def plot_bars(ax, dataMat, label):
for indSubject, subject in enumerate(subjects):
for indCond, condition in enumerate(conditions):
sessionsThisCondThisSubject = dataMat[indSubject, :, indCond]
ax.plot(np.zeros(len(sessionsThisCondThisSubject)) + (indSubject + 0.5*width + indCond*width) + pointShift,
sessionsThisCondThisSubject, marker='o', linestyle='none', mec=condColors[indCond], mfc='none')
ax.hold(1)
rects1 = ax.bar(ind, dataMat[:, :, 0].mean(1)-0.5, width, bottom=0.5, edgecolor='k', facecolor='w', lw=2, label='Saline')
rects2 = ax.bar(ind+width+0.015, dataMat[:, :, 1].mean(1)-0.5, width, bottom=0.5, edgecolor=muscimolColor, lw=2, facecolor='w', label='Muscimol')
ax.set_xticks(ind + width)
ax.set_xticklabels(np.arange(6)+1, fontsize=fontSizeLabels)
ax.set_xlabel('Mouse', fontsize=fontSizeLabels)
ax.axhline(y=0.5, color='0.5', linestyle='-')
# ax.set_ylim([0.45, 1])
ax.set_xlim([ind[0]-0.5*width, ind[-1]+2.5*width ])
ax.set_ylabel('Number of trials', fontsize=fontSizeLabels)
# ax.set_yticks([0.5, 1])
extraplots.set_ticks_fontsize(plt.gca(),fontSizeTicks)
extraplots.boxoff(ax)
ax.legend(bbox_to_anchor=(0.95, 0.6),
loc=3,
numpoints=1,
fontsize=fontSizeLabels,
ncol=1,
columnspacing=1.5,
frameon=False)
for i in [1, 3, 4]:
extraplots.significance_stars([i+0.5*width,i+1.5*width], 1000, 50, starSize=6, gapFactor=0.4, color='0.5')
def nice_psycurve_settings(ax, fitcolor=None, fontsize=20, lineweight=3, fitlineinds=[3]):
'''
A hack for setting some psycurve axes properties, especially the weight of the line and the xticks
I made this because I am using the fxn plot_psycurve_fit_and_data, which obscures handles to things
that I later need (like the lines, etc. ) This function will be useless if I make plots in a better way.
'''
extraplots.boxoff(ax)
extraplots.set_ticks_fontsize(ax, fontsize)
for lineind in fitlineinds:
fitline = ax.lines[lineind]
plt.setp(fitline, lw=lineweight)
if fitcolor:
plt.setp(fitline, color=fitcolor)
xticklabels = [item.get_text() for item in ax.get_xticklabels()]
xticks = ax.get_xticks()
newXtickLabels = np.logspace(xticks[0], xticks[-1], 3, base=2)
ax.set_xticks(np.log2(np.array(newXtickLabels)))
if min(newXtickLabels) > 1000:
ax.set_xticklabels(['{:.3}'.format(x/1000.0) for x in newXtickLabels])
else:
ax.set_xticklabels(['{:.3}'.format(x) for x in newXtickLabels])
def plot_raster_and_PSTH(sessiontype, gs, color='k'):
axRaster = plt.subplot(gs[0])
ephysData, bdata = cell.load(sessiontype)
eventOnsetTimes = ephysData['events']['stimOn']
eventOnsetTimes = spikesanalysis.minimum_event_onset_diff(
eventOnsetTimes, minEventOnsetDiff=0.5)
timeRange = [-0.3, 1.0]
(spikeTimesFromEventOnset, trialIndexForEachSpike,
indexLimitsEachTrial) = spikesanalysis.eventlocked_spiketimes(
ephysData['spikeTimes'], eventOnsetTimes, timeRange)
# pRaster, hCond, zLine = extraplots.raster_plot(spikeTimesFromEventOnset,
# indexLimitsEachTrial,
# timeRange)
axRaster.plot(spikeTimesFromEventOnset,
trialIndexForEachSpike,
'k.',
ms=1,
rasterized=True)
# plt.setp(pRaster, ms=1)
axRaster.set_xlim(timeRange)
axRaster.set_xticks([])
# axRaster.axis('off')
extraplots.boxoff(axRaster)
axRaster.set_yticks([len(eventOnsetTimes)])
axPSTH = plt.subplot(gs[1])
smoothPSTH = True
psthLineWidth = 2
smoothWinSize = 1
binsize = 10 #in milliseconds
binEdges = np.around(np.arange(timeRange[0] - (binsize / 1000.0),
timeRange[1] + 2 * (binsize / 1000.0),
(binsize / 1000.0)),
decimals=2)
winShape = np.concatenate((np.zeros(smoothWinSize),
np.ones(smoothWinSize))) # Square (causal)
winShape = winShape / np.sum(winShape)
psthTimeBase = np.linspace(timeRange[0],
timeRange[1],
num=len(binEdges) - 1)
spikeCountMat = spikesanalysis.spiketimes_to_spikecounts(
spikeTimesFromEventOnset, indexLimitsEachTrial, binEdges)
thisPSTH = np.mean(spikeCountMat, axis=0)
if smoothPSTH:
thisPSTH = np.convolve(thisPSTH, winShape, mode='same')
ratePSTH = thisPSTH / float(binsize / 1000.0)
axPSTH.plot(psthTimeBase, ratePSTH, '-', color=color, lw=psthLineWidth)
displayRange = timeRange
axPSTH.set_xlim(displayRange)
extraplots.boxoff(axPSTH)
axPSTH.set_ylim([0, max(ratePSTH)])
axPSTH.set_yticks([0, np.floor(np.max(ratePSTH))])
# axPSTH.set_ylabel('spk/s', fontsize=fontSizeLabels)
axPSTH.set_ylabel('spk/s')
def plot_bars(ax, dataMat, label):
for indSubject, subject in enumerate(subjects):
for indCond, condition in enumerate(conditions):
sessionsThisCondThisSubject = dataMat[indSubject, :, indCond]
ax.plot(np.zeros(len(sessionsThisCondThisSubject)) +
(indSubject + 0.5 * width + indCond * width) + pointShift,
sessionsThisCondThisSubject,
marker='o',
linestyle='none',
mec=condColors[indCond],
mfc='none')
ax.hold(1)
rects1 = ax.bar(ind,
dataMat[:, :, 0].mean(1) - 0.5,
width,
bottom=0.5,
edgecolor='k',
facecolor='w',
lw=2,
label='Saline')
rects2 = ax.bar(ind + width + 0.015,
dataMat[:, :, 1].mean(1) - 0.5,
width,
bottom=0.5,
edgecolor=muscimolColor,
lw=2,
facecolor='w',
label='Muscimol')
ax.set_xticks(ind + width)
ax.set_xticklabels(np.arange(6) + 1, fontsize=fontSizeLabels)
ax.set_xlabel('Mouse', fontsize=fontSizeLabels)
ax.axhline(y=0.5, color='0.5', linestyle='-')
# ax.set_ylim([0.45, 1])
ax.set_xlim([ind[0] - 0.5 * width, ind[-1] + 2.5 * width])
ax.set_ylabel('Number of trials', fontsize=fontSizeLabels)
# ax.set_yticks([0.5, 1])
extraplots.set_ticks_fontsize(plt.gca(), fontSizeTicks)
extraplots.boxoff(ax)
ax.legend(bbox_to_anchor=(0.95, 0.6),
loc=3,
numpoints=1,
fontsize=fontSizeLabels,
ncol=1,
columnspacing=1.5,
frameon=False)
for i in [1, 3, 4]:
