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381 changes: 381 additions & 0 deletions ModelF/Changed/AFIRT_calculation.R
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283 changes: 283 additions & 0 deletions ModelF/Changed/Task05_Sensitivity_Analysis_pt2.Rmd
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Original file line number Diff line number Diff line change
@@ -0,0 +1,283 @@
---
title: "Task05_Sensitivity_Analysis_pt2"
author: "Miandra Ellis"
date: "`r format(Sys.time(), '%d %B, %Y')`"
output: html_document
# output:
# html_document:
# toc: true
# toc_float: true
# code_folding: hide
---

# Preliminary stuff

```{r, warning=FALSE}
# Need this to get rxode working. I don't know why I keep having to run this.
Sys.setenv(PATH = paste(Sys.getenv("PATH"), "C:/RBuildTools/3.4/bin/",
"C:/RBuildTools/3.4/mingw_64/bin", sep = ";"))
Sys.setenv(BINPREF = "C:/RBuildTools/3.4/mingw_64/bin/")

# To be called at the top of every Rmd file. Initialization code and some useful constants.
suppressMessages(source("ams_initialize_script.R"))
```

# Create data frame for multiple drugs and parameters.

```{r, include=FALSE}

# Note: Insoluble and soluble drugs are treated differently.
# For insoluble, Tacc = M3totss/M30. For soluble, Tacc = S3totss/S30.
# We are also interested in different parameters in the SA for either case.
# See writeup for details.

# --------------------------------------------------------------------------------
# Initialize.
# --------------------------------------------------------------------------------

# Load model.
model = ivsc_4cmtct_shedct(target = TRUE)
# Drugs to explore.
drugs = c("Atezolizumab", "Herceptin", "Pembrolizumab", "Bevacizumab")
# List of parameters of interest.
parameters = c("dose", "ksynM3", "k13D", "kshedM3", "kshedDM3", "VD3")
# names(parameters) = parameters
# Create vector of soluble drugs.
soluble = "Bevacizumab"

# Create paths to data files for each drug.
paths = NULL
for (i in 1:length(drugs)) {
paths[i] = paste0("../data/ModelF_", drugs[i],"_Params.xlsx")
}

# Dose time, frequency, compartment, nominal dose
tmax = 26*7 #days
tau = 21 #days
compartment = 2
dose.nmol = scale.mpk2nmol
joined = NULL
isSoluble = FALSE

# --------------------------------------------------------------------------------
# Iterate over all the drugs.
# --------------------------------------------------------------------------------
i.dfs = 0
for (i in 1:length(drugs)){
# Load parameters.
param.as.double = read.param.file(paths[i])
df_param = as.data.frame(t(param.as.double))

# Check if drug has soluble target.
if (drugs[i] %in% soluble) {
# Change any non-shed parameters including M to S.
parameters = sapply(parameters,
function(x) {
if (!grepl("shed|dose",x)) {return(gsub("M","S", x))}
return(x)
})
isSoluble = TRUE
}

# Set range for parameters of interest in SA.
# Check which parameters are nonzero, not including dose which isn't in df_param.
nnzero = df_param[parameters[which(parameters != "dose")]] != 0
nnzero = colnames(nnzero)[which(nnzero)]
params.to.iterate = data.frame(dose = lseq(scale.mpk2nmol*.1,scale.mpk2nmol*10,7),
lapply(df_param[nnzero], function(x) lseq(x*0.1, x*10, 7)))

dfs = list()
# Iterate all of the parameters for a single drug.
for (j in 1:ncol(params.to.iterate)){
i.dfs = i.dfs+1
param.to.change = names(params.to.iterate)[j]
param.to.change.range = params.to.iterate[[j]]
soluble = isSoluble
compare_i = compare.thy.sim(model = model,
param.as.double = param.as.double,
dose.nmol = dose.nmol,
tmax = tmax,
tau = tau,
compartment = compartment,
param.to.change = param.to.change,
param.to.change.range = param.to.change.range,
soluble = soluble) %>%
mutate(drug = drugs[i], isSol = isSoluble)

dfs[[i.dfs]] = compare_i
}

# Reset isSoluble to false since the default in compare.thy.sim is false.
isSoluble = FALSE
}
joined = bind_rows(dfs)

