OPTIMIZE improved, layout changed, bug fix

R/Global.R

@@ -40,6 +40,7 @@ library(scales)
 COR_FUNC <- function(vec1, vec2) {
   df <- data.frame(v1 = vec1, v2 = vec2)
   df2 <- df[complete.cases(df),]
+  #browser()
   return(cor(df2[,1],df2[,2]))
 }
 
@@ -942,12 +943,13 @@ PlotLinPLA_FUNC <- function(circle, sigmoid, all_l2, pl_df, indS, indT) {
     truePL_df <- NULL
   }
 
+  
 
   p <- ggplot(all_l2, aes(x = log_dose, y = readout, color = factor(isRef))) +
     geom_point(size = 2) +
     # labs(title=paste("linear regression model", indS,indT), color="product") +
     scale_colour_manual(labels = c("test", "reference"), values = c("#C2173F", "#4545BA")) +
-    ylim(min(all_l2$readout), max(all_l2$readout)) +
+    
     scale_x_continuous(breaks = scales::pretty_breaks(n = 10)) +
     scale_y_continuous(breaks = scales::pretty_breaks(n = 10)) +
     theme_bw()
@@ -981,6 +983,7 @@ PlotLinPLA_FUNC <- function(circle, sigmoid, all_l2, pl_df, indS, indT) {
     x = log_dose, y = readout, shape = factor(isRef),
     size = 5, alpha = 0.2
   ), col = c("black"), inherit.aes = FALSE) +
+    ylim(min(all_l2$readout), max(all_l2$readout)) +
     scale_shape_manual(labels = c("test", "reference"), values = c(21, 21))
   # fit intercept for test and ref and common slope
 
@@ -1017,6 +1020,7 @@ PlotLinPLA_FUNC <- function(circle, sigmoid, all_l2, pl_df, indS, indT) {
       title = paste("restricted linear regression model"),
       subtitle = paste("Regression on highlighted points")
     ) +
+    ylim(min(all_l2$readout), max(all_l2$readout)) +
     theme(legend.position = "none", axis.text = element_text(size = 14))
   pr3 <- pr2 + geom_point(circle, mapping = aes(
     x = log_dose, y = readout, shape = factor(isRef),
@@ -1219,7 +1223,7 @@ tests_FUNC <- function(ro_new, Lim, PureErrFlag) {
   VCOVpure <- V_V * meanPureErr
   DFsPure <- FitAnova[4, 1]
 
-
+#browser()
   testPOTr <- logical()
   if (POTr_CI[1] * 100 > Lim[[9]] & POTr_CI[2] * 100 < Lim[[10]]) testPOTr <- 0 else testPOTr <- 1