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figures/Figure3/PlotAlphhaRhoFig3.m

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+%%
+d=1.5*1*10^(-6);%(in microm);
+g_list =[0.1000 0.5000 1.0000 2.5000 5.0000];
+
+CellNameCell{1}='L5MouseR1';
+CellNameCell{2}='BasketR1';
+CellNameCell{3}='SpinyR1';
+
+
+for  ii=1:1
+    CellName=CellNameCell{ii};
+for gg=2
+
+% Layer 5 mouse
+if strcmp(CellName,'L5MouseR1')
+z= readtable(sprintf('/Users/darshan/Dropbox/Work/VoltageWholeCellProject-2018/MultiCompProject/rhos/Different_g_syn/NMO_161366/Rm3500_Rin57_norm_%d.csv',gg));
+end
+
+% Layer 4 Spiny
+if strcmp(CellName,'SpinyR1')
+z= readtable(sprintf('/Users/darshanr/Dropbox (HHMI)/VoltageWholeCellProject-2018/MultiCompProject/rhos/Different_g_syn/JM072303/Rm1000_Rin45_norm_%d.csv',gg));
+end
+
+
+if strcmp(CellName,'BasketR1')
+z= readtable(sprintf('/Users/darshanr/Dropbox (HHMI)/VoltageWholeCellProject-2018/MultiCompProject/rhos/Different_g_syn/NMO_130658/Rm3000_Rin36_norm_%d.csv',gg));
+end
+
+
+if ii==1
+Rm=3500; Rin=57;
+end
+if ii==2
+    Rm=7000;Rin=94;
+end
+if ii==3
+    Rm=14000; Rin=162;
+end
+
+lambda(ii)=(d*Rm/(4*Rin))^0.5 *10e4 %results: 612 microM
+
+
+
+
+
+[rhoE,alphaE]=ChooseAlphaRhoFromDataEI(z,1000);
+
+
+x=z.seg_dist(2:end);
+alpha=z.alpha(2:end);
+rho=z.rho(2:end);
+figure(1)
+subplot 311
+plot(x,rho,'.')
+hold on;box off; ylim([0 1]);
+ylabel('rho')
+subplot 312
+plot(x,alpha,'.')
+hold on;box off; ylim([0 1]);
+ylabel('alpha')
+subplot 313
+plot(x,alpha.*rho,'.')
+hold on;box off; ylim([0 1]);
+ylabel('Gamma')
+
+figure(111)
+semilogy(x,rho,'.')
+hold on;box off; ylim([0 1]);
+ylabel('rho')
+
+% figure(112)
+% semilogy(x,alpha,'.')
+% hold on;box off; ylim([0 1]);
+% ylabel('alpha')
+
+figure(100*ii+12)
+plot(x,log10(alpha),'.')
+hold on;box off; 
+ylabel('alpha')
+y=alpha;
+[RsqNW,yCalc]= MyLinearReg(x,log10(y));
+plot(x,yCalc,'r')
+[RsqNW,yCalc,expAlpha(ii,:)]= MyLinearReg(x,log(y));
+ylim([-3 0]);
+
+
+figure(100*ii+13)
+plot(x,log10(alpha.*rho),'.')
+hold on;box off; 
+% ylim([0 1]);
+ylabel('Gamma')
+y=alpha.*rho;
+[RsqNW,yCalc]= MyLinearReg(x,log10(y));
+plot(x,yCalc,'r')
+ylim([-3 0]);
+[RsqNW,yCalc,expGamma(ii,:)]= MyLinearReg(x,log(y));
+
+
+
+% 
+% figure(2)
+% subplot 211
+% plot(x./lambda(ii),rho,'.')
+% hold on;box off;axis square; ylim([0 1]);
+% ylabel('rho')
+% subplot 212
+% plot(x./lambda(ii),alpha,'.')
+% hold on;box off;axis square; ylim([0 1]);
+% ylabel('alpha')
+
+figure(3)
+plot(alphaE,rhoE.*alphaE,'.')
+hold on;box off;axis square; xlim([0 1]);  ylim([0 1]);
+
+xlabel('Somatic current change (\alpha)')
+ylabel('Visability of conductance (\alpha\rho)')
+m_rho(ii,gg)=mean(rhoE);
+m_alpha(ii,gg)=mean(alphaE);
+m_mult(ii,gg)=mean(rhoE.*alphaE);
+
+
+% Distributions
+
+figure(100+ii)
+histogram2(rhoE,alphaE,0:0.05:1,0:0.05:1,'DisplayStyle','tile','ShowEmptyBins','on');
+title('rho')
+xlim([0 1]);ylim([0 1])
+axis square
+
+figure(200+ii)
+hist(alphaE,0:0.05:1)
+title('alpha')
+xlim([0 1]);
+box off
+
+figure(300+ii)
+hist(rhoE,0:0.05:1)
+title('rho')
+xlim([0 1]);
+box off
+
+
+end
+
+end
+figure(1)
+legend(['L5MouseR1, \langle\rho\rangle=' num2str(m_rho(1)) '  \langle\alpha\rangle=' num2str(m_alpha(1))],['BasketR1, \langle\rho\rangle=' num2str(m_rho(2)) '  \langle\alpha\rangle=' num2str(m_alpha(2))],['SpinyR1, \langle\rho\rangle=' num2str(m_rho(3)) '  \langle\alpha\rangle=' num2str(m_alpha(3))])
+figure(3)
+
+legend(['L5MouseR1, \langle\alpha\rho\rangle=' num2str(m_mult(1)) '  \langle\alpha\rangle=' num2str(m_alpha(1))],['BasketR1, \langle\alpha\rho\rangle=' num2str(m_mult(2)) '  \langle\alpha\rangle=' num2str(m_alpha(2))],['SpinyR1, \langle\alpha\rho\rangle=' num2str(m_mult(3)) '  \langle\alpha\rangle=' num2str(m_alpha(3))])
+alphavec=0:0.01:1;
+plot(alphavec,alphavec,'--k')
+plot(alphavec,alphavec.^2,'-r')
+%%
+close all
+for ii=1
+figure(100+ii)
+loglog(g_list,m_mult(ii,:),'-o')
+hold all
+plot(g_list,m_alpha(ii,:),'-o')
+plot(g_list,m_rho(ii,:),'-o')
+loglog(g_list,1-0.1*g_list,'-ok')
+ xlabel('g_syn')
+ legend('\langle \Gamma \rangle=\langle\alpha\rho\rangle','\langle\alpha\rangle','\langle\rho\rangle')
+end
+
+