4PL report update
This commit is contained in:
+192
-191
@@ -90,198 +90,199 @@ You can also embed plots, for example:
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```{r XLplot, echo=FALSE, warning=FALSE, fig.height=4, fig.width=6, fig.cap="Plot of models", fig.align='left'}
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plot_f <- function(dat, sigmoid,det_sig) {
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CORdat <- cor(dat[,1],dat[,ncol(dat)])
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# plot_f <- function(dat, sigmoid,det_sig) {
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# CORdat <- cor(dat[,1],dat[,ncol(dat)])
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#
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# all_l <- melt(data.frame(dat), id.vars="log_dose", variable.name="replname", value.name = "readout")
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# isRef <- rep(c(1,0),1,each=nrow(all_l)/2)
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# isSample <- rep(c(0,1),1,each=nrow(all_l)/2)
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# all_l2 <- cbind(all_l, isRef, isSample)
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#
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# if(is.null(det_sig)) {
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# if (CORdat<0) {
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# startlist <- list(a=sigmoid[3], b=-sigmoid[5],cs=sigmoid[7],
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# d=sigmoid[1],r=sigmoid[8])
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# } else {
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# startlist <- list(a=sigmoid[3],b=sigmoid[5],cs=sigmoid[7],
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# d=sigmoid[1],r=sigmoid[8])
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# }
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# } else {
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# startlist <- list(a=det_sig[5], b=det_sig[1],cs=det_sig[7],
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# d=det_sig[3],r=det_sig[7] - det_sig[8])
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# }
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# #browser()
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# tryCatch({
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# mr <- gsl_nls(fn = readout ~ a+(d-a)/(1+exp(b*(log_dose-(cs-r*isSample)))),
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# data=all_l2,
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# start=startlist,
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# control=gsl_nls_control(xtol=1e-6,ftol=1e-6, gtol=1e-6))
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# },
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# error = function(err) {
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# err$message
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# })
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# s_mr <- summary(mr)
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# a <- s_mr$coefficients[1,1]
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# b <- s_mr$coefficients[2,1]
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# cs <- s_mr$coefficients[3,1]
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# d <- s_mr$coefficients[4,1]
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# r <- s_mr$coefficients[5,1]
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#
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# log_dose <- unique(all_l$log_dose)
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# seq_x <- seq(min(log_dose),max(log_dose),0.1)
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# SAMPLE <- a+(d-a)/(1+exp(b*(seq_x-(cs-r))))
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# REF <- a+(d-a)/(1+exp(b*(seq_x-(cs))))
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#
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# if (is.null(det_sig)) {
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# SAMPLEtrue <- sigmoid[4] + (sigmoid[2] -sigmoid[4])/(1+exp(sigmoid[6]*(seq_x-(sigmoid[7]-sigmoid[8]))))
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# REFtrue <- sigmoid[3] + (sigmoid[1] -sigmoid[3])/(1+exp(sigmoid[5]*(seq_x-(sigmoid[7]))))
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# } else {
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# SAMPLEtrue <- det_sig[4] + (det_sig[6] -det_sig[4])/(1+exp(-det_sig[2]*(seq_x-(det_sig[8]))))
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# REFtrue <- det_sig[3] + (det_sig[5] -det_sig[3])/(1+exp(-det_sig[1]*(seq_x-(det_sig[7]))))
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# }
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#
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# pl_df <- cbind(seq_x, SAMPLE, REF, SAMPLEtrue, REFtrue)
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# all_l2$readout[all_l2$readout < 0] <- 0.01
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# all_l2$readouttrans <- log(all_l2$readout)
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# slopeEC50 <- b*(a-d)/4
