Added some math to the plots for the linear models

mathesong · Aug 21, 2024 · 5ae97c9 · 5ae97c9
1 parent dd62606
commit 5ae97c9
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Showing 6 changed files with 92 additions and 80 deletions.
diff --git a/R/kinfitr_loganplot.R b/R/kinfitr_loganplot.R
@@ -220,18 +220,16 @@ plot_Loganfit <- function(loganout, roiname = NULL) {
 
   xlimits <- c(0, tail(plotdf$Logan_Plasma, 1))
 
-  xlabel <- "Integ(C_Plasma)/C_Tissue"
-  ylabel <- "Integ(C_Tissue)/C_Tissue"
-
-  # xlabel <- expression(paste("", "", integral("", paste("0"), paste("", "t")),
-  #                            "C", phantom()[{paste("Plasma")}], "",
-  #                            phantom()/phantom(), "C", phantom()[{
-  #                              paste("Tissue", "")}]))
-  #
-  # ylabel <- expression(paste("", "", integral("", paste("0"), paste("", "t")),
-  #                            "C", phantom()[{paste("Tissue")}], "",
-  #                             phantom()/phantom(), "C", phantom()[{
-  #                             paste("Tissue", "")}]))
+  # xlabel <- "Integ(C_Plasma)/C_Tissue"
+  # ylabel <- "Integ(C_Tissue)/C_Tissue"
+
+  xlabel <- expression(paste("", "", integral(, paste("0"), paste("", "t")),
+                             "C", phantom()[{ paste("P") }],"(",tau,")d",tau, " / ",
+                             "C", phantom()[{ paste("T") }],"(t)"))
+
+  ylabel <- expression(paste("", "", integral(, paste("0"), paste("", "t")),
+                             "C", phantom()[{ paste("T") }],"(",tau,")d",tau, " / ",
+                             "C", phantom()[{ paste("T") }],"(t)"))
 
   outplot <- ggplot(data = plotdf, aes(x = Logan_Plasma, y = Logan_ROI, colour = Equilibrium)) +
     geom_point(aes(shape = "a", size = Weights)) +
@@ -302,20 +300,20 @@ Logan_tstar <- function(t_tac, lowroi, medroi, highroi, input, filename = NULL,
   # ylabel <- "Integ(C_Tissue)/C_Tissue"
 
   xlabel <- expression(paste("", "", integral(, paste("0"), paste("", "t")),
-                             "C", phantom()[{ paste("Plasma") }],"(t)", " / ",
-                             "C", phantom()[{ paste("Tissue") }],"(t)"))
+                             "C", phantom()[{ paste("P") }],"(",tau,")d",tau, " / ",
+                             "C", phantom()[{ paste("T") }],"(t)"))
 
   ylabel <- expression(paste("", "", integral(, paste("0"), paste("", "t")),
-                             "C", phantom()[{ paste("Tissue") }],"(t)", " / ",
-                             "C", phantom()[{ paste("Tissue") }],"(t)"))
+                             "C", phantom()[{ paste("T") }],"(",tau,")d",tau, " / ",
+                             "C", phantom()[{ paste("T") }],"(t)"))
 
   low_xlimits <- c(0, tail(lowroi_fit$fitvals$Logan_Plasma, 1))
   med_xlimits <- c(0, tail(medroi_fit$fitvals$Logan_Plasma, 1))
   high_xlimits <- c(0, tail(highroi_fit$fitvals$Logan_Plasma, 1))
 