extraplots.significance_stars([i + 0.5 * width, i + 1.5 * width],
1000,
50,
starSize=6,
gapFactor=0.4,
color='0.5')
def plot_hist(ax, dataArr, color, label):
lowFreq = 4
highFreq = 128
nFreqs = 11
freqs = np.logspace(np.log10(lowFreq), np.log10(highFreq), nFreqs)
freqs = np.round(freqs, decimals=1)
freqs = np.r_[0, freqs]
freqLabels = ['{}'.format(freq) for freq in freqs[1:]]
freqLabels = ['NS', ' '] + freqLabels
roundData = np.round(dataArr[pd.notnull(dataArr)], decimals=1)
counts = Counter(roundData)
freqsToPlot = np.r_[0, 1, freqs[1:]]
index = np.arange(len(freqsToPlot))
heights = []
for freq in freqsToPlot:
try:
heights.append(100 * counts[freq] / np.double(len(roundData)))
except KeyError:
heights.append(0)
barWidth = 0.8
rects = plt.bar(index + 0.5 * barWidth,
heights,
barWidth,
label=label,
color=color)
plt.xticks(index + barWidth, freqs)
ax.set_xticklabels(freqLabels, rotation='vertical')
plt.ylabel('% cells')
# ax.set_xlim([1.5,index[-1]+2*barWidth-0.5])
# plt.xlabel('Highest AM rate to which\ncell can synchronize (Hz)')
extraplots.boxoff(ax)
height = max(heights) * 0.05
extraplots.breakaxis(1.8, 0, 0.3, height, gap=0.4)
ax.tick_params(axis='x', length=0)
plt.ylim([0, max(heights) + 1])
labelText = '{}, N={}'.format(label, len(roundData))
ax.annotate(labelText,
xy=(0.1, 0.9),
xycoords='axes fraction',
fontsize=9,
fontweight='bold')
return rects
def plot_band_psychometric(validPerSNR, rightPerSNR, possibleSNRs, colour = 'k', linestyle='-', xlabel=True, ylabel=True):
from statsmodels.stats.proportion import proportion_confint
performance = []
upper = []
lower = []
for inds in range(len(possibleSNRs)):
CIthisSNR = np.array(proportion_confint(rightPerSNR[inds], validPerSNR[inds], method = 'wilson'))
performance.append(100.0*rightPerSNR[inds]/validPerSNR[inds])
upper.append(100.0*CIthisSNR[1]-performance[-1])
lower.append(performance[-1]-100.0*CIthisSNR[0])
plt.plot(np.arange(len(possibleSNRs)), performance, linestyle, marker='o', color=colour, mec=colour, lw=3, ms=10)
plt.errorbar(np.arange(len(possibleSNRs)), performance, yerr = [lower, upper], color=colour, lw=2, ls=linestyle)
if ylabel:
plt.ylabel("% rightward", fontsize=16)
if xlabel:
plt.xlabel('SNR (dB)', fontsize=16)
plt.xticks(np.arange(len(possibleSNRs)), possibleSNRs)
plt.ylim((0,100))
ax = plt.gca()
extraplots.boxoff(ax)
def plot_events_in_time(timeStamps,nBins=50,fontsize=8):
'''
Plot histogram of inter-spike interval (in msec, log scale)
Parameters
----------
timeStamps : array (float in sec)
'''
ax = plt.gca()
timeBinEdges = np.linspace(timeStamps[0],timeStamps[-1],nBins) # in microsec
# FIXME: Limits depend on the time of the first spike (not of recording)
(nEvents,binEdges) = np.histogram(timeStamps,bins=timeBinEdges)
hp, = plt.plot((binEdges-timeStamps[0])/60.0, np.r_[nEvents,0], drawstyle='steps-post')
plt.setp(hp,lw=1,color='k')
plt.xlabel('Time (min)')
plt.axis('tight')
ax.set_yticks(plt.ylim())
extraplots.boxoff(ax)
extraplots.set_ticks_fontsize(ax,fontsize)
return hp
def multisession_events_in_time(timeStamps, nBins=50, fontsize=8):
'''
Plot the spike timestamps throughout the recording session.
IF the acquisition system is restarted at a site, then the timestamps will
also reset and cause a failure in the traditional implementation of this method
(spikesorting.plot_events_in_time). This method finds any negative ISIs (which mark
the spot where the timestamps were reset), adds the value of the ts immediatly before
the reset to all remaining timestamps, and plots a red line at this time point to indicate
that there is an uncertain amount of time between the spikes before and after this point.
TODO: Still need to implement the fix I described above and then use the method in the
multisession report
Parameters
----------
timeStamps : array (float in sec)
'''
# ISI = np.diff(timeStamps)
# if np.any(ISI<0):
ax = plt.gca()
timeBinEdges = np.linspace(timeStamps[0], timeStamps[-1],
nBins) # in microsec
# FIXME: Limits depend on the time of the first spike (not of recording)
(nEvents, binEdges) = np.histogram(timeStamps, bins=timeBinEdges)
hp, = plt.plot((binEdges - timeStamps[0]) / 60.0,
np.r_[nEvents, 0],
drawstyle='steps-post')
plt.setp(hp, lw=1, color='k')
plt.xlabel('Time (min)')
plt.axis('tight')
ax.set_yticks(plt.ylim())
extraplots.boxoff(ax)
extraplots.set_ticks_fontsize(ax, fontsize)
return hp
color=colorNoise,
clip_on=False)
spikeCountMat = spikesanalysis.spiketimes_to_spikecounts(
spikeTimesFromEventOnset, indexLimitsEachTrial, binEdges)
thisPSTH = np.mean(spikeCountMat, axis=0)
if smoothPSTH:
thisPSTH = np.convolve(thisPSTH, winShape, mode='same')
ratePSTH = thisPSTH / float(binsize / 1000.0)
axThalNoisePSTH.plot(psthTimeBase,
ratePSTH,
'-',
color=colorPSTH,
lw=psthLineWidth)
axThalNoisePSTH.set_xlim(displayRange)
extraplots.boxoff(axThalNoisePSTH)
axThalNoisePSTH.set_ylim([0, max(ratePSTH)])
axThalNoisePSTH.set_yticks([0, np.floor(np.max(ratePSTH))])
axThalNoisePSTH.set_ylabel('spk/s', fontsize=fontSizeLabels)
axThalNoisePSTH.set_xticks([0, 0.3])
extraplots.set_ticks_fontsize(axThalNoisePSTH, fontSizeTicks)
## -- Thalamus Laser -- ##
spikeTimesFromEventOnset = None
trialIndexForEachSpike = None
indexLimitsEachTrial = None
sessiontype = 'laserpulse'
cell = ephyscore.Cell(rowThal)
ephysData, bdata = cell.load(sessiontype)
spikeTimes = ephysData['spikeTimes']
eventOnsetTimes = ephysData['events']['stimOn']
ftraceEachTrial[cellInd1, trialsHighFreq],
'o',
ms=markerSize,
mew=3,
mec=color1,
mfc='none',
rasterized=RASTERIZED)
#plt.axis('square')
