import matplotlib
matplotlib.use('Agg')
import numpy
from pylab import *
import mytools
import pickle
import sys
import time
from os.path import exists
coeffCoeffs = [[0.25,0],[0.125,0],[0.5,0],[0.5,1.0/3],[0.5,2.0/3],[0.5,1.0],[-0.25,0],[-0.125,0],[-0.5,0]]
import mutation_stuff
MT = mutation_stuff.getMT()
defVals = mutation_stuff.getdefvals()
geneNames = mutation_stuff.getgenenames()
keyList = defVals.keys()
for idefval in range(0,len(keyList)):
if type(defVals[keyList[idefval]]) is not list:
defVals[keyList[idefval]] = [defVals[keyList[idefval]], defVals[keyList[idefval]]] #make the dictionary values [somatic, apical]
updatedVars = ['somatic','apical','basal'] # the possible classes of segments that defVals may apply to
whichDefVal = [0,1,0] # use the defVal[0] for somatic and basal segments and defVal[1] for apical segments
variants = [[0,5,1],[2,4,7],[1,2,13],[3,1,0],[5,0,0],[8,3,0],[12,2,0],[13,4,0]] #from drawallmeangains (maxCountersAll) #Removed KCNN3!
rates = [0.1*x for x in range(4,17)]
icell = 0
gsyn = 1.07
gNoise = 1.07
cols = ['#666666','#012345','#cc00aa','#bbaa00','#ee6600','#ff0000', '#00aaaa','#772277','#00cc00']
col_control = '#2222ff'
if exists('nSpikes_control.sav'):
unpicklefile = open('nSpikes_control.sav', 'r')
unpickledlist = pickle.load(unpicklefile)
unpicklefile.close()
nSpikes_control = unpickledlist[0]
else:
nSpikes_control = []
for irate in range(0,len(rates)):
myrate = rates[irate]
nSpikesThisRate = []
print "loading control rate="+str(myrate)
for myseed in range(1,10):
if exists('spikes_parallel150_mutID0_'+str(myrate)+'_gNoise'+str(gNoise)+'_gsyn'+str(gsyn)+'_seed'+str(myseed)+'.sav'):
unpicklefile = open('spikes_parallel150_mutID0_'+str(myrate)+'_gNoise'+str(gNoise)+'_gsyn'+str(gsyn)+'_seed'+str(myseed)+'.sav', 'r')
unpickledlist = pickle.load(unpicklefile)
unpicklefile.close()
Nplaced = 0
spikedCells_all = []
for j in range(0,len(unpickledlist[1])):
spikedCells = unpickledlist[1][j]
spikedCellsUnique = unique(spikedCells)
spikedCells2 = zeros(spikedCells.shape)
for i in range(0,len(spikedCellsUnique)):
spikedCells2[spikedCells == spikedCellsUnique[i]] = Nplaced + i
Nplaced = Nplaced + len(spikedCellsUnique)
spikedCells_all = hstack([spikedCells_all, spikedCells2])
spikes = [hstack(unpickledlist[0]),spikedCells_all]
nSpikesThisRate.append(len(spikes[0]))
else:
print 'spikes_parallel150_mutID0_'+str(myrate)+'_gNoise'+str(gNoise)+'_gsyn'+str(gsyn)+'_seed'+str(myseed)+'.sav not found'
nSpikes_control.append(nSpikesThisRate[:])
file = open('nSpikes_control.sav', 'w')
pickle.dump([nSpikes_control],file)
file.close()
for counter in range(0,461):
if not exists('nSpikes'+str(counter)+'.sav'):
nSpikesThisIter = []
print "loading mutID="+str(counter)
for irate in range(0,len(rates)):
myrate = rates[irate]
nSpikesThisRate = []
print "loading rate="+str(myrate)
for myseed in range(1,10):
if exists('spikes_parallel150_mutID'+str(counter)+'_'+str(myrate)+'_gNoise'+str(gNoise)+'_gsyn'+str(gsyn)+'_seed'+str(myseed)+'.sav'):
unpicklefile = open('spikes_parallel150_mutID'+str(counter)+'_'+str(myrate)+'_gNoise'+str(gNoise)+'_gsyn'+str(gsyn)+'_seed'+str(myseed)+'.sav', 'r')
unpickledlist = pickle.load(unpicklefile)
unpicklefile.close()
else:
continue
Nplaced = 0
spikedCells_all = []
for j in range(0,len(unpickledlist[1])):
spikedCells = unpickledlist[1][j]
spikedCellsUnique = unique(spikedCells)
spikedCells2 = zeros(spikedCells.shape)
for i in range(0,len(spikedCellsUnique)):
spikedCells2[spikedCells == spikedCellsUnique[i]] = Nplaced + i
Nplaced = Nplaced + len(spikedCellsUnique)
spikedCells_all = hstack([spikedCells_all, spikedCells2])
spikes = [hstack(unpickledlist[0]),spikedCells_all]
nSpikesThisRate.append(len(spikes[0]))
if len(spikes[0]) < 20:
print str(spikes[0])
nSpikesThisIter.append(nSpikesThisRate[:])
file = open('nSpikes'+str(counter)+'.sav', 'w')
pickle.dump([nSpikesThisIter],file)
file.close()
print "Loading control f-I curves..."