-  low_linplot <- qplot(lowroi_fit$fitvals$Logan_Plasma, lowroi_fit$fitvals$Logan_ROI) + ggtitle("Low") + xlab(xlabel) + ylab(ylabel) + xlim(low_xlimits)
-  med_linplot <- qplot(medroi_fit$fitvals$Logan_Plasma, medroi_fit$fitvals$Logan_ROI) + ggtitle("Medium") + xlab(xlabel) + ylab(ylabel) + xlim(med_xlimits)
-  high_linplot <- qplot(highroi_fit$fitvals$Logan_Plasma, highroi_fit$fitvals$Logan_ROI) + ggtitle("High") + xlab(xlabel) + ylab(ylabel) + xlim(high_xlimits)
+  low_linplot <- qplot(lowroi_fit$fitvals$Logan_Plasma, lowroi_fit$fitvals$Logan_ROI) + ggtitle("Low") + xlim(low_xlimits) + xlab(xlabel) + ylab(ylabel)
+  med_linplot <- qplot(medroi_fit$fitvals$Logan_Plasma, medroi_fit$fitvals$Logan_ROI) + ggtitle("Medium") + xlim(med_xlimits) + xlab(xlabel) + ylab(ylabel)
+  high_linplot <- qplot(highroi_fit$fitvals$Logan_Plasma, highroi_fit$fitvals$Logan_ROI) + ggtitle("High") + xlim(high_xlimits) + xlab(xlabel) + ylab(ylabel)
 
   tstarInclFrames <- 3:frames
   zeros <- rep(0, length(tstarInclFrames))

diff --git a/R/kinfitr_mlloganplot.R b/R/kinfitr_mlloganplot.R
@@ -208,10 +208,14 @@ plot_mlLoganfit <- function(mlloganout, roiname = NULL) {
   names(myColors) <- levels(plotdf$Equilibrium)
   colScale <- scale_colour_manual(name = paste0(roiname, "\nEquilibrium"), values = myColors)
 
+  xlabel <- "Fitted Values"
+  ylabel <- expression(paste("", "", integral(, paste("0"), paste("", "t")),
+                             "C", phantom()[{ paste("T") }],"(",tau,")d",tau))
+
   outplot <- ggplot(data = plotdf, aes(x = Fitted, y = Term1_DV, colour = Equilibrium)) +
     geom_point(aes(shape = "a", size = Weights)) +
     geom_abline(slope = 1, intercept = 0) +
-    xlab("Fitted Values") + ylab("Integ(C_Tissue)") + colScale +
+    xlab(xlabel) + ylab(ylabel) + colScale +
     guides(shape = "none", color = guide_legend(order = 1)) +
     scale_size(range = c(1, 3))
 
@@ -265,7 +269,7 @@ mlLogan_tstar <- function(t_tac, lowroi, medroi, highroi, input, filename = NULL
 
   xlabel <- "Fitted Values"
   ylabel <- expression(paste("", "", integral(, paste("0"), paste("", "t")),
-                       "C", phantom()[{ paste("Tissue") }],"(t)"))
+                             "C", phantom()[{ paste("T") }],"(",tau,")d",tau))
 
   low_linplot <- qplot(lowroi_fit$fitvals$Fitted, lowroi_fit$fitvals$Term1_DV) + ggtitle("Low") + xlab(xlabel) + ylab(ylabel)
   med_linplot <- qplot(medroi_fit$fitvals$Fitted, medroi_fit$fitvals$Term1_DV) + ggtitle("Medium") + xlab(xlabel) + ylab(ylabel)

diff --git a/R/kinfitr_patlakplot.R b/R/kinfitr_patlakplot.R
@@ -203,18 +203,12 @@ plot_Patlakfit <- function(patlakout, roiname = NULL) {
 
   xlimits <- c(0, tail(plotdf$Patlak_Plasma, 1))
 
-  xlabel <- "Integ(C_Plasma)/C_Tissue"
-  ylabel <- "Integ(C_Tissue)/C_Tissue"
-
-  # xlabel <- expression(paste("", "", integral("", paste("0"), paste("", "t")),
-  #                            "C", phantom()[{paste("Plasma")}], "",
-  #                            phantom()/phantom(), "C", phantom()[{
-  #                              paste("Plasma", "")}]))
-  #
-  # ylabel <- expression(paste("", "", integral("", paste("0"), paste("", "t")),
-  #                            "C", phantom()[{paste("Tissue")}], "",
-  #                            phantom()/phantom(), "C", phantom()[{
-  #                              paste("Plasma", "")}]))
+  xlabel <- expression(paste("", "", integral(, paste("0"), paste("", "t")),
+                             "C", phantom()[{ paste("P") }],"(",tau,")d",tau, " / ",
+                             "C", phantom()[{ paste("P") }],"(t)"))
+
+  ylabel <- expression(paste("C", phantom()[{ paste("T") }],"(t)", " / ",
+                             "C", phantom()[{ paste("P") }],"(t)"))
 