#plt.xlim()
#plt.ylim()
plt.axis([4866, 6238, 4407, 7830])
ax0.set_xticklabels([])
ax0.set_yticklabels([])
ax0.tick_params('both', direction='in')
extraplots.boxoff(ax0)
fontSize = 18
plt.xlabel('Response: Neuron {}'.format(cellsToPlot[0]), fontsize=fontSize)
plt.ylabel('Response: Neuron {}'.format(cellsToPlot[1]), fontsize=fontSize)
plt.show()
# -- Classifier --
if 1:
from sklearn import svm
nClass0 = np.sum(trialsLowFreq)
nClass1 = np.sum(trialsHighFreq)
class0 = np.vstack([
ftraceEachTrial[cellInd0, trialsLowFreq],
ftraceEachTrial[cellInd1, trialsLowFreq]
]).T
edgecolor='k',
facecolor='w')
rects2 = ax2.bar(ind + width + 0.015,
dataMat[:, :, 1].mean(1) - 0.5,
width,
bottom=0.5,
edgecolor='r',
facecolor='w')
ax2.set_xticks(ind + width)
ax2.set_xticklabels(np.arange(6) + 1, fontsize=fontSizeLabels)
ax2.set_xlabel('Mouse', fontsize=fontSizeLabels)
ax2.axhline(y=0.5, color='0.5', linestyle='-')
# ax2.set_ylim([0.45, 1])
ax2.set_xlim([ind[0] - 0.5 * width, ind[-1] + 2.5 * width])
ax2.set_ylabel('Number of Trials', fontsize=fontSizeLabels)
# ax2.set_yticks([0.5, 1])
extraplots.set_ticks_fontsize(plt.gca(), fontSizeTicks)
extraplots.boxoff(ax2)
# ax2.annotate('C', xy=(labelPosX[0],labelPosY[0]), xycoords='axes fraction', fontsize=fontSizePanel, fontweight='bold')
plt.show()
for indSubject in range(5):
subDataSal = dataMat[indSubject, :, 0]
subDataMus = dataMat[indSubject, :, 1]
print indSubject
print stats.ranksums(subDataSal, subDataMus)
def plot_ave_psycurve_reward_change(animal, sessions):
FREQCOLORS = [
'0.3', colorpalette.TangoPalette['Orange2'],
colorpalette.TangoPalette['SkyBlue2']
]
allBehavDataThisAnimal = behavioranalysis.load_many_sessions(
animal, sessions)
targetFrequency = allBehavDataThisAnimal['targetFrequency']
choice = allBehavDataThisAnimal['choice']
valid = allBehavDataThisAnimal['valid'] & (
choice != allBehavDataThisAnimal.labels['choice']['none'])
choiceRight = choice == allBehavDataThisAnimal.labels['choice']['right']
currentBlock = allBehavDataThisAnimal['currentBlock']
blockTypes = [
allBehavDataThisAnimal.labels['currentBlock']['same_reward'],
allBehavDataThisAnimal.labels['currentBlock']['more_left'],
allBehavDataThisAnimal.labels['currentBlock']['more_right']
]
#blockTypes = [allBehavDataThisAnimal.labels['currentBlock']['more_left'],allBehavDataThisAnimal.labels['currentBlock']['more_right']]
blockLabels = ['same_reward', 'more_left', 'more_right']
#blockLabels = ['more_left','more_right']
trialsEachType = behavioranalysis.find_trials_each_type(
currentBlock, blockTypes)
nFreqs = len(np.unique(targetFrequency))
#print trialsEachType
nBlocks = len(blockTypes)
#thisAnimalPos = inda
#ax1=plt.subplot(gs[thisAnimalPos])
#plt.clf()
fontsize = 12
allPline = []
blockLegends = []
fractionHitsEachValueAllBlocks = np.empty((nBlocks, nFreqs))
for blockType in range(nBlocks):
if np.any(trialsEachType[:, blockType]):
targetFrequencyThisBlock = targetFrequency[
trialsEachType[:, blockType]]
validThisBlock = valid[trialsEachType[:, blockType]]
choiceRightThisBlock = choiceRight[trialsEachType[:, blockType]]
#currentBlockValue = currentBlock[trialsEachBlock[0,block]]
(possibleValues,fractionHitsEachValue,ciHitsEachValue,nTrialsEachValue,nHitsEachValue)=\
behavioranalysis.calculate_psychometric(choiceRightThisBlock,targetFrequencyThisBlock,validThisBlock)
logPossibleValues = np.log2(possibleValues)
lowerFreqConstraint = logPossibleValues[1]
upperFreqConstraint = logPossibleValues[-2]
maxFreq = max(logPossibleValues)
minFreq = min(logPossibleValues)
constraints = ('Uniform({}, {})'.format(lowerFreqConstraint,
upperFreqConstraint),
'Uniform(0,5)', 'Uniform(0,1)', 'Uniform(0,1)')
estimate = extrastats.psychometric_fit(logPossibleValues,
nTrialsEachValue,
nHitsEachValue, constraints)
fractionHitsEachValueAllBlocks[
blockType, :] = fractionHitsEachValue
upperWhisker = ciHitsEachValue[1, :] - fractionHitsEachValue
lowerWhisker = fractionHitsEachValue - ciHitsEachValue[0, :]
xRange = logPossibleValues[-1] - logPossibleValues[1]
fitxvals = np.linspace(logPossibleValues[0] - 0.1 * xRange,
logPossibleValues[-1] + 0.1 * xRange, 40)
fityvals = extrastats.psychfun(fitxvals, *estimate)
# (pline, pcaps, pbars, pdots) = extraplots.plot_psychometric(1e-3*possibleValues,fractionHitsEachValue, ciHitsEachValue,xTickPeriod=1)
ax = plt.gca()
ax.hold(True)
(pline, pcaps, pbars) = ax.errorbar(
logPossibleValues,
100 * fractionHitsEachValue,
yerr=[100 * lowerWhisker, 100 * upperWhisker],
ecolor=FREQCOLORS[blockType],
fmt=None,
clip_on=False)
pdots = ax.plot(logPossibleValues,
100 * fractionHitsEachValue,
'o',
ms=6,
mec='None',
mfc=FREQCOLORS[blockType],
clip_on=False)
if blockType == 0:
pfit = ax.plot(fitxvals,
100 * fityvals,
color=FREQCOLORS[blockType],
lw=2,
clip_on=False,
linestyle='--')
else:
pfit = ax.plot(fitxvals,
100 * fityvals,
color=FREQCOLORS[blockType],
lw=2,
clip_on=False)
# plt.setp((pline, pcaps, pbars), color=FREQCOLORS[blockType])
# plt.setp((pline, pbars), color=FREQCOLORS[blockType])
# plt.setp(pdots, mfc=FREQCOLORS[blockType], mec=FREQCOLORS[blockType])
allPline.append(pline)
blockLegends.append(blockLabels[blockType])
if blockType == nBlocks - 1:
plt.xlabel('Frequency (kHz)', fontsize=fontsize)
plt.ylabel('Rightward trials (%)', fontsize=fontsize)
extraplots.set_ticks_fontsize(plt.gca(), fontsize)
ax.set_xticks(logPossibleValues)
tickLabels = [''] * len(possibleValues)
tickLabels[0] = 6.2
tickLabels[-1] = 19.2
ax.set_xticklabels(tickLabels)
ax.axhline(y=50, linestyle='-', color='0.7')
extraplots.boxoff(ax)