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#
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# Xbendl3 <- cs-(1.31696/b)
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# Xbendu3 <- cs+(1.31696/b)
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# XbendlT <- cs-r-(1.31696/b)
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# XbenduT <- cs-r+(1.31696/b)
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# bendpoints <- c(bendREF_lower = round(Xbendl3,3), bendREF_upper=round(Xbendu3,3),
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# bendSAMPLE_lower = round(XbendlT,3), bendSAMPLE_upper=round(XbenduT,3))
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#
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# p <- ggplot(all_l2, aes(x=log_dose, y=readout, color=factor(isRef))) +
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# geom_point(shape=factor(isRef), alpha=0.8) +
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# labs(title = paste("restricted 4pl; bendp:", round(Xbendl3,3),round(Xbendu3,3),round(XbendlT,3),round(XbenduT,3)),
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# color="product") +
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# scale_color_manual(labels=c("test","reference"), values=c("red","blue")) +
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# scale_shape_manual(labels=c("test","reference")) +
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# theme_bw() +
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# theme(axis.text = element_text(size=14))
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#
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# p2 <- p + geom_line(data=as.data.frame(pl_df), aes(x=seq_x, y=SAMPLE), color="red",
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# inherit.aes = F) +
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# geom_line(data=as.data.frame(pl_df), aes(x=seq_x, y=REF), color="blue",
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# inherit.aes = F) +
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# geom_line(data=as.data.frame(pl_df), aes(x=seq_x, y=SAMPLEtrue), color="red", linetype=2, alpha=0.4,
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# inherit.aes = F) +
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# geom_line(data=as.data.frame(pl_df), aes(x=seq_x, y=REFtrue), color="blue", linetype=2, alpha=0.4,
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# inherit.aes = F) +
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# geom_vline(xintercept=c(Xbendl3, Xbendu3), col="blue",linetype=2) +
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# geom_vline(xintercept=c(XbendlT, XbenduT), col="red",linetype=2) +
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# annotate("text", x=cs, y=a+(d-a)/2, label="0", size=5) +
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# theme(legend.position="none")
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#
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#
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# # transformed plots
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# p_rt <- ggplot(all_l2, aes(x=log_dose, y=readouttrans, color=factor(isRef))) +
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# geom_point(shape=factor(isRef), alpha=0.8) +
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# labs(title = paste("restricted transformed 4pl"), color="product") +
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# scale_color_manual(labels=c("test","reference"), values=c("red","blue")) +
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# theme_bw()
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#
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# mrt <- gsl_nls(fn = readouttrans ~ a+(d-a)/(1+exp(b*(log_dose-(cs-r*isSample)))),
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# data=all_l2,
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# start=startlist,
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# control=gsl_nls_control(xtol=1e-6,ftol=1e-6, gtol=1e-6))
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# s_mrt <- summary(mrt)
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# a_trans <- s_mrt$coefficients[1,1]
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# b_trans <- s_mrt$coefficients[2,1]
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# cs_trans <- s_mrt$coefficients[3,1]
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# d_trans <- s_mrt$coefficients[4,1]
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# r_trans <- s_mrt$coefficients[5,1]
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#
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# XbendlTrans <- cs_trans-(1.31696/b_trans)
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# XbenduTrans <- cs_trans+(1.31696/b_trans)
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# XbendlTransT <- cs_trans-r_trans-(1.31696/b_trans)
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# XbenduTransT <- cs_trans-r_trans+(1.31696/b_trans)
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# bendpointsTRANS <- c(bendREF_lower = round(XbendlTrans,3), bendREF_upper=round(XbenduTrans,3),