   outplot <- ggplot(data = plotdf, aes(x = Patlak_Plasma, y = Patlak_ROI, colour = Equilibrium)) +
     geom_point(aes(shape = "a", size = Weights)) +
@@ -272,20 +266,17 @@ Patlak_tstar <- function(t_tac, lowroi, medroi, highroi, input, filename = NULL,
   medroi_fit <- Patlakplot(t_tac, medroi, input, tstarIncludedFrames = frames, inpshift = inpshift, vB = vB, frameStartEnd = frameStartEnd)
   highroi_fit <- Patlakplot(t_tac, highroi, input, tstarIncludedFrames = frames, inpshift = inpshift, vB = vB, frameStartEnd = frameStartEnd)
 
-  #xlabel <- "Integ(C_Plasma) / C_Plasma"
-  #ylabel <- "C_Tissue / C_Plasma"
-
-  xlabel <- expression(paste("", "", integral(, paste("0"), paste("", "t")),
-                             "C", phantom()[{ paste("Plasma") }],"(t)", " / ",
-                             "C", phantom()[{ paste("Plasma") }],"(t)"))
-
-  ylabel <- expression(paste("C", phantom()[{ paste("Tissue") }],"(t)", " / ",
-                             "C", phantom()[{ paste("Plasma") }],"(t)"))
-
   low_xlimits <- c(0, tail(lowroi_fit$fitvals$Patlak_Plasma, 1))
   med_xlimits <- c(0, tail(medroi_fit$fitvals$Patlak_Plasma, 1))
   high_xlimits <- c(0, tail(highroi_fit$fitvals$Patlak_Plasma, 1))
 
+  xlabel <- expression(paste("", "", integral(, paste("0"), paste("", "t")),
+                             "C", phantom()[{ paste("P") }],"(",tau,")d",tau, " / ",
+                             "C", phantom()[{ paste("P") }],"(t)"))
+
+  ylabel <- expression(paste("C", phantom()[{ paste("T") }],"(t)", " / ",
+                             "C", phantom()[{ paste("P") }],"(t)"))
+
   low_linplot <- qplot(lowroi_fit$fitvals$Patlak_Plasma, lowroi_fit$fitvals$Patlak_ROI) + ggtitle("Low") + xlab(xlabel) + ylab(ylabel) + xlim(low_xlimits)
   med_linplot <- qplot(medroi_fit$fitvals$Patlak_Plasma, medroi_fit$fitvals$Patlak_ROI) + ggtitle("Medium") + xlab(xlabel) + ylab(ylabel) + xlim(med_xlimits)
   high_linplot <- qplot(highroi_fit$fitvals$Patlak_Plasma, highroi_fit$fitvals$Patlak_ROI) + ggtitle("High") + xlab(xlabel) + ylab(ylabel) + xlim(high_xlimits)

diff --git a/R/kinfitr_refPatlak.R b/R/kinfitr_refPatlak.R
@@ -152,13 +152,20 @@ plot_refPatlakfit <- function(refpatlakout, roiname = NULL) {
   names(myColors) <- levels(plotdf$Equilibrium)
   colScale <- scale_colour_manual(name = paste0(roiname, "\nEquilibrium"), values = myColors)
 