# legend = plt.legend(allPline,blockLegends,loc=2) #Add the legend manually to the current Axes.
# ax = plt.gca().add_artist(legend)
#plt.hold(True)
#plt.legend(bbox_to_anchor=(1, 1), bbox_transform=plt.gcf().transFigure)
#plt.show()
# plt.title('%s %s-%s'%(animal,sessions[0],sessions[-1]))
return fractionHitsEachValueAllBlocks
bandIndexLimitsEachTrial = cell['indexLimitsEachTrial']
rasterTimeRange = cell['rasterTimeRange']
trialsEachCond = cell['trialsEachCond']
trialsEachCond = trialsEachCond[:,1:] #don't include pure tone
trialsEachCond = trialsEachCond[:-70,:] #remove last couple of trials where baseline seems to increase
possibleBands = cell['possibleBands']
possibleBands = possibleBands[1:]
bandLabels = possibleBands.tolist()
bandLabels[-1] = 'WN'
colorEachCond = colours[indCell]*(len(possibleBands)/2+1)
pRaster, hcond, zline = extraplots.raster_plot(bandSpikeTimesFromEventOnset,bandIndexLimitsEachTrial,rasterTimeRange,
trialsEachCond=trialsEachCond,labels=bandLabels,colorEachCond=colorEachCond)
axRaster.annotate(panelLabels[indCell], xy=(labelPosX[1],labelPosY[indCell]), xycoords='figure fraction',
fontsize=fontSizePanel, fontweight='bold')
plt.setp(pRaster, ms=3, color='k')
extraplots.boxoff(axRaster)
if indCell != 2:
axRaster.set_xticklabels('')
plt.ylabel('Bandwidth (oct)',fontsize=fontSizeLabels)
yLims = np.array(plt.ylim())
rect = patches.Rectangle((0.0,yLims[1]*1.02),1.0,yLims[1]*0.04,linewidth=1,edgecolor=soundColor,facecolor=soundColor,clip_on=False)
axRaster.add_patch(rect)
extraplots.set_ticks_fontsize(plt.gca(),fontSizeTicks)
plt.xlabel('Time from sound onset (s)',fontsize=fontSizeLabels)
# -- Plots of sustained bandwidth tuning --
def plot_example_with_rate(subplotSpec, exampleName, color='k'):
fig = plt.gcf()
gs = gridspec.GridSpecFromSubplotSpec(1,
4,
subplot_spec=subplotSpec,
wspace=-0.45,
hspace=0.0)
specRaster = gs[0:2]
axRaster = plt.Subplot(fig, specRaster)
fig.add_subplot(axRaster)
spikeTimes = exampleSpikeTimes[exampleName]
indexLimitsEachTrial = exampleIndexLimitsEachTrial[exampleName]
timeRange = [-0.2, 0.7]
freqEachTrial = exampleFreqEachTrial[exampleName]
possibleFreq = np.unique(freqEachTrial)
freqLabels = ['{0:.1f}'.format(freq) for freq in possibleFreq]
trialsEachCondition = behavioranalysis.find_trials_each_type(
freqEachTrial, possibleFreq)
pRaster, hCond, zline = extraplots.raster_plot(spikeTimes,
indexLimitsEachTrial,
timeRange,
trialsEachCondition,
labels=freqLabels)
plt.setp(pRaster, ms=2)
ax = plt.gca()
ax.set_xticks([0, 0.5])
ax.set_xlabel('Time from sound onset (s)')
ax.set_ylabel('AM Rate (Hz)')
# ax.annotate('A', xy=(labelPosX[0],labelPosY[0]), xycoords='figure fraction',
# fontsize=fontSizePanel, fontweight='bold')
countRange = [0.1, 0.5]
spikeCountMat = spikesanalysis.spiketimes_to_spikecounts(
spikeTimes, indexLimitsEachTrial, countRange)
numSpikesInTimeRangeEachTrial = np.squeeze(spikeCountMat)
numSpikesInTimeRangeEachTrial = np.squeeze(
np.diff(indexLimitsEachTrial, axis=0))
if len(numSpikesInTimeRangeEachTrial) == len(freqEachTrial) + 1:
numSpikesInTimeRangeEachTrial = numSpikesInTimeRangeEachTrial[:-1]
conditionMatShape = np.shape(trialsEachCondition)
numRepeats = np.product(conditionMatShape[1:])
nSpikesMat = np.reshape(numSpikesInTimeRangeEachTrial.repeat(numRepeats),
conditionMatShape)
spikesFilteredByTrialType = nSpikesMat * trialsEachCondition
avgSpikesArray = np.sum(spikesFilteredByTrialType, 0) / np.sum(
trialsEachCondition, 0).astype('float') / np.diff(np.array(countRange))
stdSpikesArray = np.std(spikesFilteredByTrialType, 0) / np.diff(
np.array(countRange))
specRate = gs[3]
axRate = plt.Subplot(fig, specRate)
fig.add_subplot(axRate)
nRates = len(possibleFreq)
plt.hold(True)
plt.plot(avgSpikesArray,
range(nRates),
'ro-',
mec='none',
ms=7,
lw=3,
color=color)
plt.plot(avgSpikesArray - stdSpikesArray, range(len(possibleFreq)), 'k:')
plt.plot(avgSpikesArray + stdSpikesArray, range(len(possibleFreq)), 'k:')
axRate.set_ylim([-0.5, nRates - 0.5])
axRate.set_yticks(range(nRates))
axRate.set_yticklabels([])
#ax = plt.gca()
axRate.set_xlabel('Firing rate (spk/s)')
extraplots.boxoff(axRate)
# extraplots.boxoff(ax, keep='right')
return (axRaster, axRate)
markerThisCond = markerEachCond[indc]
for indSubject, oneSubject in enumerate(subjectsThisCond):
sessionsThisSubject = sessionsThisCond & (subject==oneSubject)
samples = (180/np.pi) * np.concatenate(deltaHeadAngle[sessionsThisSubject])# From radians to degrees
samples = samples[:maxSamplesToInclude]
xvals = np.tile(xPos[indc]+0.1*indSubject-0.1,len(samples))
plt.plot(xvals,samples,'o',marker=markerEachSubject[indSubject],mfc='none',mec='0.75', zorder=-1,clip_on=False)
meanVal = np.mean(samples)
seVal = np.std(samples)/np.sqrt(len(samples))
meanEachCondEachSubject[indc].append(meanVal)
subjectIndFromAll = list(possibleSubjects).index(oneSubject)
#print samples
dataEachCondEachSubject[subjectIndFromAll][indc] = samples
#[pline,pcap,pbar] = plt.errorbar(xPos[indc]+0.1*indSubject-0.2, meanVal, seVal, color=colorThisCond)
pmark = plt.plot(xPos[indc]+0.1*indSubject-0.1, meanVal,markerThisCond,mfc=colorThisCond,mec='None')
extraplots.boxoff(ax3)
plt.ylabel('Change in angle (deg)')
ax3.set_yticks(np.arange(-200,300,100))
#plt.ylim([-200,200])
plt.ylim(300*np.array([-1,1]))
plt.xlim([-0.7,4.1])
ax3.axes.get_xaxis().set_visible(False)
ax3.spines['bottom'].set_visible(False)
signifYpos = 300 #220
extraplots.significance_stars([xPos[0],xPos[1]], signifYpos, 20, starSize=10, gapFactor=0.2, color='0.5')
extraplots.significance_stars([xPos[2],xPos[3]], signifYpos, 20, starSize=10, gapFactor=0.2, color='0.5')
plt.text(np.mean(xPos[0:2]), -signifYpos, 'Left', ha='center', fontsize=fontSizeLabels+2)
plt.text(np.mean(xPos[2:4]), -signifYpos, 'Right', ha='center', fontsize=fontSizeLabels+2)
plt.show()
axLatency.plot(pos,
D1PopStat * 1000,
'o',
mec=colorD1,
mfc='None',
alpha=markerAlpha)
medline(axLatency, np.median(D1PopStat) * 1000, 1, 0.5)
axLatency.set_ylabel('Latency (ms)', fontsize=fontSizeTicks)
# tickLabels = ['ATh:Str', 'AC:Str']
tickLabels = [
'nD1:Str\nn={}'.format(len(nD1PopStat)),
'D1:Str\nn={}'.format(len(D1PopStat))
]
axLatency.set_xticks(range(2))
axLatency.set_xlim([-0.5, 1.5])
extraplots.boxoff(axLatency)
axLatency.set_ylim([-0.001, 65])
extraplots.set_ticks_fontsize(axLatency, fontSizeTicks)
axLatency.set_xticklabels(tickLabels, fontsize=fontSizeLabels, rotation=45)
zstat, pVal = stats.ranksums(nD1PopStat, D1PopStat)
# print "Ranksums test between thalamus and AC population stat ({}) vals: p={}".format(popStatCol, pVal) Remove Matt
messages.append("{} p={}".format(popStatCol, pVal))
'''
if pVal<0.05:
starMarker='*'
else:
starMarker='n.s.'
extraplots.new_significance_stars([0, 1], yStars, yStarHeight, starMarker=starMarker,
#Is this the correct thing to get to calculate psychometrics?