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# bendSAMPLE_lower = round(XbendlTransT,3), bendSAMPLE_upper=round(XbenduTransT,3))
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#
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# SAMPLEtrans <- a_trans+(d_trans-a_trans)/(1+exp(b_trans*(seq_x-(cs_trans-r_trans))))
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# REFtrans <- a_trans+(d_trans-a_trans)/(1+exp(b_trans*(seq_x-(cs_trans))))
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#
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# pl_df_trans <- cbind(seq_x, SAMPLEtrans, REFtrans)
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# p_rt2 <- p_rt + geom_line(data=as.data.frame(pl_df_trans), aes(x=seq_x, y=SAMPLEtrans), color="red",
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# inherit.aes = F) +
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# geom_line(data=as.data.frame(pl_df_trans), aes(x=seq_x, y=REFtrans), color="blue",
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# inherit.aes = F) +
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# geom_vline(xintercept=c(XbendlTrans, XbenduTrans), col="blue",linetype=2) +
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# geom_vline(xintercept=c(XbendlTransT, XbenduTransT), col="red",linetype=2) +
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# theme(legend.position = "none", axis.text=element_text(size=14))
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#
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# if (is.null(det_sig)) {
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# unrestr <- drm(readout ~ exp(log_dose), isSample, data=all_l2, fct=LL.4(),
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# pmodels=data.frame(isSample, isSample,isSample,isSample))
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# Sum_u <- summary(unrestr)
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# ast <- Sum_u$coefficients[3,1]
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# ate <- Sum_u$coefficients[4,1]
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# bst <- Sum_u$coefficients[1,1]
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# bte <- Sum_u$coefficients[2,1]
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# cst <- log(Sum_u$coefficients[7,1])
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# cte <- log(Sum_u$coefficients[8,1])
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# dst <- Sum_u$coefficients[5,1]
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# dte <- Sum_u$coefficients[6,1]
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# } else {
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# ast <- det_sig[5]
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# ate <- det_sig[6]
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# bst <- det_sig[1]
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# bte <- det_sig[2]
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# cst <- det_sig[7]
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# cte <- det_sig[8]
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# dst <- det_sig[3]
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# dte <- det_sig[4]
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# }
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# REFu <- ast + (dst-ast)/(1+exp(bst*(seq_x-cst)))
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# SAMPLEu <- ate + (dte-ate)/(1+exp(bte*(seq_x-cte)))
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# pl_df2 <- cbind(seq_x, SAMPLEu, REFu)
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# #browser()
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# pu <- ggplot(all_l2, aes(x=log_dose, y=readout, color=factor(isRef))) +
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# geom_point() +
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# labs(title="unrestricted 4_pl-Model", color="product") +
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# scale_color_manual(labels = c("test","reference"), values=c("red","blue")) +
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# theme_bw()
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# pu2 <- pu + geom_line(data=as.data.frame(pl_df2), aes(x=seq_x, y=SAMPLEu),
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# color="red", inherit.aes = F) +
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# geom_line(data=as.data.frame(pl_df2), aes(x=seq_x, y=REFu),
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# color="blue", inherit.aes = F,
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# show.legend = F)
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# pu2_ <- pu2 +
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# theme(legend.position = "none", axis.text = element_text(size=14))
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# putrans <- ggplot(all_l2, aes(x=log_dose, y=readouttrans, color=factor(isRef))) +
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# geom_point() +
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# labs(title="unrestricted transformed 4_pl-Model", color="product") +