+  ylabel <- expression(paste("C", phantom()[{ paste("T") }],"(t)", " / ",
+                                  "C", phantom()[{ paste("R") }],"(t)"))
+
+  xlabel <- expression(paste("", "", integral(, paste("0"), paste("", "t")),
+                                  "C", phantom()[{ paste("R") }],"(",tau,")d",tau, " / ",
+                                  "C", phantom()[{ paste("R") }],"(t)"))
+
   outplot <- ggplot(data = plotdf, aes(x = Patlak_ref, y = Patlak_roi, colour = Equilibrium)) +
     geom_point(aes(shape = "a", size = Weights)) +
     geom_abline(
       slope = as.numeric(refpatlakout$fit$coefficients[2]),
       intercept = as.numeric(refpatlakout$fit$coefficients[1])
     ) +
-    xlab("Integ(C_Ref) / C_Ref") + ylab("C_Tissue / C_Ref") + colScale +
+    xlab(xlabel) + ylab(ylabel) + colScale +
     guides(shape = "none", color = guide_legend(order = 1)) + scale_size(range = c(1, 3))
 
   return(outplot)
@@ -200,20 +207,16 @@ refPatlak_tstar <- function(t_tac, reftac, lowroi, medroi, highroi, filename = N
   medroi_fit <- refPatlak(t_tac, reftac, medroi, length(reftac), frameStartEnd = frameStartEnd)
   highroi_fit <- refPatlak(t_tac, reftac, highroi, length(reftac), frameStartEnd = frameStartEnd)
 
-  patlak_xlab <- "Integ(C_Ref) / C_Ref"
-  patlak_ylab <- "C_Tissue / C_Ref"
-
-  patlak_ylab <- expression(paste("C", phantom()[{ paste("Target") }],"(t)", " / ",
-                                  "C", phantom()[{ paste("Ref") }],"(t)"))
-
-  patlak_xlab <- expression(paste("", "", integral(, paste("0"), paste("", "t")),
-                             "C", phantom()[{ paste("Ref") }],"(t)", " / ",
-                             "C", phantom()[{ paste("Ref") }],"(t)"))
+  ylabel <- expression(paste("C", phantom()[{ paste("T") }],"(t)", " / ",
+                             "C", phantom()[{ paste("R") }],"(t)"))
 
+  xlabel <- expression(paste("", "", integral(, paste("0"), paste("", "t")),
+                             "C", phantom()[{ paste("R") }],"(",tau,")d",tau, " / ",
+                             "C", phantom()[{ paste("R") }],"(t)"))
 
-  low_linplot <- qplot(lowroi_fit$fitvals$Patlak_Ref, lowroi_fit$fitvals$Patlak_ROI) + ggtitle("Low") + xlab(patlak_xlab) + ylab(patlak_ylab)
-  med_linplot <- qplot(medroi_fit$fitvals$Patlak_Ref, medroi_fit$fitvals$Patlak_ROI) + ggtitle("Medium") + xlab(patlak_xlab) + ylab(patlak_ylab)
-  high_linplot <- qplot(highroi_fit$fitvals$Patlak_Ref, highroi_fit$fitvals$Patlak_ROI) + ggtitle("High") + xlab(patlak_xlab) + ylab(patlak_ylab)
+  low_linplot <- qplot(lowroi_fit$fitvals$Patlak_Ref, lowroi_fit$fitvals$Patlak_ROI) + ggtitle("Low") + xlab(xlabel) + ylab(ylabel)
+  med_linplot <- qplot(medroi_fit$fitvals$Patlak_Ref, medroi_fit$fitvals$Patlak_ROI) + ggtitle("Medium") + xlab(xlabel) + ylab(ylabel)
+  high_linplot <- qplot(highroi_fit$fitvals$Patlak_Ref, highroi_fit$fitvals$Patlak_ROI) + ggtitle("High") + xlab(xlabel) + ylab(ylabel)
 
   tstarInclFrames <- 3:frames
   zeros <- rep(0, length(tstarInclFrames))

diff --git a/R/kinfitr_reflogan.R b/R/kinfitr_reflogan.R
@@ -148,13 +148,25 @@ plot_refLoganfit <- function(refloganout, roiname = NULL) {
   names(myColors) <- levels(plotdf$Equilibrium)
   colScale <- scale_colour_manual(name = paste0(roiname, "\nEquilibrium"), values = myColors)
 