choiceRight = choice==bdata.labels['choice']['right']
targetFreq = bdata['targetFrequency']
noLaserTrials = valid&(bdata['trialType']==0)
(possibleValues,fractionHitsEachValue,ciHitsEachValue,nTrialsEachValue,nHitsEachValue)=\
behavioranalysis.calculate_psychometric(choiceRight, targetFreq, noLaserTrials)
(pline, pcaps, pbars, pdots) = extraplots.plot_psychometric(1e-3*possibleValues,fractionHitsEachValue,ciHitsEachValue,xTickPeriod=1)
allPlines.append(pline)
ax = pline.axes
extraplots.boxoff(ax)
extraplots.set_ticks_fontsize(ax, fontsize)
#plt.title(subject+' - '+sessions[0]+'-'+sessions[-1], fontsize=fontsize)
plt.xlabel('Frequency (kHz)',fontsize=fontsize)
plt.ylabel('Rightward trials (%)',fontsize=fontsize)
extraplots.set_ticks_fontsize(plt.gca(),fontsize)
plt.setp(pline, color='k')
plt.setp(pcaps, color='k')
plt.setp(pbars, color='k')
plt.setp(pdots, markerfacecolor='k')
legend = plt.legend(allPlines, ['No Laser', 'Laser'])
plt.hold(True)
laserTrials = valid&(bdata['trialType']==1)
color=colours[indCell][laser])
lines.append(line)
#plt.legend([lines[-1],lines[0]],['{}, SI = {:.2f}'.format(figLegends[indCell], SIs[1]),'Control, SI = {:.2f}'.format(SIs[0])], loc='best', frameon=False, fontsize=fontSizeLabels)
plt.legend([lines[-1], lines[0]], [figLegends[indCell], 'Control'],
loc='best',
frameon=False,
fontsize=fontSizeLabels)
axCurve.annotate(panelLabels[indCell],
xy=(labelPosX[0], labelPosY[indCell]),
xycoords='figure fraction',
fontsize=fontSizePanel,
fontweight='bold')
axCurve.set_ylim(bottom=0)
axCurve.set_xticks(bands[1:])
axCurve.tick_params(top=False, right=False, which='both')
extraplots.boxoff(axCurve)
extraplots.set_ticks_fontsize(plt.gca(), fontSizeTicks)
if not indCell:
axCurve.set_xticklabels('')
if indCell:
axCurve.set_xticks(bands)
bands = bands.tolist()
bands[-1] = 'WN'
bands[1::2] = [''] * len(
bands[1::2]) #remove every other label so x axis less crowded
axCurve.set_xticklabels(bands)
plt.xlabel('Bandwidth (oct)', fontsize=fontSizeLabels)
plt.ylabel('Firing rate (spk/s)', fontsize=fontSizeLabels)
plt.xlim(-0.1, 7) #expand x axis so you don't have dots on y axis
if PANELS[1]:
def plot_example_with_rate(axRaster, axFR, exampleName, color='k'):
spikeTimes = exampleSpikeTimes[exampleName]
indexLimitsEachTrial = exampleIndexLimitsEachTrial[exampleName]
timeRange = [-0.2, 0.7]
freqEachTrial = exampleFreqEachTrial[exampleName]
possibleFreq = np.unique(freqEachTrial)
freqLabels = ['{0:.0f}'.format(freq) for freq in possibleFreq]
trialsEachCondition = behavioranalysis.find_trials_each_type(
freqEachTrial, possibleFreq)
plt.sca(axRaster)
pRaster, hCond, zline = extraplots.raster_plot(spikeTimes,
indexLimitsEachTrial,
timeRange,
trialsEachCondition,
labels=freqLabels)
plt.setp(pRaster, ms=figparams.rasterMS)
blankLabels = [''] * 11
for labelPos in [0, 5, 10]:
blankLabels[labelPos] = freqLabels[labelPos]
axRaster.set_yticklabels(blankLabels)
# ax = plt.gca()
axRaster.set_xticks([0, 0.5])
axRaster.set_xlabel('Time from\nsound onset (s)',
fontsize=fontSizeLabels,
labelpad=-1)
axRaster.set_ylabel('AM rate (Hz)', fontsize=fontSizeLabels, labelpad=-5)
# ax.annotate('A', xy=(labelPosX[0],labelPosY[0]), xycoords='figure fraction',
# fontsize=fontSizePanel, fontweight='bold')
countRange = [0.1, 0.5]
# spikeCountMat = spikesanalysis.spiketimes_to_spikecounts(spikeTimes, indexLimitsEachTrial, countRange)
# numSpikesInTimeRangeEachTrial = np.squeeze(spikeCountMat)
numSpikesInTimeRangeEachTrial = np.squeeze(
np.diff(indexLimitsEachTrial, axis=0))
if len(numSpikesInTimeRangeEachTrial) == len(freqEachTrial) + 1:
numSpikesInTimeRangeEachTrial = numSpikesInTimeRangeEachTrial[:-1]
conditionMatShape = np.shape(trialsEachCondition)
numRepeats = np.product(conditionMatShape[1:])
nSpikesMat = np.reshape(numSpikesInTimeRangeEachTrial.repeat(numRepeats),
conditionMatShape)
spikesFilteredByTrialType = nSpikesMat * trialsEachCondition
avgSpikesArray = np.sum(spikesFilteredByTrialType, 0) / np.sum(
trialsEachCondition, 0).astype('float') / np.diff(np.array(countRange))
stdSpikesArray = np.std(spikesFilteredByTrialType, 0) / np.diff(
np.array(countRange))
axRate = plt.subplot(axFR)
plt.sca(axRate)
nRates = len(possibleFreq)
plt.hold(True)
plt.plot(avgSpikesArray,
range(nRates),
'ro-',
mec='none',
ms=6,
lw=3,
color=color)
plt.plot(avgSpikesArray - stdSpikesArray, range(len(possibleFreq)), 'k:')
plt.plot(avgSpikesArray + stdSpikesArray, range(len(possibleFreq)), 'k:')
axRate.set_ylim([-0.5, nRates - 0.5])
axRate.set_yticks(range(nRates))
axRate.set_yticklabels([])
# ax = plt.gca()
axRate.set_xlabel('Firing rate\n(spk/s)',
fontsize=fontSizeLabels,
labelpad=-1)
extraplots.boxoff(axRate)
plt.setp(markers, ms=dataMS)
plt.hold(1)
medline(np.median(acPopStat), 1, 0.5)
plt.hold(1)
axSummary.set_yticks(yticks)
axSummary.set_yticklabels(ytickLabels)
# tickLabels = ['ATh:Str\nn={}'.format(len(thalPopStat)), 'AC:Str\nn={}'.format(len(acPopStat))]
tickLabels = ['ATh:Str', 'AC:Str']
axSummary.set_xticks(range(2))
axSummary.set_xticklabels(tickLabels, rotation=45)
axSummary.set_xlim([-0.5, 1.5])
extraplots.set_ticks_fontsize(axSummary, fontSizeLabels)
extraplots.boxoff(axSummary)
# axSummary.set_yticks(np.unique(thalPopStat))
# axSummary.set_yticklabels(possibleFreqLabels)
# axSummary.set_ylim([-0.001, 0.161])
yDataMax = max([max(acPopStat), max(thalPopStat)])
yStars = yDataMax + yDataMax * starYfactor
yStarHeight = (yDataMax * starYfactor) * starHeightFactor
zVal, pVal = stats.mannwhitneyu(thalPopStat, acPopStat)
messages.append("{} p={}".format(popStatCol, pVal))
# if pVal < 0.05:
# extraplots.new_significance_stars([0, 1], np.log(170), np.log(1.1), starMarker='*',
# fontSize=fontSizeStars, gapFactor=starGapFactor)
# else:
# extraplots.new_significance_stars([0, 1], np.log(170), np.log(1.1), starMarker='n.s.',
capthick=1)
patches.append(
mpatches.Patch(color=bandColours[band], label=numBands[band]))
plt.legend(handles=patches,
borderaxespad=0.3,
prop={'size': 12},
loc='best')
axPsyCurve.set_xticks(range(len(numSNRs)))
axPsyCurve.set_xticklabels(numSNRs)