```

# Plot the output AFIRT.

```{r}
# I only wanted a subset of the parameters for gather.
joined.A = joined[c("fold.change","AFIRT.Kssd", "AFIRT.Kss", "AFIRT.Kd", "AFIRT.sim", "param","drug", "isSol")]

# Use gather to make the long data frame for ggplot.
plots.A = joined.A %>% gather(key, AFIRT.value, -param, -fold.change,-drug, -isSol) %>%
filter(!is.na(AFIRT.value)) %>%
# Group by isSoluble to create to separate plots.
group_by(isSol)%>%
do(plot = ggplot(., aes(fold.change, AFIRT.value, color=key)) +
scale.x.log10() +
scale.y.log10() +
geom_line() +
geom_point() +
facet_grid(drug ~ param))
plots.A$plot
```

# Plot the output TFIRT.

```{r}
# I only wanted a subset of the parameters for gather.
joined.T = joined[c("fold.change","TFIRT.Kssd", "TFIRT.Kss", "TFIRT.Kd", "TFIRT.sim", "param","drug", "isSol")]

# Use gather to make the long data frame for ggplot.
plots.T = joined.T %>% gather(key, TFIRT.value, -param, -fold.change,-drug, -isSol) %>%
filter(!is.na(TFIRT.value)) %>%
# Group by isSoluble to create to separate plots.
group_by(isSol)%>%
do(plot = ggplot(., aes(fold.change, TFIRT.value, color=key)) +
scale.x.log10() +
scale.y.log10() +
geom_line() +
geom_point() +
facet_grid(drug ~ param))
plots.T$plot
```

# Create data frame for multiple drugs and parameters.
# This is redone for no target in order to compare Cmin.
# The only difference is 'target = FALSE' is the input for the model.

```{r, include=FALSE}

# Note: Insoluble and soluble drugs are treated differently.
# For insoluble, Tacc = M3totss/M30. For soluble, Tacc = S3totss/S30.
# We are also interested in different parameters in the SA for either case.
# See writeup for details.

# --------------------------------------------------------------------------------
# Initialize.
# --------------------------------------------------------------------------------

# Load model.
model = ivsc_4cmtct_shedct(target = FALSE)
# Drugs to explore.
drugs = c("Atezolizumab", "Herceptin", "Pembrolizumab", "Bevacizumab")
# List of parameters of interest.
parameters = c("dose", "ksynM3", "k13D", "kshedM3", "kshedDM3", "VD3")
# names(parameters) = parameters
# Create vector of soluble drugs.
soluble = "Bevacizumab"

# Create paths to data files for each drug.
paths = NULL
for (i in 1:length(drugs)) {
paths[i] = paste0("../data/ModelF_", drugs[i],"_Params.xlsx")
}

# Dose time, frequency, compartment, nominal dose
tmax = 26*7 #days
tau = 21 #days
compartment = 2
dose.nmol = scale.mpk2nmol
joined = NULL
isSoluble = FALSE

# --------------------------------------------------------------------------------
# Iterate over all the drugs.
# --------------------------------------------------------------------------------

for (i in 1:length(drugs)){
# Load parameters.
param.as.double = read.param.file(paths[i])
df_param = as.data.frame(t(param.as.double))

# Check if drug has soluble target.
if (drugs[i] %in% soluble) {
# Change any non-shed parameters including M to S.
parameters = sapply(parameters,
function(x) {
if (!grepl("shed|dose",x)) {return(gsub("M","S", x))}
return(x)
})
isSoluble = TRUE
}

# Set range for parameters of interest in SA.
# Check which parameters are nonzero, not including dose which isn't in df_param.
nnzero = df_param[parameters[which(parameters != "dose")]] != 0
nnzero = colnames(nnzero)[which(nnzero)]
params.to.iterate = data.frame(dose = lseq(scale.mpk2nmol*.1,scale.mpk2nmol*10,7),
lapply(df_param[nnzero], function(x) lseq(x*0.1, x*10, 7)))

dfs = list()
# Iterate all of the parameters for a single drug.
for (j in 1:ncol(params.to.iterate)){
i.dfs = i.dfs + 1
dfs[[i.dfs]] = compare.thy.sim(model = model,
param.as.double = param.as.double,
dose.nmol = dose.nmol,
tmax = tmax,
tau = tau,
compartment = compartment,
param.to.change = names(params.to.iterate)[j],
param.to.change.range = params.to.iterate[[j]],
soluble = isSoluble) %>%
mutate(drug = drugs[i], isSol = isSoluble)
}
# Reset isSoluble to false since the default in compare.thy.sim is false.
isSoluble = FALSE
}
joined = bind_rows(dfs)