+  xlabel <- expression(paste("(", "",
+                                    paste(integral(, paste("0"), paste("", "t")),
+                                          "C", phantom()[{ paste("R") }],"(",tau,")d",tau, " + ",
+                                          frac(paste("C", phantom()[{ paste("R") }],"(t)"),
+                                               paste("k",phantom()[{ paste("2") }],"\'",))),")",
+                                      " / ",
+                                 "C", phantom()[{ paste("T") }],"(t)"))
+
+  ylabel <- expression(paste("", "", integral(, paste("0"), paste("", "t")),
+                                 "C", phantom()[{ paste("T") }],"(",tau,")d",tau, " / ",
+                                 "C", phantom()[{ paste("T") }],"(t)"))
+
   outplot <- ggplot(data = plotdf, aes(x = Logan_ref, y = Logan_roi, colour = Equilibrium)) +
     geom_point(aes(shape = "a", size = Weights)) +
     geom_abline(
       slope = as.numeric(refloganout$fit$coefficients[2]),
       intercept = as.numeric(refloganout$fit$coefficients[1])
     ) +
-    xlab("[Integ(C_Ref)+C_Ref/k2prime] / C_Tissue") + ylab("Integ(C_Tissue) / C_Tissue") + colScale +
+    xlab(xlabel) + ylab(ylabel) + colScale +
     guides(shape = "none", color = guide_legend(order = 1)) + scale_size(range = c(1, 3))
 
   return(outplot)
@@ -198,21 +210,21 @@ refLogan_tstar <- function(t_tac, reftac, lowroi, medroi, highroi, k2prime, file
   medroi_fit <- refLogan(t_tac, reftac, medroi, k2prime, length(reftac), frameStartEnd = frameStartEnd)
   highroi_fit <- refLogan(t_tac, reftac, highroi, k2prime, length(reftac), frameStartEnd = frameStartEnd)
 
-  # logan_xlab <- "[Integ(C_Ref)+C_Ref/k2prime] / C_Tissue"
-  # logan_ylab <- "Integ(C_Tissue) / C_Tissue"
-
-  logan_xlab <- expression(paste("(", "", integral(, paste("0"), paste("", "t")),
-                             "C", phantom()[{ paste("Ref") }],"(t)", " + ",
-                             "C", phantom()[{ paste("Ref") }],"(t)","/k",phantom()[{ paste("2") }],"\' ) / ",
-                             "C", phantom()[{ paste("Target") }],"(t)"))
-
-  logan_ylab <- expression(paste("", "", integral(, paste("0"), paste("", "t")),
-                                 "C", phantom()[{ paste("Tissue") }],"(t)", " / ",
-                                 "C", phantom()[{ paste("Tissue") }],"(t)"))
-
-  low_linplot <- qplot(lowroi_fit$fitvals$Logan_Ref, lowroi_fit$fitvals$Logan_ROI) + ggtitle("Low") + xlab(logan_xlab) + ylab(logan_ylab)
-  med_linplot <- qplot(medroi_fit$fitvals$Logan_Ref, medroi_fit$fitvals$Logan_ROI) + ggtitle("Medium") + xlab(logan_xlab) + ylab(logan_ylab)
-  high_linplot <- qplot(highroi_fit$fitvals$Logan_Ref, highroi_fit$fitvals$Logan_ROI) + ggtitle("High") + xlab(logan_xlab) + ylab(logan_ylab)
+  xlabel <- expression(paste("(", "",
+                             paste(integral(, paste("0"), paste("", "t")),
+                                   "C", phantom()[{ paste("R") }],"(",tau,")d",tau, " + ",
+                                   frac(paste("C", phantom()[{ paste("R") }],"(t)"),
+                                        paste("k",phantom()[{ paste("2") }],"\'",))),")",
+                             " / ",
+                             "C", phantom()[{ paste("T") }],"(t)"))
+
+  ylabel <- expression(paste("", "", integral(, paste("0"), paste("", "t")),
+                             "C", phantom()[{ paste("T") }],"(",tau,")d",tau, " / ",
+                             "C", phantom()[{ paste("T") }],"(t)"))
+
+  low_linplot <- qplot(lowroi_fit$fitvals$Logan_Ref, lowroi_fit$fitvals$Logan_ROI) + ggtitle("Low") + xlab(xlabel) + ylab(ylabel)
+  med_linplot <- qplot(medroi_fit$fitvals$Logan_Ref, medroi_fit$fitvals$Logan_ROI) + ggtitle("Medium") + xlab(xlabel) + ylab(ylabel)
+  high_linplot <- qplot(highroi_fit$fitvals$Logan_Ref, highroi_fit$fitvals$Logan_ROI) + ggtitle("High") + xlab(xlabel) + ylab(ylabel)
 
