# NOT RUN {
# }
# NOT RUN {
#############################################################
# Fit volume distribution data for A10 vSMC cell cultures
# as described in the above referenced paper
#############################################################
## load the volume distributions in the "A10_vSMC_volume_data" dataset
data("A10_vSMC_volume_data")
labs <- c("a","b","c","d")
## the volume distributions representing 0 nM aphidicolin concentration
Aph0 <- list(Aph0_a, Aph0_b, Aph0_c, Aph0_d)
## the associated cell cycle times
tAph0 <- c(tAph0_a, tAph0_b, tAph0_c, tAph0_d)
## fit each dataset
Aph0res <- list()
Aph0tab <- matrix(ncol=2,nrow=4)
for(i in 1:length(Aph0)) {
Aph0res[[i]] <- fitVolDist(vol=volumes_A10_vSMC, freq=Aph0[[i]],
r=100,sigma_r=44, t=tAph0[i])
Aph0tab[i,] <- coef(Aph0res[[i]])
}
Aph0tab <- rbind(Aph0tab, colMeans(Aph0tab))
colnames(Aph0tab) <- c("r", "sigma_r")
rownames(Aph0tab) <- c(labs, "mean values")
## plot results
par(mfrow=c(3,2))
for(i in 1:length(Aph0)) {
pe <- signif(coef(Aph0res[[i]]),3)
plot(volumes_A10_vSMC, Aph0[[i]], type="l", main= substitute(paste(
"r: ", p1, ", ", sigma[r],": ",p2),
list(p1=pe[1], p2=pe[2])),
xlab = expression(paste("volume (",mu, m^3,")", sep="")),
sub=paste("vol. dist. Aphidicolin 0 nM", labs[i]), ylab="frequency")
lines(volumes_A10_vSMC, fitted(Aph0res[[i]]), col=2)
}
textplot("(Above) Volume distribution data
representing A10 vSMC cells
cultured with 0 nM aphidicolin
concentration (black)
and model fit (red).
(Right) Parameter estimates and
mean estimates over the four fits",fixed.width=FALSE)
textplot(signif(Aph0tab,3))
## the volume distributions representing 50 nM aphidicolin concentration
Aph50 <- list(Aph50_a, Aph50_b, Aph50_c, Aph50_d)
## the associated cell cycle times
tAph50 <- c(tAph50_a, tAph50_b, tAph50_c, tAph50_d)
## fit each dataset
Aph50res <- list()
Aph50tab <- matrix(ncol=2,nrow=4)
for(i in 1:length(Aph50)) {
Aph50res[[i]] <- fitVolDist(vol=volumes_A10_vSMC, freq=Aph50[[i]],
r=100,sigma_r=44, t=tAph50[i])
Aph50tab[i,] <- coef(Aph50res[[i]])
}
Aph50tab <- rbind(Aph50tab, colMeans(Aph50tab))
colnames(Aph50tab) <- c("r", "sigma_r")
rownames(Aph50tab) <- c(labs, "mean values")
## plot results
par(mfrow=c(3,2))
for(i in 1:length(Aph50)) {
pe <- signif(coef(Aph50res[[i]]),3)
plot(volumes_A10_vSMC, Aph50[[i]], type="l", main= substitute(paste(
"r: ", p1, ", ", sigma[r],": ",p2),
list(p1=pe[1], p2=pe[2])),
xlab = expression(paste("volume (", mu, m^3,")", sep="")),
sub=paste("vol. dist. Aphidicolin 50 nM", labs[i]), ylab="frequency")
lines(volumes_A10_vSMC, fitted(Aph50res[[i]]), col=2)
}
textplot("(Above) Volume distribution data
representing A10 vSMC cells
cultured with 50 nM aphidicolin
concentration (black)
and model fit (red).