ispDef = 0
Is = [0.35+0.05*x for x in range(0,22)]
unpicklefile = open('../haymod/ifcurvesmut_cs'+str(icell)+'_0_0_0.sav', 'r')
unpickledlist = pickle.load(unpicklefile)
unpicklefile.close()
spTimesThisMutVal = unpickledlist[1+ispDef]
nSpikes_control_if = [sum([1 for x in spTimesThisMutVal[5][j] if x >= 500]) for j in range(0,len(Is))]
counter = 0
close("all")
f, axarr = plt.subplots(2, len(variants)+1)
lenvarper2 = 4 # len(variants)/2
for ix in range(0,lenvarper2):
for iy in range(0,2):
axarr[0,ix+lenvarper2*iy].set_position([0.1+0.176*ix, 0.1+0.44*(1-iy), 0.176, 0.37])
axarr[1,ix+lenvarper2*iy].set_position([0.121+0.176*ix, 0.33+0.44*(1-iy), 0.075, 0.11])
axarr[0,8].set_position([0.1+0.176*4, 0.1+0.44*(1-1), 0.176, 0.37])
axarr[1,8].set_position([0.121+0.176*4, 0.33+0.44*(1-1), 0.075, 0.11])
timesAll = []
VsomaAll = []
spikeFreqsAll = []
for igene in range(0,len(MT)):
for imut in range(0,len(MT[igene])):
nVals = len(MT[igene][imut])*[0]
thesemutvars = []
for imutvar in range(0,len(MT[igene][imut])):
thesemutvars.append(MT[igene][imut][imutvar][0])
if type(MT[igene][imut][imutvar][1]) is int or type(MT[igene][imut][imutvar][1]) is float:
MT[igene][imut][imutvar][1] = [MT[igene][imut][imutvar][1]]
nVals[imutvar] = len(MT[igene][imut][imutvar][1])
cumprodnVals = cumprod(nVals)
allmutvars = cumprodnVals[len(MT[igene][imut])-1]*[thesemutvars]
allmutvals = []
for iallmutval in range(0,cumprodnVals[len(MT[igene][imut])-1]):
allmutvals.append([0]*len(thesemutvars))
for iallmutval in range(0,cumprodnVals[len(MT[igene][imut])-1]):
for imutvar in range(0,len(MT[igene][imut])):
if imutvar==0:
allmutvals[iallmutval][imutvar] = MT[igene][imut][imutvar][1][iallmutval%nVals[imutvar]]
else:
allmutvals[iallmutval][imutvar] = MT[igene][imut][imutvar][1][(iallmutval/cumprodnVals[imutvar-1])%nVals[imutvar]]
for iallmutval in range(0,cumprodnVals[len(MT[igene][imut])-1]):
mutval = allmutvals[iallmutval]
mutText = ""
for imutvar in range(0,len(MT[igene][imut])):
if imutvar > 0 and imutvar%2==0:
mutText = mutText+"\n"
mutvars = allmutvars[iallmutval][imutvar]
mutvals = allmutvals[iallmutval][imutvar]
if type(mutvars) is str:
mutvars = [mutvars]
mutText = mutText + str(mutvars) + ": "
for kmutvar in range(0,len(mutvars)):
mutvar = mutvars[kmutvar]
if mutvar.find('offm') > -1 or mutvar.find('offh') > -1 or mutvar.find('ehcn') > -1:
newVal = [x+mutvals for x in defVals[mutvar]]
if mutvals >= 0 and kmutvar==0:
mutText = mutText + "+" + str(mutvals) +" mV"
elif kmutvar==0:
mutText = mutText + str(mutvals) +" mV"
else:
newVal = [x*mutvals for x in defVals[mutvar]]
if kmutvar==0:
mutText = mutText + "*" + str(mutvals)
if kmutvar < len(mutvars)-1:
mutText = mutText + ", "
iters = [0, 2, 6, 8]
iters_if = [0, 2, 5, 6, 8, -1]
doSkip = True
ivar = -1
for iiter in range(0,len(iters)):
iter = iters[iiter]
counter = counter+1
for ivar2 in range(0,len(variants)):
if igene == variants[ivar2][0] and imut == variants[ivar2][1] and iallmutval == variants[ivar2][2]:
ivar = ivar2
doSkip = False
break
if doSkip:
continue
if exists('nSpikes'+str(counter)+'.sav'):
unpicklefile = open('nSpikes'+str(counter)+'.sav', 'r')
unpickledlist = pickle.load(unpicklefile)
unpicklefile.close()
nSpikesThisIter = unpickledlist[0]
else:
print 'nSpikes'+str(counter)+'.sav not found!'