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# scale_color_manual(labels = c("test","reference"), values=c("red","blue")) +
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# theme_bw()
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#
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# unrestr_trans <- drm(readouttrans ~ exp(log_dose), isSample, data=all_l2, fct=LL.4(),
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# pmodels=data.frame(isSample, isSample,isSample,isSample))
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# Sum_ut <- summary(unrestr_trans)
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# ast_t <- Sum_ut$coefficients[3,1]
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# ate_t <- Sum_ut$coefficients[4,1]
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# bst_t <- Sum_ut$coefficients[1,1]
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# bte_t <- Sum_ut$coefficients[2,1]
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# cst_t <- log(Sum_ut$coefficients[7,1])
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# cte_t <- log(Sum_ut$coefficients[8,1])
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# dst_t <- Sum_ut$coefficients[5,1]
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# dte_t <- Sum_ut$coefficients[6,1]
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#
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# REFu_trans <- ast_t + (dst_t-ast_t)/(1+exp(bst_t*(seq_x-cst_t)))
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# SAMPLEu_trans <- ate_t + (dte_t-ate_t)/(1+exp(bte_t*(seq_x-cte_t)))
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# pl_df2u_t <- cbind(seq_x, SAMPLEu_trans, REFu_trans)
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#
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# pu2_t <- putrans + geom_line(data=as.data.frame(pl_df2u_t), aes(x=seq_x, y=SAMPLEu_trans),
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# color="red", inherit.aes = F) +
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# geom_line(data=as.data.frame(pl_df2u_t), aes(x=seq_x, y=REFu_trans),
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# color="blue", inherit.aes = F,
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# show.legend = F)
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# pu3_t <- pu2_t
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# grid.arrange(p2,p_rt2,pu2_,pu3_t, nrow=2)
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# }
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#
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# plot_f(XLdat2, sigmoid=NULL, det_sig=coeffs)
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all_l <- melt(data.frame(dat), id.vars="log_dose", variable.name="replname", value.name = "readout")
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isRef <- rep(c(1,0),1,each=nrow(all_l)/2)
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isSample <- rep(c(0,1),1,each=nrow(all_l)/2)
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all_l2 <- cbind(all_l, isRef, isSample)
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if(is.null(det_sig)) {
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if (CORdat<0) {
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startlist <- list(a=sigmoid[3], b=-sigmoid[5],cs=sigmoid[7],
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d=sigmoid[1],r=sigmoid[8])
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} else {
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startlist <- list(a=sigmoid[3],b=sigmoid[5],cs=sigmoid[7],
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d=sigmoid[1],r=sigmoid[8])
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}
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} else {
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startlist <- list(a=det_sig[5], b=det_sig[1],cs=det_sig[7],
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d=det_sig[3],r=det_sig[7] - det_sig[8])
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}
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#browser()
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tryCatch({
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mr <- gsl_nls(fn = readout ~ a+(d-a)/(1+exp(b*(log_dose-(cs-r*isSample)))),
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data=all_l2,
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start=startlist,
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control=gsl_nls_control(xtol=1e-6,ftol=1e-6, gtol=1e-6))
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},
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error = function(err) {
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err$message
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})
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s_mr <- summary(mr)
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a <- s_mr$coefficients[1,1]
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b <- s_mr$coefficients[2,1]
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cs <- s_mr$coefficients[3,1]
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d <- s_mr$coefficients[4,1]
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r <- s_mr$coefficients[5,1]