```

# Plot the output Cmin.

```{r}

# I only wanted a subset of the parameters for gather.
joined.Cmin = joined[c("fold.change","Cmin", "param","drug", "isSol")]

# Use gather to make the long data frame for ggplot.
plots.Cmin = joined.Cmin %>% gather(key, Cmin.value, -param, -fold.change,-drug, -isSol) %>%
filter(!is.na(Cmin.value)) %>%
# Group by isSoluble to create to separate plots.
group_by(isSol)%>%
do(plot = ggplot(., aes(fold.change, Cmin.value, color=key)) +
scale.x.log10() +
scale.y.log10() +
geom_line() +
geom_point() +
facet_grid(drug ~ param))
plots.Cmin$plot

```


















487 changes: 487 additions & 0 deletions ModelF/Task03_Explore_Bevacizumab.html
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302 changes: 302 additions & 0 deletions ModelF/Task04_Sensitivity_Analysis.html
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224 changes: 224 additions & 0 deletions ModelF/Task04_Sensitivity_Analysis_Individual.html
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32 changes: 13 additions & 19 deletions ModelF/Task05_Sensitivity_Analysis_Aggregate.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -149,7 +149,7 @@ plots.A.Kssd = plots.A.Kssd %>%
param = str_replace(param,"S","T"),
key = str_replace(key,"_",""),
key = str_replace(key,"AFIRT\\.",""),
key = str_replace(key,"Kssd","Theory (AFTIR*)"),
key = str_replace(key,"Kssd","Theory (AFTIR)"),
key = str_replace(key,"sim","Simulation"),
Target = ifelse(isSol,"Soluble","Membrane-Bd"),
Target = factor(Target,levels=c("Soluble","Membrane-Bd")))
Expand All @@ -158,7 +158,7 @@ plots.T.Kssd = plots.T.Kssd %>%
param = str_replace(param,"S","T"),
key = str_replace(key,"_",""),
key = str_replace(key,"TFIRT\\.",""),
key = str_replace(key,"Kssd","Theory (TFTIR*)"),
key = str_replace(key,"Kssd","Theory (TFTIR)"),
key = str_replace(key,"sim","Simulation"),
Target = ifelse(isSol,"Soluble","Membrane-Bd"),
Target = factor(Target,levels=c("Soluble","Membrane-Bd")))
Expand All @@ -168,7 +168,7 @@ plots.A.Kss = plots.A.Kss %>%
param = str_replace(param,"S","T"),
key = str_replace(key,"_",""),
key = str_replace(key,"AFIRT\\.",""),
key = str_replace(key,"Kss","Theory (AFTIR*)"),
key = str_replace(key,"Kss","Theory (AFTIR)"),
key = str_replace(key,"sim","Simulation"),
Target = ifelse(isSol,"Soluble","Membrane-Bd"),
Target = factor(Target,levels=c("Soluble","Membrane-Bd")))
Expand All @@ -177,7 +177,7 @@ plots.T.Kss = plots.T.Kss %>%
param = str_replace(param,"S","T"),
key = str_replace(key,"_",""),
key = str_replace(key,"TFIRT\\.",""),
key = str_replace(key,"Kss","Theory (TFTIR*)"),
key = str_replace(key,"Kss","Theory (TFTIR)"),
key = str_replace(key,"sim","Simulation"),
Target = ifelse(isSol,"Soluble","Membrane-Bd"),
Target = factor(Target,levels=c("Soluble","Membrane-Bd")))
Expand All @@ -187,7 +187,7 @@ plots.A.Kd = plots.A.Kd %>%