continue
axarr[0,ivar].plot(rates, [mean(x)/150./11.0 for x in nSpikesThisIter], 'b-',color=cols[iter])
print "igene="+str(igene)+", imut="+str(imut)+", iallmutval="+str(iallmutval)+", ivar="+str(ivar)+", counter="+str(counter)+", iter="+str(iter)
if doSkip:
continue
print mutText
print "Loading f-I curves..."
unpicklefile = open('../haymod/ifcurvesmut_cs'+str(icell)+'_'+str(igene)+'_'+str(imut)+'_'+str(iallmutval)+'.sav', 'r')
unpickledlist = pickle.load(unpicklefile)
unpicklefile.close()
spTimesThisMutVal = unpickledlist[1+ispDef]
for iiter in range(0,len(iters_if)):
iter = iters_if[iiter]
if iter == 5 or iter == -1:
continue
nSpikes_if = [sum([1 for x in spTimesThisMutVal[iiter][j] if x >= 500]) for j in range(0,len(Is))]
axarr[1,ivar].plot(Is, [x/7.5 for x in nSpikes_if], 'b-', color=cols[iter])
axarr[1,ivar].plot(Is, [x/7.5 for x in nSpikes_control_if], 'b-', color=col_control)
axarr[0,ivar].plot(rates, [mean(x)/150.0/11. for x in nSpikes_control], 'b-',color=col_control)
axarr[0,ivar].set_title(geneNames[igene])
axarr[0,ivar].set_xlim([0.4,1.6])
axarr[0,ivar].set_ylim([0,12])
axarr[0,ivar].set_xticks([0.6, 1.0, 1.4])
axarr[0,ivar].set_yticks([0, 3, 6, 9, 12])
if ivar < lenvarper2:
axarr[0,ivar].set_xticklabels(['', '', ''])
elif ivar==6:
#axarr[0,ivar].set_xlabel('rate factor r ')
axarr[0,ivar].set_xlabel('rate factor $r$')
#axarr[0,ivar].set_xlabel('rate factor $c_{\mathrm{rate}}$ ')
if ivar % lenvarper2 > 0:
axarr[0,ivar].set_yticklabels(['', '', '', '', ''])
else:
axarr[0,ivar].set_ylabel('$f$ (Hz)')
axarr[1,ivar].set_xlim([0.35,1.4])
axarr[1,ivar].set_ylim([0,20])
axarr[1,ivar].set_xticks([0.5,1.0])
axarr[1,ivar].set_yticks([0,10,20])
axarr[1,ivar].set_xlabel('$I$ (nA)',fontsize=8)
for tick in axarr[1,ivar].xaxis.get_major_ticks()+axarr[1,ivar].yaxis.get_major_ticks():
tick.label.set_fontsize(6)
axarr[1,ivar].yaxis.set_tick_params(pad=3)
f.savefig("fig1c.eps")
iters = [0, 2, 6, 8]
iters_if = [0, 2, 6, 8]
combmutIDnums = [1, 0, 2, 3]
ivar = 8
for iiter in range(0,len(iters)):
iter = iters[iiter]
combmutIDnum = combmutIDnums[iiter]
if not exists('nSpikes_comb_'+str(iiter)+'.sav'):
nSpikesThisIter = []
print "loading mutID="+str(combmutIDnum)
for irate in range(0,len(rates)):
myrate = rates[irate]
nSpikesThisRate = []
print "loading rate="+str(myrate)
for myseed in range(1,12):
if exists('spikes_parallel150_mutcombID'+str(combmutIDnum)+'_'+str(myrate)+'_gNoise'+str(gNoise)+'_gsyn'+str(gsyn)+'_seed'+str(myseed)+'.sav'):
unpicklefile = open('spikes_parallel150_mutcombID'+str(combmutIDnum)+'_'+str(myrate)+'_gNoise'+str(gNoise)+'_gsyn'+str(gsyn)+'_seed'+str(myseed)+'.sav', 'r')
