulse_dur)
+
+% spikes = cell array of a single unit's spike times with length of number of trials.
+% Fs = sampling rate (in sec)
+% prestim = time before visual stimulus onset (in sec)
+% totaltime = total time of trial(in sec)
+% light_trialtypes = 1xnumtrials vector defining each trial's light
+    % condition
+% light_start = time when the light started (in sec)
+% pulse_dur = duration of light pulse (in sec)
+    % pulse_dur in trains experiments)
+
+spike_raster = make_raster(spikes,Fs,totaltime);
+num_trials = length(spikes);
+    color_mat = [0 0 0; 0 .8 1; 0 0 1; 0 0.5 .4; 0 .7 .2]; % for graphing purposes (first is black, last is green)
+
+time_vec = linspace(-prestim,totaltime-prestim,size(spike_raster,2));      % for x-axis 
+cond_colors = ones(1,num_trials);      % just in case you have multiple conditions
+
+% if light experiment, add blue shading on raster
+if length(unique(light_trialtypes)) > 1         % it was an opto experiment if there's more than one "light" condition (one condition would be nolight)
+    [cond,idx] = sort(light_trialtypes);    % sort trials by light conditions
+    diff_conds = unique(cond);
+    new_spike_rast = spike_raster(idx,:);             % reordered according to light condition
+    new_spike_rast(find(~new_spike_rast)) = nan;        % so that you don't plot absence of spikes as y=0
+    for c = 1:length(diff_conds)
+        cond_colors(find(cond==diff_conds(c)))=c;
+    end
+    start_patch = find(cond>0,1,'first');     % first trial with light
+    end_patch = num_trials;         % assumes all trials where cond > 0 had light
+    x1 = light_start-prestim;       % when the light starts
+
+    for c = 1:length(diff_conds)
+        start_patch = find(cond==diff_conds(c),1,'first')-1;
+        end_patch = find(cond==diff_conds(c),1,'last')-1;
+        if sum(diff_conds>10)         % if it was a trains experiment
+            for p = 1:(light_trialtypes(idx(end_patch)))
+                space = 1/(light_trialtypes(idx(end_patch)));
+                patch([x1+((p-1)*space) x1+((p-1)*space) x1+pulse_dur+((p-1)*space) x1+pulse_dur+((p-1)*space) x1+((p-1)*space)],[start_patch end_patch end_patch start_patch start_patch], [0.9 0.9 0.9], 'LineStyle', 'none')
+            end
+        elseif diff_conds(c)         % any other light condition
+            patch([x1 x1 x1+pulse_dur x1+pulse_dur x1],[start_patch end_patch end_patch start_patch start_patch], [0.9 0.9 0.9], 'LineStyle', 'none')
+        end
+        line([-prestim totaltime-prestim], [end_patch end_patch]','Color','r','LineStyle','--')
+    end
+
+
+%         patch([x1 x1 border border x1],[start_patch end_patch end_patch start_patch start_patch], [0.9 0.9 0.9], 'LineStyle', 'none')
+    hold on
+end
+
+if exist('xrange','var')        
+    rasterrange = [find(time_vec==.4):find(time_vec==.8)];
+else
+    rasterrange = 1:size(new_spike_rast,2);
+end
+
+% draw raster
+for t = 1:num_trials     % for each trial
+    new_spike_rast(t,find(new_spike_rast(t,:))) = new_spike_rast(t,find(new_spike_rast(t,:)))+(t-1);        % plot 'ones' in vector so that y = trial number
+    plot(time_vec(rasterrange),new_spike_rast(t,rasterrange),'.','Color',color_mat(cond_colors(t),:),'MarkerSize',6)    
+    hold on
+end
+ylim([0 num_trials])
+xlim([-prestim totaltime-prestim])
+
+xlabel('Time from visual stimulus onset (sec)','fontsize',14)
+ylabel('Trial (by condition)','fontsize',14)
+
+return