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log_dose <- unique(all_l$log_dose)
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seq_x <- seq(min(log_dose),max(log_dose),0.1)
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SAMPLE <- a+(d-a)/(1+exp(b*(seq_x-(cs-r))))
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REF <- a+(d-a)/(1+exp(b*(seq_x-(cs))))
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if (is.null(det_sig)) {
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SAMPLEtrue <- sigmoid[4] + (sigmoid[2] -sigmoid[4])/(1+exp(sigmoid[6]*(seq_x-(sigmoid[7]-sigmoid[8]))))
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REFtrue <- sigmoid[3] + (sigmoid[1] -sigmoid[3])/(1+exp(sigmoid[5]*(seq_x-(sigmoid[7]))))
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} else {
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SAMPLEtrue <- det_sig[4] + (det_sig[6] -det_sig[4])/(1+exp(-det_sig[2]*(seq_x-(det_sig[8]))))
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REFtrue <- det_sig[3] + (det_sig[5] -det_sig[3])/(1+exp(-det_sig[1]*(seq_x-(det_sig[7]))))
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}
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pl_df <- cbind(seq_x, SAMPLE, REF, SAMPLEtrue, REFtrue)
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all_l2$readout[all_l2$readout < 0] <- 0.01
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all_l2$readouttrans <- log(all_l2$readout)
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slopeEC50 <- b*(a-d)/4
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Xbendl3 <- cs-(1.31696/b)
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Xbendu3 <- cs+(1.31696/b)
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XbendlT <- cs-r-(1.31696/b)
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XbenduT <- cs-r+(1.31696/b)
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bendpoints <- c(bendREF_lower = round(Xbendl3,3), bendREF_upper=round(Xbendu3,3),
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bendSAMPLE_lower = round(XbendlT,3), bendSAMPLE_upper=round(XbenduT,3))
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p <- ggplot(all_l2, aes(x=log_dose, y=readout, color=factor(isRef))) +
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geom_point(shape=factor(isRef), alpha=0.8) +
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labs(title = paste("restricted 4pl; bendp:", round(Xbendl3,3),round(Xbendu3,3),round(XbendlT,3),round(XbenduT,3)),
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color="product") +
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scale_color_manual(labels=c("test","reference"), values=c("red","blue")) +
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scale_shape_manual(labels=c("test","reference")) +
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theme_bw() +
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theme(axis.text = element_text(size=14))
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p2 <- p + geom_line(data=as.data.frame(pl_df), aes(x=seq_x, y=SAMPLE), color="red",
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inherit.aes = F) +
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geom_line(data=as.data.frame(pl_df), aes(x=seq_x, y=REF), color="blue",
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inherit.aes = F) +
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geom_line(data=as.data.frame(pl_df), aes(x=seq_x, y=SAMPLEtrue), color="red", linetype=2, alpha=0.4,
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inherit.aes = F) +
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geom_line(data=as.data.frame(pl_df), aes(x=seq_x, y=REFtrue), color="blue", linetype=2, alpha=0.4,
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inherit.aes = F) +
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geom_vline(xintercept=c(Xbendl3, Xbendu3), col="blue",linetype=2) +
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geom_vline(xintercept=c(XbendlT, XbenduT), col="red",linetype=2) +
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annotate("text", x=cs, y=a+(d-a)/2, label="0", size=5) +
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theme(legend.position="none")
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# transformed plots
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p_rt <- ggplot(all_l2, aes(x=log_dose, y=readouttrans, color=factor(isRef))) +
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geom_point(shape=factor(isRef), alpha=0.8) +
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labs(title = paste("restricted transformed 4pl"), color="product") +
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scale_color_manual(labels=c("test","reference"), values=c("red","blue")) +
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theme_bw()
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mrt <- gsl_nls(fn = readouttrans ~ a+(d-a)/(1+exp(b*(log_dose-(cs-r*isSample)))),
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data=all_l2,
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start=startlist,
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control=gsl_nls_control(xtol=1e-6,ftol=1e-6, gtol=1e-6))