param = str_replace(param,"S","T"),
key = str_replace(key,"_",""),
key = str_replace(key,"AFIRT\\.",""),
key = str_replace(key,"Kd","Theory (AFTIR*)"),
key = str_replace(key,"Kd","Theory (AFTIR)"),
key = str_replace(key,"sim","Simulation"),
Target = ifelse(isSol,"Soluble","Membrane-Bd"),
Target = factor(Target,levels=c("Soluble","Membrane-Bd")))
Expand All @@ -196,7 +196,7 @@ plots.T.Kd = plots.T.Kd %>%
param = str_replace(param,"S","T"),
key = str_replace(key,"_",""),
key = str_replace(key,"TFIRT\\.",""),
key = str_replace(key,"Kd","Theory (TFTIR*)"),
key = str_replace(key,"Kd","Theory (TFTIR)"),
key = str_replace(key,"sim","Simulation"),
Target = ifelse(isSol,"Soluble","Membrane-Bd"),
Target = factor(Target,levels=c("Soluble","Membrane-Bd")))
Expand All @@ -208,10 +208,9 @@ g = g + geom_line()
g = g + facet_grid(drug + Target ~ param, switch = "y")
g = g + scale_linetype_manual(values = c("solid","longdash"))
g = g + labs(x="Fold Change in Parameter",
y="Average Free Tissue target to\nInitial target Ratio (AFTIR)",
y="Average Free Tissue target to\nInitial target Ratio (AFTIR)")
# color = "Estimate",
# linetype = "Estimate",
caption = "Kssd")
# linetype = "Estimate")
g = g + theme(legend.position="bottom",
text=element_text(size=15),
axis.title.x=element_text(size=20),
Expand All @@ -224,30 +223,25 @@ height = 7
plot(g)
ggsave("../results/Task05_AFTIR.Kssd.pdf",width = width,height=height)
g = g %+% plots.T.Kssd
g = g + labs(y="Trough Free Tissue target to\ninitial target Ratio (TFTIR)",
caption = "Kssd")
g = g + labs(y="Trough Free Tissue target to\ninitial target Ratio (TFTIR)")
plot(g)
ggsave("../results/Task05_TFTIR.Kssd.pdf",width = width,height=height)

g = g %+% plots.A.Kss
g = g + labs(y="Average Free Tissue target to\nInitial target Ratio (AFTIR)",
caption = "Kss")
g = g + labs(y="Average Free Tissue target to\nInitial target Ratio (AFTIR)")
plot(g)
ggsave("../results/Task05_AFTIR.Kss.pdf",width = width,height=height)
g = g %+% plots.T.Kss
g = g + labs(y="Trough Free Tissue target to\ninitial target Ratio (TFTIR)",
caption = "Kss")
g = g + labs(y="Trough Free Tissue target to\ninitial target Ratio (TFTIR)")
plot(g)
ggsave("../results/Task05_TFTIR.Kss.pdf",width = width,height=height)

g = g %+% plots.A.Kd
g = g + labs(y="Average Free Tissue target to\nInitial target Ratio (AFTIR)",
caption = "Kd")
g = g + labs(y="Average Free Tissue target to\nInitial target Ratio (AFTIR)")
plot(g)
ggsave("../results/Task05_AFTIR.Kd.pdf",width = width,height=height)
g = g %+% plots.T.Kd
g = g + labs(y="Trough Free Tissue target to\ninitial target Ratio (TFTIR)",
caption = "Kd")
g = g + labs(y="Trough Free Tissue target to\ninitial target Ratio (TFTIR)")
plot(g)
ggsave("../results/Task05_TFTIR.Kd.pdf",width = width,height=height)
```
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