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Task02a_Sensitivity_SCIM_k_pars_all_drugs.R
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Task02a_Sensitivity_SCIM_k_pars_all_drugs.R
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source("ams_initialize_script.R")
#rxSetIni0(FALSE)
source("SCIM_calculation.R")
source("ivsc_2cmt_RR_V1.R")
dirs$Rscript.name = "Task02a_Sensitivity_SCIM_k_pars.R"
dirs$output.prefix= str_extract(dirs$Rscript.name,"^Task\\d\\d\\w?_")
model = ivsc_2cmt_RR_v1()
#Drug list to loop through for finding file names
drugs_list = list("Pembro","VEGFR1","VEGFR2","Atezoli","Ramuc","Siltux","Tociliz") #ADD THIS LINE
dfs = data.frame() #ADD THIS LINE
# Create paths to data files for each drug.
param = NULL #ADD THIS LINE
i = 1 #ADD THIS LINE
#Get params for all the drugs
for (drugs in drugs_list) { #ADD THIS LOOP
filename = list.files(path = "parameters/",pattern = drugs) #change filename line to this
if (length(filename)>1)
stop("check and see if you have any temp files open or something. maybe close excel")
param[[i]] = paste0("parameters/",filename)
i = i+1
}
# List of parameters of interest.
parameters = c("ksynT", "keDT","koff_TL", "kon_TL", "koff_DT","kon_DT")
# Dose time, frequency, compartment, nominal dose
tmax = 52*7 #days
tau = 21 #days
compartment = 2
dose.nmol = 100*scale.mpk2nmol
param.list = list()
all_params <- data.frame() #ADD THIS LINE
for (i in 1:length(drugs_list)){ #loop over all the drugs in the list
# Load parameters.
param.as.double = read.param.file(param[i]) #ADD THIS LINE (CHANGED VARIABLE NAME TO PARAM)
df_param = as.data.frame(t(param.as.double))
param.list[[i]] = data.frame(t(param.as.double)) %>%
mutate(drug = drugs_list[[i]]) %>%
dplyr::select(drug,everything())
# 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(lapply(df_param[nnzero], function(x) lseq(x*0.000001, x*1000000, 13)))
dfs = list() #Reset the temp list for every drug
temp_dfs <- data.frame() #Reset the temporary dataframe
# Iterate all of the parameters for a single drug.
for (j in 1:ncol(params.to.iterate)){
param.to.change = names(params.to.iterate)[j]
param.to.change.range = params.to.iterate[[j]]
dfs[[j]] = 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)
}
#ADD THESE LINES
temp_dfs <- bind_rows(dfs) #create a temp dataframe for all the data
temp_dfs$drug <- as.character(drugs_list[i])
all_params <- rbind(all_params,temp_dfs) #Cat data frame
}
param.table = bind_rows(param.list) %>%
mutate(Kd_DT = koff_DT/kon_DT,
Kss_DT = (koff_DT + keDT)/kon_DT,
Kd_TL = koff_TL/kon_TL,
Kss_TL = (koff_TL + keTL)/kon_TL)
#View(param.table)
drug = param.table$drug
param.tablet = param.table %>%
dplyr::select(-drug) %>%
t() %>%
as.data.frame() %>%
setNames(drug)
#View(param.tablet)
write.csv(all_params, file = "results/Task02a_sensitivity_all drugs and params_100_updated 04_24.csv")
data.plot = all_params %>%
dplyr::select(fold.change.param, SCIM_sim, SCIM_thy_keTL_negroot, SCIM_thy_keTL0, AFIR_thy, drug,param) %>%
gather(key,value,-c(fold.change.param,drug,param))
g = ggplot(data.plot, aes(x=fold.change.param,y=value,color=key,linetype=key))
g = g + geom_line(size = 1, alpha = .5)
g = g + facet_grid(drug ~ param,scales = "free_y", switch = "y")
g = g + scale_x_log10()
g = g + scale_y_log10()
g = g + scale_color_manual (values = c(SCIM_sim = "black",
SCIM_thy_keTL0 = "blue",
SCIM_thy_keTL_negroot = "green",
AFIR_thy = "red"))
g = g + scale_linetype_manual(values = c(SCIM_sim = "solid",
SCIM_thy_keTL0 = "dotted",
SCIM_thy_keTL_negroot = "dashed",
AFIR_thy = "solid"))
print(g)
# Compare simplified SCIM eqns.
# SCIM_thy_keTL_negroot is the most complex i.e not simplified version of SCIM
# SCIM_sim is the SCIM from the simulation
# 26, 29, and 31 refer to the eqn numbers in the latex doc. for the simplified SCIMs
data.SCIMs = all_params %>%
dplyr::select(fold.change.param, SCIM_sim, SCIM_thy_keTL_negroot, SCIM_thy_keTL_negroot26, SCIM_thy_keTL_negroot31, drug,param) %>%
gather(key,value,-c(fold.change.param,drug,param))
g <- ggplot(data.SCIMs, aes(x=fold.change.param,y=value,color=key,linetype=key)) +
geom_line(size = 1, alpha = .6) +
facet_grid(drug ~ param,scales = "free_y", switch = "y") +
scale_x_log10() +
scale_y_log10() +
scale_color_manual(values = c(SCIM_sim = "gray25",
SCIM_thy_keTL_negroot = "green3",
SCIM_thy_keTL_negroot26 = "dodgerblue4",
#SCIM_thy_keTL_negroot29 = "yellow",
SCIM_thy_keTL_negroot31 = "darkorange")) +
scale_linetype_manual(values = c(SCIM_sim = "solid",
SCIM_thy_keTL_negroot = "dashed",
SCIM_thy_keTL_negroot26 = "dotdash",
#SCIM_thy_keTL_negroot29 = "dotted",
SCIM_thy_keTL_negroot31 = "dashed"))
print(g)
# Compare simplified SCIMs and AFIR.
data.SCIMs2 = all_params %>%
dplyr::select(fold.change.param, SCIM_sim, SCIM_thy_keTL_negroot, SCIM_thy_keTL_negroot26, AFIR_thy, drug,param) %>%
gather(key,value,-c(fold.change.param,drug,param))
g <- ggplot(data.SCIMs2, aes(x=fold.change.param,y=value,color=key,linetype=key)) +
geom_line(size = 1, alpha = .6) +
facet_grid(drug ~ param,scales = "free_y", switch = "y") +
scale_x_log10() +
scale_y_log10() +
scale_color_manual (values = c(SCIM_sim = "gray25",
SCIM_thy_keTL_negroot = "green3",
SCIM_thy_keTL_negroot26 = "dodgerblue4",
AFIR_thy = "red")) +
scale_linetype_manual(values = c(SCIM_sim = "solid",
SCIM_thy_keTL_negroot = "dashed",
SCIM_thy_keTL_negroot26 = "dotdash",
AFIR_thy = "solid"))
print(g)