update

_render.R

@@ -43,3 +43,4 @@ for (f in list.files('_book', '[.]html$', full.names = TRUE)) {
 if (length(formats) > 1) bookdown::publish_book()
 
 setwd(owd)
+

simulation/run.R

@@ -4,6 +4,8 @@ library(ggpubr)
 library(rlang)
 library(httpgd)
 library(ggthemes)
+library(ggsci)
+library(ggpubr)
 mod <- mread_cache('simulation/TMDD.cpp')
 mod <- param(mod, list(KINT = 0.003,
                        KOFF = 0.001,
@@ -15,12 +17,11 @@ mod <- param(mod, list(KINT = 0.003,
                        VC = 0.04,
                        KON = 0.002
 ))
-install.packages('bookdown')
 #### Change of dose  ####
 
 amt_vec <- c(10, 15, 20, 25)
-
-dose_change_plot <- mod %>%
+amt_vec2 <- c(3, 5, 10, 15)
+dose_change_plotA <- mod %>%
   data_set(as_data_set(data.frame(amt = amt_vec, ID = 1:4, cmt = 2) %>% mutate(dose = amt))) %>%
   carry_out(dose) %>%
   zero_re() %>%
@@ -33,16 +34,26 @@ dose_change_plot <- mod %>%
   labs(x = "Time (hr)",
        y = "Concentration (nM/L)",
        col = "Dose (nM)")+
-  theme_few() + 
-  scale_color_calc()
-dose_change_plot
+  scale_y_continuous(limits = c(0.05, 1000), breaks = c( 0.1, 1, 10, 100, 1000), trans = "log10") +
+  scale_x_continuous(limits = c(0, 3000)) +
+  scale_color_npg() +
+  theme_bw()
+
+plot_grid(dose_change_plotA, dose_change_plotA, labels = c("A", "B"), label_size = 18)
+dose_change_plotA
 ggsave('media-07/TMDD_dose.png', width = 7.5, height = 6, unit = "in")
 dose_change_plot_log <- dose_change_plot + scale_y_continuous(trans = 'log10')
 
 dose_change_plot_log
 ggarrange(dose_change_plot_log, dose_change_plot, common.legend = TRUE, labels = c("A", "B"))
 ggsave("media-07/DOSEA.png", width = 6, height = 4, unit = "in")
+
 #### Change of parameter ####
+library(scales)
+NotFancy <- function(l) {
+  l <- format(l, scientific = FALSE)
+  parse(text = l)
+}
 
 param_change <- function(PAR, SEQ, TIME = 800) {
   PAR2 <- as_name(enquo(PAR))
@@ -60,9 +71,9 @@ param_change <- function(PAR, SEQ, TIME = 800) {
     labs(x = "Time (hr)",
          y = "Concentration (nM/L)",
          col = paste0(as_label(enquo(PAR)), " (nM)")) +
-    theme_few() +
-    scale_color_calc() +
-    scale_y_continuous(breaks = c(0, 50, 100), limits = c(0, 130))
+    theme_bw() +
+    scale_color_npg(labels = c("0.0005", "0.001", "0.005", "0.01", "0.05")) +
+    scale_y_continuous(breaks = c(0, 50, 100), limits = c(0, 130)) 
   p1
   #p2 <- p1 + scale_y_continuous(trans = "log10")
   #ggarrange(p1, p2, common.legend = TRUE, labels = c("A", "B"))
@@ -75,9 +86,9 @@ param_change(R0, seq(1, 20, length.out = 5), 100)
 ggsave('media-07/R0.png', width = 7.5, height = 6, unit = "in")
 param_change(KEL, seq(0.00015, 0.01, length.out = 5), 300)
 ggsave('media-07/KEL.png', width = 6, height = 4, unit = "in")
-param_change(KDEG, seq(0.00015, 0.01, length.out = 5), 300)
+param_change(KDEG, c(0.00015, 0.0015, 0.015, 0.15, 1.5), 300)
 ggsave('media-07/KDEG.png', width = 6, height = 4, unit = "in")
-param_change(KINT, seq(0.00015, 0.01, length.out = 5), 1000) + scale_y_continuous(trans = 'log10') + labs(color = "Kec (nM)")
+param_change(KINT, c(0.0005, 0.001, 0.005, 0.01, 0.05), 1000) + scale_y_continuous(trans = "log10") + labs(color = "Kec (nM)")
 ggsave('media-07/KINT.png', width = 6, height = 4, unit = "in")
 param_change(KON, seq(0.00015, 0.01, length.out = 5), 300)
 ggsave('media-07/KON.png', width = 6, height = 4, unit = "in")
@@ -105,7 +116,6 @@ dose_change_plot <- mod %>%
     col = "Dose (nM)"
   )
 