axPsyCurve.set_xlabel('SNR (dB)')
axPsyCurve.set_ylim(0, 100)
axPsyCurve.set_ylabel('% trials tone reported')
extraplots.boxoff(axPsyCurve)
# -- plot accuracies for each bandwidth and laser presentation --
axAccuracy = plt.subplot(gs[0, 1])
barLoc = np.array([-0.24, 0.24])
xLocs = np.arange(len(numBands))
xTickLabels = numBands
for band in range(len(numBands)):
accuracy = np.zeros(len(numLasers))
for laser in range(len(numLasers)):
accuracy[laser] = 100.0 * np.sum(
correct[trialsEachCond[:, laser, band]]) / np.sum(
valid[trialsEachCond[:, laser, band]])
plt.axvline(x=0, linewidth=1, color='darkgrey')
plt.xlim(timeRange)
yLims = [0, 50]
soundBarHeight = 0.1 * yLims[-1]
plt.fill([0, 0.1, 0.1, 0],
yLims[-1] + np.array([0, 0, soundBarHeight, soundBarHeight]),
ec='none',
fc=soundColor,
clip_on=False)
plt.ylim(yLims)
plt.yticks(yLims)
plt.xticks(np.arange(-0.2, 0.6, 0.2))
plt.xlabel('Time from sound onset (s)', fontsize=fontSizeLabels)
plt.ylabel('Firing rate\n(spk/s)',
fontsize=fontSizeLabels) #, labelpad=labelDis)
extraplots.boxoff(plt.gca())
# -- Panel C: representative sound-evoked raster from psychometric task, modulated -- #
#ax4 = plt.subplot(gs[2, 0:2])
ax4 = plt.subplot(gs01[0:2, 0:])
ax4.annotate('C',
xy=(labelPosX[1], labelPosY[1]),
xycoords='figure fraction',
fontsize=fontSizePanel,
fontweight='bold')
if PANELS[1]:
rasterFilename = 'example_psychometric_midfreq_soundaligned_raster_test089_20160124a_T4_c6.npz'
rasterFullPath = os.path.join(dataDir, rasterFilename)
rasterExample = np.load(rasterFullPath)
amplitudeColor = cp.TangoPalette['ScarletRed1']
distanceColor = cp.TangoPalette['SkyBlue2']
velocityColor = cp.TangoPalette['Chameleon3']
markerSize = 8
fig = plt.gcf()
fig.clf()
fig.set_facecolor('w')
gs = gridspec.GridSpec(2, 3)
gs.update(left=0.15, right=0.85, wspace=1, hspace=0.5)
ax1 = plt.subplot(gs[0, :])
plt.plot(np.random.randn(20),np.random.randn(20),'o-',ms=markerSize, color='0.75',mfc=amplitudeColor,mec='w')
extraplots.boxoff(plt.gca())
plt.xlabel('Time (s)', fontsize=fontSizeLabels)
plt.ylabel('Amplitude (V)', fontsize=fontSizeLabels)
extraplots.set_ticks_fontsize(plt.gca(),fontSizeTicks)
ax1.annotate('A', xy=(labelPosX[0],labelPosY[0]), xycoords='figure fraction',
fontsize=fontSizePanel, fontweight='bold')
ax2 = plt.subplot(gs[1,:-1])
plt.plot(np.random.randn(20),np.random.randn(20),'o-',ms=markerSize,color='0.75',mfc=distanceColor,mec='w')
extraplots.boxoff(plt.gca())
extraplots.set_ticks_fontsize(plt.gca(),fontSizeTicks)
plt.xlabel('Time (s)', fontsize=fontSizeLabels)
plt.ylabel('Distance (m)', fontsize=fontSizeLabels)
ax2.annotate('B', xy=(labelPosX[0],labelPosY[1]), xycoords='figure fraction', fontsize=fontSizePanel, fontweight='bold')
ax3 = plt.subplot(gs[1:, -1])
rects1 = ax3.bar(ind, 1000*subjectMeans[:,0], width, bottom=0.5, edgecolor='k', facecolor='w', lw=2, label='Saline', align='edge')
rects2 = ax3.bar(ind+width+0.015, 1000*subjectMeans[:,1], width, bottom=0.5, edgecolor=muscimolColor, lw=2, facecolor='w', label='Muscimol', align='edge')
# plt.ylim([250,730])
ymax = 730
ymin = 250
plt.ylim([ymin,ymax])
xticks = range(5)
xticklabels = range(1,6)
plt.ylabel('Time from center port exit\nto reward port entry (ms)')
plt.xlabel('Mouse')
ax3.set_xlim([ind[0]-0.5*width, ind[-1]+2.5*width ])
ax3.set_xticks(ind + width)
ax3.set_xticklabels(np.arange(6)+1, fontsize=fontSizeTicks)
extraplots.boxoff(ax3)
for sigSubjectInd in [4]:
extraplots.significance_stars([sigSubjectInd+0.5*width,sigSubjectInd+1.5*width], ymax, (ymax-ymin)*starLineHeightFactor, starSize=6, gapFactor=0.4, color='0.5')
# extraplots.significance_stars(sigSubjectInd+np.array([-0.25,0.25]), 710, 25, starSize=6, gapFactor=0.4, color='0.5')
# -- Stats -- #
for inds, subject in enumerate(subjects):
zScore, pVal = stats.ranksums(centerToSideFile['{}validmeansaline'.format(subject)], centerToSideFile['{}validmeanmuscimol'.format(subject)])
print 'For mouse {}, using only mean of valid trials in saline condition and in muscimol condition in a ranksums test, p value for the difference in time from centerOut to sideIn is {}.'.format(inds+1, pVal)
# -- Panel C: response times -- #
ax4 = plt.subplot(gs[1, 0])
soundToCoutFilename = 'muscimol_response_time_summary.npz'
soundToCoutFullPath = os.path.join(dataDir,soundToCoutFilename)
soundToCoutFile = np.load(soundToCoutFullPath)
colorEachCond=colorEachCond,
fillWidth=None,
labels=None)
plt.setp(pRaster, ms=msRaster)
soundTimesFromEventOnset = intData['soundTimesFromEventOnset']
trialsToUse = np.sum(trialsEachCond, axis=1).astype('bool')
yLims = plt.gca().get_ylim()
plt.hold('on')
bplot = plt.boxplot(soundTimesFromEventOnset[trialsToUse],
sym='',
vert=False,
positions=[yLims[-1] * 1.05],
widths=[yLims[-1] * 0.04])
extraplots.boxoff(plt.gca())
plt.autoscale(enable=True, axis='y', tight=True)
#plt.axis('off')
for element in ['boxes', 'whiskers', 'fliers', 'caps']:
plt.setp(bplot[element], color='grey', linewidth=1)
plt.setp(bplot['whiskers'], linestyle='-')
plt.setp(bplot['medians'], color='orange')
sideInTimesFromEventOnset = intData['sideInTimesFromEventOnset']
plt.hold('on')
bplot = plt.boxplot(sideInTimesFromEventOnset[trialsToUse],
sym='',
vert=False,
positions=[yLims[-1] * 1.05],
widths=[yLims[-1] * 0.04])
extraplots.boxoff(plt.gca())
pdots = ax1.plot(logPossibleValues, 100*fractionHitsEachValue, 'o', ms=6, mec='None', mfc=color,
clip_on=False)
#ax1.set_xticks(logPossibleValues)
#freqLabels = ['{:.03}'.format(x) for x in possibleValues/1000.0]
#ax1.set_xticklabels(freqLabels)
#ax1.set_xlabel('Frequency (kHz)', fontsize=fontSizeLabels)
pfit, = ax1.plot(fitxvals, 100*fityvals, color=color, lw=2, clip_on=False)
plotHandles.append(pfit)
ax1.annotate('B', xy=(labelPosX[0],labelPosY[0]), xycoords='axes fraction',
fontsize=fontSizePanel, fontweight='bold')
extraplots.boxoff(ax1)
#xticks = ax1.get_xticks()
#newXtickLabels = np.logspace(xticks[0], xticks[-1], 3, base=2)
#ax1.set_xticks(np.log2(np.array(newXtickLabels)))
#ax1.set_xticklabels(['{:.3}'.format(x/1000.0) for x in newXtickLabels])