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s_mrt <- summary(mrt)
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a_trans <- s_mrt$coefficients[1,1]
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b_trans <- s_mrt$coefficients[2,1]
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cs_trans <- s_mrt$coefficients[3,1]
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d_trans <- s_mrt$coefficients[4,1]
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r_trans <- s_mrt$coefficients[5,1]
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XbendlTrans <- cs_trans-(1.31696/b_trans)
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XbenduTrans <- cs_trans+(1.31696/b_trans)
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XbendlTransT <- cs_trans-r_trans-(1.31696/b_trans)
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XbenduTransT <- cs_trans-r_trans+(1.31696/b_trans)
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bendpointsTRANS <- c(bendREF_lower = round(XbendlTrans,3), bendREF_upper=round(XbenduTrans,3),
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bendSAMPLE_lower = round(XbendlTransT,3), bendSAMPLE_upper=round(XbenduTransT,3))
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SAMPLEtrans <- a_trans+(d_trans-a_trans)/(1+exp(b_trans*(seq_x-(cs_trans-r_trans))))
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REFtrans <- a_trans+(d_trans-a_trans)/(1+exp(b_trans*(seq_x-(cs_trans))))
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|
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pl_df_trans <- cbind(seq_x, SAMPLEtrans, REFtrans)
|
||||
p_rt2 <- p_rt + geom_line(data=as.data.frame(pl_df_trans), aes(x=seq_x, y=SAMPLEtrans), color="red",
|
||||
inherit.aes = F) +
|
||||
geom_line(data=as.data.frame(pl_df_trans), aes(x=seq_x, y=REFtrans), color="blue",
|
||||
inherit.aes = F) +
|
||||
geom_vline(xintercept=c(XbendlTrans, XbenduTrans), col="blue",linetype=2) +
|
||||
geom_vline(xintercept=c(XbendlTransT, XbenduTransT), col="red",linetype=2) +
|
||||
theme(legend.position = "none", axis.text=element_text(size=14))
|
||||
|
||||
if (is.null(det_sig)) {
|
||||
unrestr <- drm(readout ~ exp(log_dose), isSample, data=all_l2, fct=LL.4(),
|
||||
pmodels=data.frame(isSample, isSample,isSample,isSample))
|
||||
Sum_u <- summary(unrestr)
|
||||
ast <- Sum_u$coefficients[3,1]
|
||||
ate <- Sum_u$coefficients[4,1]
|
||||
bst <- Sum_u$coefficients[1,1]
|
||||
bte <- Sum_u$coefficients[2,1]
|
||||
cst <- log(Sum_u$coefficients[7,1])
|
||||
cte <- log(Sum_u$coefficients[8,1])
|
||||
dst <- Sum_u$coefficients[5,1]
|
||||
dte <- Sum_u$coefficients[6,1]
|
||||
} else {
|
||||
ast <- det_sig[5]
|
||||
ate <- det_sig[6]
|
||||
bst <- det_sig[1]
|
||||
bte <- det_sig[2]
|
||||
cst <- det_sig[7]
|
||||
cte <- det_sig[8]
|
||||
dst <- det_sig[3]
|
||||
dte <- det_sig[4]
|
||||
}
|
||||
REFu <- ast + (dst-ast)/(1+exp(bst*(seq_x-cst)))
|
||||
SAMPLEu <- ate + (dte-ate)/(1+exp(bte*(seq_x-cte)))
|
||||
pl_df2 <- cbind(seq_x, SAMPLEu, REFu)
|
||||
#browser()
|
||||
pu <- ggplot(all_l2, aes(x=log_dose, y=readout, color=factor(isRef))) +
|
||||
geom_point() +
|
||||
labs(title="unrestricted 4_pl-Model", color="product") +
|
||||
scale_color_manual(labels = c("test","reference"), values=c("red","blue")) +
|
||||
theme_bw()
|
||||
pu2 <- pu + geom_line(data=as.data.frame(pl_df2), aes(x=seq_x, y=SAMPLEu),
|
||||
color="red", inherit.aes = F) +
|
||||
geom_line(data=as.data.frame(pl_df2), aes(x=seq_x, y=REFu),
|
||||
color="blue", inherit.aes = F,
|
||||
show.legend = F)
|
||||
pu2_ <- pu2 +
|
||||
theme(legend.position = "none", axis.text = element_text(size=14))
|
||||
putrans <- ggplot(all_l2, aes(x=log_dose, y=readouttrans, color=factor(isRef))) +
|
||||
geom_point() +
|
||||
labs(title="unrestricted transformed 4_pl-Model", color="product") +
|
||||
scale_color_manual(labels = c("test","reference"), values=c("red","blue")) +
|
||||
theme_bw()
|
||||
|
||||
unrestr_trans <- drm(readouttrans ~ exp(log_dose), isSample, data=all_l2, fct=LL.4(),
|
||||
pmodels=data.frame(isSample, isSample,isSample,isSample))
|
||||
Sum_ut <- summary(unrestr_trans)
|
||||
ast_t <- Sum_ut$coefficients[3,1]
|
||||
ate_t <- Sum_ut$coefficients[4,1]
|
||||
bst_t <- Sum_ut$coefficients[1,1]
|
||||
bte_t <- Sum_ut$coefficients[2,1]
|
||||
cst_t <- log(Sum_ut$coefficients[7,1])
|
||||
cte_t <- log(Sum_ut$coefficients[8,1])
|
||||
dst_t <- Sum_ut$coefficients[5,1]
|
||||
dte_t <- Sum_ut$coefficients[6,1]
|
||||
|
||||
REFu_trans <- ast_t + (dst_t-ast_t)/(1+exp(bst_t*(seq_x-cst_t)))
|
||||
SAMPLEu_trans <- ate_t + (dte_t-ate_t)/(1+exp(bte_t*(seq_x-cte_t)))
|
||||
pl_df2u_t <- cbind(seq_x, SAMPLEu_trans, REFu_trans)
|
||||
|
||||
pu2_t <- putrans + geom_line(data=as.data.frame(pl_df2u_t), aes(x=seq_x, y=SAMPLEu_trans),
|
||||
color="red", inherit.aes = F) +
|
||||
geom_line(data=as.data.frame(pl_df2u_t), aes(x=seq_x, y=REFu_trans),
|
||||
color="blue", inherit.aes = F,
|
||||
show.legend = F)
|
||||
pu3_t <- pu2_t
|
||||
grid.arrange(p2,p_rt2,pu2_,pu3_t, nrow=2)
|
||||
}
|
||||
|
||||
plot_f(XLdat2, sigmoid=NULL, det_sig=coeffs)
|
||||
|
||||
|
||||
```
|
||||
|
||||
Reference in New Issue
Block a user