-
 mod %>%
   ev(amt = 10, cmt = 2) %>%
   mrgsim(nid = 5, end = 1800) %>%
@@ -145,21 +155,24 @@ moddata <- mod2 %>%
 
 savedata2 <- moddata
 finaldata <- moddata
-
+head(moddata)
 moddata %>%
-  filter(CP > 1E-8, time %in% sample) %>% 
-  filter(!(ID %in% 1:4 & time > 1000)) %>%
+  filter(CP > 1E-2, time %in% sample) %>% 
+  # filter(!(ID %in% 1:4 & time > 1000)) %>%
+  mutate(ADA = ifelse(ID %in% c(1, 2, 3, 4), "ADA (+)", "ADA (-)")) %>%
   ggplot(aes(x = time, y = CP, col = as.factor(ID))) +
-  geom_point() +
+  geom_point(alpha = 0.5) +
   geom_line() + 
   scale_y_continuous(trans = "log10") +
+  facet_grid(cols = vars(ADA))+
   theme_bw() +
   labs(
     x = "Time (hr)",
     y = "Concentration",
     col = "ID"
-  )
-
+  ) +
+  scale_color_npg()
+?facet_grid
 ggsave('media-07/ADA.png', width = 6, height = 4, unit = "in")
 
 write.csv(finaldata, "simulation/adadata.csv", row.names= F)
@@ -168,6 +181,7 @@ moddata <- read_csv('simulation/adadata.csv')
 
 #### MM model VS TMDD model ####
 mod <- mread_cache("simulation/TMDD.cpp")
+mod_mm <- mread_cache("simulation/MMmodel.cpp")
 mod <- param(mod, list(
   KINT = 0.003,
   KOFF = 0.001,
@@ -182,7 +196,7 @@ mod <- param(mod, list(
 
 amt_vec <- c(1, 5, 10, 15, 20)
 
-dose_change_plot <- mod %>%
+dose_change_plot_log <- mod %>%
   data_set(as_data_set(data.frame(amt = amt_vec, ID = 1:5, cmt = 2) %>% mutate(dose = amt))) %>%
   carry_out(dose) %>%
   zero_re() %>%
@@ -196,38 +210,21 @@ dose_change_plot <- mod %>%
   theme_bw() +
   labs(
     x = "Time (hr)",
-    y = "Concentration (nM/L)",
-    col = "Dose (nM)"
-  )
-
-dose_change_plot_log <- dose_change_plot + scale_y_continuous(trans = "log10")
-
-dose_change_plot_log
+    y = "Concentration (ng/mL)",
+    col = "Dose (mg)"
+  ) +
+  scale_y_continuous(trans = "log10", limits = c(0.01, 500))
 
 
-ggarrange(dose_change_plot, dose_change_plot_log, common.legend = TRUE, labels = c("A", "B"))
-ggsave("media-07/DOSE.png", width = 6, height = 4, unit = "in")
-mod_mm <- mread_cache('simulation/MMmodel.cpp')
-
-mod_mm %>%
-  ev(amt = 100) %>%
-  mrgsim() %>%
-  plot()
-
-param(mod_mm)
-mod_mm <- param(mod_mm, list(
-  VMAX = 100,
-  KM = 10
-))
-amt_vec <- c(10, 30, 50, 70, 100)
-
-mod_mm %>%
-   data_set(as_data_set(data.frame(amt = 100*amt_vec, ID = 1:5, cmt = 1) %>% mutate(dose = amt))) %>%
+tmdd.plot <- dose_change_plot_log + scale_color_npg()
+tmdd.plot
+dose_change_plot_log_mm <-mod_mm %>%
+   data_set(as_data_set(data.frame(amt = 300*amt_vec, ID = 1:5, cmt = 1) %>% mutate(dose = amt))) %>%
    carry_out(dose) %>%
    zero_re() %>%
    mrgsim(end = 1000) %>%
    as.data.frame() %>%
-   mutate(dose = as.factor(dose/100)) %>%
+   mutate(dose = as.factor(dose/100/3)) %>%
    filter(CP > 1E-2) %>%
    ggplot(aes(x = time, y = CP, col = dose)) +
    geom_line() +
@@ -238,6 +235,11 @@ mod_mm %>%
      y = "Concentration (ng/mL)",
      col = "Dose (mg)"
    ) +
-   scale_y_continuous(trans = 'log10')
-
-ggsave('media-07/MM.png', width = 6, height = 4, unit = "in")
+   scale_y_continuous(trans = 'log10', limits = c(0.01, 500)) 
+scale_y_continuous
+mm.plot <- dose_change_plot_log_mm + scale_color_npg()
+mm.plot
+library(cowplot)
+plot_grid(tmdd.plot, mm.plot, ncol = 2, labels = c("A", "B"), label_size = 18)
+grid.arrange(tmdd.plot, mm.plot, ncol = 2)
+library(gridExtra)