unpickledlist = pickle.load(unpicklefile)
unpicklefile.close()
Nplaced = 0
spikedCells_all = []
for j in range(0,len(unpickledlist[1])):
spikedCells = unpickledlist[1][j]
spikedCellsUnique = unique(spikedCells)
spikedCells2 = zeros(spikedCells.shape)
for i in range(0,len(spikedCellsUnique)):
spikedCells2[spikedCells == spikedCellsUnique[i]] = Nplaced + i
Nplaced = Nplaced + len(spikedCellsUnique)
spikedCells_all = hstack([spikedCells_all, spikedCells2])
spikes = [hstack(unpickledlist[0]),spikedCells_all]
nSpikesThisRate.append(len(spikes[0]))
if len(spikes[0]) < 20:
print str(spikes[0])
else:
print 'spikes_parallel150_mutcombID'+str(combmutIDnum)+'_'+str(myrate)+'_gNoise'+str(gNoise)+'_gsyn'+str(gsyn)+'_seed'+str(myseed)+'.sav not found'
nSpikesThisIter.append(nSpikesThisRate[:])
file = open('nSpikes_comb_'+str(iiter)+'.sav', 'w')
pickle.dump([nSpikesThisIter],file)
file.close()
if exists('nSpikes_comb_'+str(iiter)+'.sav'):
unpicklefile = open('nSpikes_comb_'+str(iiter)+'.sav', 'r')
unpickledlist = pickle.load(unpicklefile)
unpicklefile.close()
nSpikesThisIter = unpickledlist[0]
else:
print 'nSpikes_comb_'+str(iiter)+'.sav not found!'
continue
axarr[0,ivar].plot(rates, [mean(x) for x in nSpikesThisIter], 'b-',color=cols[iter])
unpicklefile = open('../haymod/ifcurves_comb_cs'+str(icell)+'.sav', 'r')
unpickledlist = pickle.load(unpicklefile)
unpicklefile.close()
spTimesThisMutVal = unpickledlist[1+ispDef]
for iiter in range(0,len(iters_if)):
iter = iters_if[iiter]
if iter == 5 or iter == -1:
continue
nSpikes_if = [sum([1 for x in spTimesThisMutVal[iiter][j] if x >= 500]) for j in range(0,len(Is))]
axarr[1,ivar].plot(Is, [x/7.5 for x in nSpikes_if], 'b-', color=cols[iter])
print "Comb nSpikes="+str(nSpikes_if)
axarr[1,ivar].plot(Is, [x/7.5 for x in nSpikes_control_if], 'b-', color=col_control)
axarr[0,ivar].plot(rates, [mean(x) for x in nSpikes_control], 'b-',color=col_control)
axarr[0,ivar].set_title("Combination")
axarr[0,ivar].set_xlim([0.4,1.6])
axarr[0,ivar].set_ylim([0,20000])
axarr[0,ivar].set_xticks([0.6, 1.0, 1.4])
axarr[0,ivar].set_yticks([0, 5000, 10000, 15000, 20000])
axarr[0,ivar].set_yticklabels(['', '', '', '', ''])
axarr[1,ivar].set_xlim([0,1.4])
axarr[1,ivar].set_ylim([0,20])
axarr[1,ivar].set_xticks([0,0.5,1.0])
axarr[1,ivar].set_yticks([0,10,20])
axarr[1,ivar].set_xlabel('$I$ (nA)',fontsize=8)
for tick in axarr[1,ivar].xaxis.get_major_ticks()+axarr[1,ivar].yaxis.get_major_ticks():
tick.label.set_fontsize(6)
f.text(0.025, 0.88, 'C', fontsize=36)
f.savefig("fig1c.eps")