xTicks = np.array([6,11,19])
ax1.set_xticks(np.log2(xTicks*1000))
freqLabels = ['{:d}'.format(x) for x in xTicks]
ax1.set_xticklabels(freqLabels)
ax1.set_xlabel('Frequency (kHz)', fontsize=fontSizeLabels)
ax1.set_xlim([fitxvals[0],fitxvals[-1]])
ax1.set_ylim([0, 100])
ax1.set_ylabel('Rightward trials (%)', fontsize=fontSizeLabels)
lines.append(line)
#plt.legend([lines[-1],lines[0]],['{}, SI = {:.2f}'.format(figLegends[indCell], SIs[1]),'Control, SI = {:.2f}'.format(SIs[0])], loc='best', frameon=False, fontsize=fontSizeLabels)
plt.legend([lines[-1], lines[0]], [figLegends[indCell], 'control'],
loc=legendLocs[indCell],
frameon=False,
fontsize=fontSizeLegend,
borderpad=2.0)
axCurve.annotate(panelLabels[indCell],
xy=(labelPosX[2], labelPosY[indCell]),
xycoords='figure fraction',
fontsize=fontSizePanel,
fontweight='bold')
axCurve.set_ylim(bottom=0)
axCurve.set_xticks(bands[1:])
axCurve.tick_params(top=False, right=False, which='both')
extraplots.boxoff(axCurve)
extraplots.set_ticks_fontsize(plt.gca(), fontSizeTicks)
# if not indCell:
# axCurve.set_xticklabels('')
# if indCell:
#axCurve.set_xticks(bands)
bands = bands.tolist()
bands[-1] = 'WN'
#bands[1::2] = ['']*len(bands[1::2]) #remove every other label so x axis less crowded
axCurve.set_xticklabels(bands[1:])
#plt.xticks(rotation=-45)
plt.xlabel('Bandwidth (oct)', fontsize=fontSizeLabels)
plt.ylabel('Firing rate (spk/s)', fontsize=fontSizeLabels)
plt.xlim(0.2, 7) #expand x axis so you don't have dots on y axis
# bottom three panels have their own gridspec of sorts
pRaster, hcond, zline = extraplots.raster_plot(spikeTimesFromEventOnset,
indexLimitsEachTrial,
timeRangeSound,
trialsEachCond=trialsEachCond,
colorEachCond=colorEachFreq,
labels=labels)
plt.setp(pRaster, ms=msRaster)
plt.setp(hcond,zorder=3)
movementTimesFromEventOnset = rasterExample['movementTimesFromEventOnset']
trialsToUse = np.sum(trialsEachCond, axis=1).astype('bool')
yLims = plt.gca().get_ylim()
plt.hold('on')
bplot = plt.boxplot(movementTimesFromEventOnset[trialsToUse], sym='', vert=False, positions=[yLims[-1]+15], widths=[25])
extraplots.boxoff(plt.gca())
plt.autoscale(enable=True, axis='y', tight=True)
plt.axis('off')
for element in ['boxes', 'whiskers', 'fliers', 'caps']:
plt.setp(bplot[element], color='grey', linewidth=1)
plt.setp(bplot['whiskers'], linestyle='-')
plt.setp(bplot['medians'], color='orange')
#plt.xlabel('Time from sound onset (s)',fontsize=fontSizeLabels, labelpad=labelDis)
plt.gca().set_xticklabels('')
plt.ylabel('Frequency (kHz)',fontsize=fontSizeLabels) #, labelpad=labelDis)
plt.xlim(timeRangeSound[0],timeRangeSound[1])
ax6 = plt.subplot(gs00[3,:])
psthFilename = 'example_freq_tuning_2afc_psth_adap017_20160317a_T5_c3.npz'
nD1PopStat = nD1[popStatCol][pd.notnull(nD1[popStatCol])]
pos = jitter(np.ones(len(nD1PopStat))*0, 0.20)
axBW.plot(pos, nD1PopStat, 'o', mec=colornD1, mfc='None', alpha=markerAlpha)
medline(axBW, np.median(nD1PopStat), 0, 0.5)
pos = jitter(np.ones(len(D1PopStat))*1, 0.20)
axBW.plot(pos, D1PopStat, 'o', mec=colorD1, mfc='None', alpha=markerAlpha)
medline(axBW, np.median(D1PopStat), 1, 0.5)
axBW.set_ylabel('BW10', fontsize=fontSizeLabels)
tickLabels = ['nD1:Str\nn={}'.format(len(nD1PopStat)), 'D1:Str\nn={}'.format(len(D1PopStat))]
axBW.set_xticks(range(2))
axBW.set_xlim([-0.5, 1.5])
ylim = [-0.5, 6]
axBW.set_ylim(ylim)
extraplots.boxoff(axBW)
extraplots.set_ticks_fontsize(axBW, fontSizeTicks)
axBW.set_xticklabels(tickLabels, fontsize=fontSizeLabels, rotation=45)
zstat, pVal = stats.mannwhitneyu(nD1PopStat, D1PopStat, alternative='two-sided') # Nick used stats.ranksum
messages.append("{} p={}".format(popStatCol, pVal))
yDataMax = max([max(D1PopStat), max(nD1PopStat)])
# yStars = yDataMax + yDataMax*starYfactor
yStars = max(ylim) * 1.05
yStarHeight = (yDataMax*starYfactor)*starHeightFactor
plt.sca(axBW)
starString = None if pVal < 0.05 else 'n.s.'
extraplots.significance_stars([0, 1], yStars, yStarHeight, starMarker='*',
starSize=fontSizeStars+2, starString=starString,
def plot_am_with_rate(subplotSpec,
spikeTimes,
indexLimitsEachTrial,
currentFreq,
uniqFreq,
color='k'):
fig = plt.gcf()
gs = gridspec.GridSpecFromSubplotSpec(4,
4,
subplot_spec=subplotSpec,
wspace=-0.45,
hspace=0.0)
axRaster = plt.ubplot(fig, specRaster)
# Possible issue in matplotlib backend preventing subplot from working properly. Based on pylab we use TkAgg
fig.add_subplot(axRaster)
timeRange = [-0.2, 0.7]
freqLabels = ['{0:.0f}'.format(freq) for freq in uniqFreq]
trialsEachCondition = behavioranalysis.find_trials_each_type(
currentFreq, uniqFreq)
pRaster, hCond, zline = extraplots.raster_plot(spikeTimes,
indexLimitsEachTrial,
timeRange,
trialsEachCondition,
labels=freqLabels)
plt.setp(pRaster, ms=figparams.rasterMS)
blankLabels = [''] * 11
for labelPos in [0, 5, 10]:
blankLabels[labelPos] = freqLabels[labelPos]
axRaster.set_yticklabels(blankLabels)
ax = plt.gca()
ax.set_xticks([0, 0.5])
ax.set_xlabel('Time from\nsound onset (s)',
fontsize=fontSizeLabels,
labelpad=-1)
ax.set_ylabel('AM rate (Hz)', fontsize=fontSizeLabels, labelpad=-5)
# ax.annotate('A', xy=(labelPosX[0],labelPosY[0]), xycoords='figure fraction',
# fontsize=fontSizePanel, fontweight='bold')
countRange = [0.1, 0.5]
spikeCountMat = spikesanalysis.spiketimes_to_spikecounts(
spikeTimes, indexLimitsEachTrial, countRange)
# numSpikesInTimeRangeEachTrial = np.squeeze(spikeCountMat)
numSpikesInTimeRangeEachTrial = np.squeeze(
np.diff(indexLimitsEachTrial, axis=0))
if len(numSpikesInTimeRangeEachTrial) == len(currentFreq) + 1:
numSpikesInTimeRangeEachTrial = numSpikesInTimeRangeEachTrial[:-1]
conditionMatShape = np.shape(trialsEachCondition)
numRepeats = np.product(conditionMatShape[1:])
nSpikesMat = np.reshape(numSpikesInTimeRangeEachTrial.repeat(numRepeats),
conditionMatShape)
spikesFilteredByTrialType = nSpikesMat * trialsEachCondition
avgSpikesArray = np.sum(spikesFilteredByTrialType, 0) / np.sum(
trialsEachCondition, 0).astype('float') / np.diff(np.array(countRange))
stdSpikesArray = np.std(spikesFilteredByTrialType, 0) / np.diff(