   tstarInclFrames <- 3:frames
   zeros <- rep(0, length(tstarInclFrames))

diff --git a/R/kinfitr_refmllogan.R b/R/kinfitr_refmllogan.R
@@ -162,10 +162,15 @@ plot_refmlLoganfit <- function(refmlloganout, roiname = NULL) {
   names(myColors) <- levels(plotdf$Equilibrium)
   colScale <- scale_colour_manual(name = paste0(roiname, "\nEquilibrium"), values = myColors)
 
+  xlabel <- "Fitted Values"
+
+  ylabel <- expression(paste("", "", integral(, paste("0"), paste("", "t")),
+                                   "C", phantom()[{ paste("T") }],"(",tau,")d",tau))
+
   outplot <- ggplot(data = plotdf, aes(x = Fitted, y = Term1_DV, colour = Equilibrium)) +
     geom_point(aes(shape = "a", size = Weights)) +
     geom_abline(slope = 1, intercept = 0) +
-    xlab("Fitted Values") + ylab("Integ(C_Tissue)") + colScale +
+    xlab(xlabel) + ylab(ylabel) + colScale +
     guides(shape = "none", color = guide_legend(order = 1)) + scale_size(range = c(1, 3))
 
   return(outplot)
@@ -212,15 +217,14 @@ refmlLogan_tstar <- function(t_tac, reftac, lowroi, medroi, highroi, k2prime, fi
   medroi_fit <- refmlLogan(t_tac, reftac, medroi, k2prime, length(reftac), frameStartEnd = frameStartEnd)
   highroi_fit <- refmlLogan(t_tac, reftac, highroi, k2prime, length(reftac), frameStartEnd = frameStartEnd)
 
-  mllogan_xlab <- "Fitted Values"
-  # mllogan_ylab <- "Integ(C_Tissue)"
+  xlabel <- "Fitted Values"
 
-  mllogan_ylab <- expression(paste("", "", integral(, paste("0"), paste("", "t")),
-                                 "C", phantom()[{ paste("Tissue") }],"(t)"))
+  ylabel <- expression(paste("", "", integral(, paste("0"), paste("", "t")),
+                             "C", phantom()[{ paste("T") }],"(",tau,")d",tau))
 
-  low_linplot <- qplot(lowroi_fit$fitvals$Fitted, lowroi_fit$fitvals$Term1_DV) + ggtitle("Low") + xlab(mllogan_xlab) + ylab(mllogan_ylab)
-  med_linplot <- qplot(medroi_fit$fitvals$Fitted, medroi_fit$fitvals$Term1_DV) + ggtitle("Medium") + xlab(mllogan_xlab) + ylab(mllogan_ylab)
-  high_linplot <- qplot(highroi_fit$fitvals$Fitted, highroi_fit$fitvals$Term1_DV) + ggtitle("High") + xlab(mllogan_xlab) + ylab(mllogan_ylab)
+  low_linplot <- qplot(lowroi_fit$fitvals$Fitted, lowroi_fit$fitvals$Term1_DV) + ggtitle("Low") + xlab(xlabel) + ylab(ylabel)
+  med_linplot <- qplot(medroi_fit$fitvals$Fitted, medroi_fit$fitvals$Term1_DV) + ggtitle("Medium") + xlab(xlabel) + ylab(ylabel)
+  high_linplot <- qplot(highroi_fit$fitvals$Fitted, highroi_fit$fitvals$Term1_DV) + ggtitle("High") + xlab(xlabel) + ylab(ylabel)
 
   tstarInclFrames <- 3:frames
   zeros <- rep(0, length(tstarInclFrames))