(Right) Parameter estimates and
mean estimates over the four fits",fixed.width=FALSE)
textplot(signif(Aph50tab,3))
## the volume distributions representing 100 nM aphidicolin concentration
Aph100 <- list(Aph100_a, Aph100_b, Aph100_c, Aph100_d)
## the associated cell cycle times
tAph100 <- c(tAph100_a, tAph100_b, tAph100_c, tAph100_d)
## fit each dataset
Aph100res <- list()
Aph100tab <- matrix(ncol=2,nrow=4)
for(i in 1:length(Aph100)) {
Aph100res[[i]] <- fitVolDist(vol=volumes_A10_vSMC, freq=Aph100[[i]],
r=100,sigma_r=44, t=tAph100[i])
Aph100tab[i,] <- coef(Aph100res[[i]])
}
Aph100tab <- rbind(Aph100tab, colMeans(Aph100tab))
colnames(Aph100tab) <- c("r", "sigma_r")
rownames(Aph100tab) <- c(labs, "mean values")
## plot results
par(mfrow=c(3,2))
for(i in 1:length(Aph100)) {
pe <- signif(coef(Aph100res[[i]]),3)
plot(volumes_A10_vSMC, Aph100[[i]], type="l", main= substitute(paste(
"r: ", p1, ", ", sigma[r],": ",p2),
list(p1=pe[1], p2=pe[2])),
xlab = expression(paste("volume (",mu, m^3,")", sep="")),
sub=paste("vol. dist. Aphidicolin 100 nM", labs[i]), ylab="frequency")
lines(volumes_A10_vSMC, fitted(Aph100res[[i]]), col=2)
}
textplot("(Above) Volume distribution data
representing A10 vSMC cells
cultured with 100 nM aphidicolin
concentration (black)
and model fit (red).
(Right) Parameter estimates and
mean estimates over the four fits",fixed.width=FALSE)
textplot(signif(Aph100tab,3))
# }
# NOT RUN {
#############################################################
# Fit volume distribution data for NIH3T3 cell cultures
# as described in the above referenced paper
#############################################################
## load the volume distributions in the "NIH3T3_volume_data" dataset
data("NIH3T3_volume_data")
labs <- c("a","b","c","d")
## the volume distributions representing NIH3T3 cells
NIH3T3 <- list(NIH3T3_a, NIH3T3_b, NIH3T3_c, NIH3T3_d)
## the associated cell cycle times
tNIH3T3 <- c(tNIH3T3_a, tNIH3T3_b, tNIH3T3_c, tNIH3T3_d)
## fit each dataset
NIH3T3res <- list()
NIH3T3tab <- matrix(ncol=2,nrow=4)
for(i in 1:length(NIH3T3)) {
NIH3T3res[[i]] <- fitVolDist(vol=volumes_nih3t3, freq=NIH3T3[[i]],
r=100,sigma_r=44, t=tNIH3T3[i])
NIH3T3tab[i,] <- coef(NIH3T3res[[i]])
}
NIH3T3tab <- rbind(NIH3T3tab, colMeans(NIH3T3tab))
colnames(NIH3T3tab) <- c("r", "sigma_r")
rownames(NIH3T3tab) <- c(labs, "mean values")
## plot results
par(mfrow=c(3,2))
for(i in 1:length(NIH3T3)) {
pe <- signif(coef(NIH3T3res[[i]]),3)
plot(volumes_nih3t3, NIH3T3[[i]], type="l", main= substitute(paste(
"r: ", p1, ", ", sigma[r],": ",p2),
list(p1=pe[1], p2=pe[2])),
xlab = expression(paste("volume (",mu, m^3,")", sep="")),
sub=paste("vol. dist. NIH3T3", labs[i]), ylab="frequency")
lines(volumes_nih3t3, fitted(NIH3T3res[[i]]), col=2)
}
textplot("(Above) Volume distribution data
representing NIH3T3 cells
cultured under normal
conditions (black)
and model fit (red).
(Right) Parameter estimates and
mean estimates over the four fits",fixed.width=FALSE)
textplot(signif(NIH3T3tab,3))
# }
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