np.array(countRange))
specRate = gs[0:3, 3]
axRate = plt.Subplot(fig, specRate)
fig.add_subplot(axRate)
nRates = len(uniqFreq)
plt.hold(True)
plt.plot(avgSpikesArray,
range(nRates),
'ro-',
mec='none',
ms=6,
lw=3,
color=color)
plt.plot(avgSpikesArray - stdSpikesArray, range(len(uniqFreq)), 'k:')
plt.plot(avgSpikesArray + stdSpikesArray, range(len(uniqFreq)), 'k:')
axRate.set_ylim([-0.5, nRates - 0.5])
axRate.set_yticks(range(nRates))
axRate.set_yticklabels([])
# ax = plt.gca()
axRate.set_xlabel('Firing rate\n(spk/s)',
fontsize=fontSizeLabels,
labelpad=-1)
extraplots.boxoff(axRate)
# extraplots.boxoff(ax, keep='right')
return axRaster, axRate
SIs = EXC_CELLS['fitSustainedSuppressionIndexNoZeroHighAmp']
slope, intercept, rVal, pVal, stdErr = stats.linregress(depths, SIs)
print "SI vs cortical depth linear regression: \ncorrelation coefficient (r): {}\np Value: {}".format(
rVal, pVal)
axScatter = plt.subplot(gs[0, 1])
plt.hold(True)
plt.plot(depths, SIs, 'o', color=excColor)
xvals = np.linspace(-2, 2, 200)
yvals = slope * xvals + intercept
plt.plot(xvals, yvals, '--', color=excColor, zorder=-1)
plt.xlim(-0.1, 1.1)
plt.ylim(-0.1, 1.1)
plt.xlabel('Depth from pia \n(fraction cortical width)',
fontsize=fontSizeLabels)
plt.ylabel('Suppression Index', fontsize=fontSizeLabels)
extraplots.boxoff(axScatter)
axScatter.annotate(panelLabel,
xy=(labelPosX[1], labelPosY),
xycoords='figure fraction',
fontsize=fontSizePanel,
fontweight='bold')
if SAVE_FIGURE:
extraplots.save_figure(figFilename, figFormat, figSize, outputDir)
color=thisColor,
mec='none',
lw=3,
ms=10,
clip_on=False)
pHandles.append(thisPlot)
plt.errorbar(np.arange(len(possibleSNRs)),
performance,
yerr=[lower, upper],
color=thisColor,
clip_on=False)
plt.xticks(np.arange(len(possibleSNRs)), possibleSNRs)
plt.xlim([-0.2, len(possibleSNRs) - 1 + 0.2])
plt.ylim((0, 100))
plt.legend(pHandles, ['Control', 'No E cells'],
loc='upper left',
numpoints=1,
markerscale=1,
handlelength=1.5,
frameon=False)
extraplots.boxoff(ax1)
#plt.ylabel('Rightward choice (%)', fontsize=fontSizeLabels)
plt.ylabel('Signal detection rate (%)', fontsize=fontSizeLabels)
plt.xlabel('Signal to noise ratio (dB)', fontsize=fontSizeLabels)
plt.show()
if SAVE_FIGURE:
extraplots.save_figure(figFilename, figFormat, figSize, outputDir)
fontSizeTicks = 10
panelsToPlot=[0, 1]
gs = gridspec.GridSpec(5, 1)
# gs.update(left=0.15, right=0.95, bottom=0.15, wspace=0.5, hspace=0.5)
summaryFilename = 'muscimol_reaction_time_summary.npz'
summaryFullPath = os.path.join(dataDir,summaryFilename)
fcFile = np.load(summaryFullPath)
subjects = fcFile['subjects']
conditions = fcFile['conditions']
for indsubject, subject in enumerate(subjects):
ax = plt.subplot(gs[indsubject, 0])
#ax.hist(fcFile['{}allsaline'.format(subject)], bins=100, histtype='step', color='k')
ax.hist(fcFile['{}validsaline'.format(subject)], bins=100, histtype='step', color='k')
#ax.hist(fcFile['{}allmuscimol'.format(subject)], bins=100, histtype='step', color='r')
ax.hist(fcFile['{}validmuscimol'.format(subject)], bins=100, histtype='step', color='r')
ax.set_xlim([0.2, 1.0])
extraplots.boxoff(ax)
z, pVal = stats.ranksums(fcFile['{}validsaline'.format(subject)], fcFile['{}validmuscimol'.format(subject)])
print 'mouse {}'.format(indsubject+1), ' Compare reaction times (side-in minus center-out) between saline and muscimol sessions using ranksum test, p value is {}'.format(pVal)
plt.show()
if SAVE_FIGURE:
extraplots.save_figure(figFilename, figFormat, figSize, outputDir)
ax0.set_xlim([0.8, 2.2])
ax0.set_xticks([1, 2])
ax0.set_xticklabels([])
ax0.set_yticks([0, 0.1, 0.2])
ax0.set_ylim([-0.03, 0.23])
ax0.set_title('Leftward trials', fontsize=fontSizeLabels + 1)
plt.sca(ax0)
extraplots.significance_stars([1, 2],
0.2,
0.01,
starSize=12,
starString='n.s.',
gapFactor=0.2,
color='0.5')
extraplots.set_ticks_fontsize(ax0, fontSizeTicks)
extraplots.boxoff(ax0)
zScore, pVal = stats.wilcoxon(allMiceMeanLeftMore, allMiceMeanRightMore)
print('reaction time leftward p={}'.format(pVal))
ax1.annotate('C',
xy=(labelPosX[2], labelPosY[0]),
xycoords='figure fraction',
fontsize=fontSizePanel,
fontweight='bold')
allMiceMeanLeftMore = []
allMiceMeanRightMore = []
for (animal, shape) in animalShapes.items():
reactionTimeRightwardLeftMore = summary[animal +
'_reactionTimeRightChoiceMoreLeft']
meanReactionTimeRightwardLeftMore = np.mean(reactionTimeRightwardLeftMore)
reactionTimeRightwardRightMore = summary[
fontsize=fontSizePanel,
fontweight='bold')
axRaster.annotate(panelTitles[indCell],
xy=(cellLabelPosX[indCell], cellLabelPosY[indCell]),
xycoords='figure fraction',
fontsize=fontSizePanel,
fontweight='bold')
plt.setp(pRaster, ms=3, color='k')
# is there a better way to remove these things??
while len(hcond) > 0:
bar = hcond.pop(0)
bar.remove()
extraplots.boxoff(axRaster)
xticks = np.arange(rasterTimeRange[0], rasterTimeRange[1] + 0.1, 0.1)
axRaster.set_xticks(xticks)
if indCell != 2:
axRaster.set_xticklabels('')
else:
plt.xlabel('Time from laser onset (s)', fontsize=fontSizeLabels)
plt.ylabel('Trial', fontsize=fontSizeLabels)
yLims = np.array(plt.ylim())
rect = patches.Rectangle((0, yLims[1] * 1.03),
0.1,
yLims[1] * 0.04,
linewidth=1,
edgecolor=laserColor,
facecolor=laserColor,
labels = ['%.1f' % freq for freq in (2**plt.xticks()[0]) / 1000]
thisAx.set_xticks(plt.xticks()[0])
thisAx.set_xticklabels(labels)
plt.xlim(11.5, 15.5)
plt.ylim(-0.1, 1.1)
plt.title("{} cells".format(cellTypeLabels[cellType]),
color=cellTypeColours[cellType],
fontsize=fontSizeLabels)
if cellType == 0:
plt.ylabel('Suppression Index', fontsize=fontSizeLabels)
else:
thisAx.set_yticklabels([''])
if cellType == 1:
plt.xlabel('Preferred frequency (kHz)', fontsize=fontSizeLabels)
extraplots.boxoff(thisAx)
thisAx.annotate(panelLabel,
xy=(labelPosX, labelPosY[0]),
xycoords='figure fraction',
fontsize=fontSizePanel,
fontweight='bold')
# --- plots of suppression index vs AM rate ---
if PANELS[1]:
dataFullPath = os.path.join(AMDataDir, AMFileName)
data = np.load(dataFullPath)
axScatter = plt.subplot(gs[1, 0])
panelLabel = 'B'