article_resources/figures_source_code/figure_7_S9.R
In Thibaudpmx/QSPVP: Parameter Space Mapping algorithms to accelerate the creation of plausible Virtual Patients
## ---------------------------
## Script name: Figure R article
##
## Purpose of script: production of figure 7
##c
## Author: Thibaud Derippe
##
## Date Created: 2022-04-18 (trial codes previously in "eval_performance" file)
##
## Under GPL-3 License
## Email: thibaud.derippe@gmail.com
## GitHub: https://github.com/Thibaudpmx/PaSM
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##
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##
##
##
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library(PaSM)
plotLindner <- function(obj, npatient = 2000, title = ""){
obj$poolVP %>%
arrange(id) %>%
mutate(test = map_lgl(simul, ~class(.x)[[1]] == "tbl_df")) %>%
filter(test) %>%
mutate(protocol = case_when(protocol == "ABT737" ~ "ABT-737",
protocol == "apog" ~ "ApoG2",
protocol == "synergy" ~ "Combination",
T~ protocol))-> temp
temp <- temp %>% left_join(temp %>%
group_by(id) %>%
tally )
idtosample <- temp$id[temp$n == max(temp$n)] %>% unique
temp %>%
filter(id%in% sample(idtosample, min(npatient, length(idtosample))) ) %>%
# slice(1:(min(npatient * obj$targets$protocol %>% unique %>% length(), nrow(temp)))) %>%
unnest(simul) %>%
mutate(protocol = if_else(protocol == "unique", "No Drug" , protocol)) %>%
ggplot()+
geom_line(aes(time, Pore, group = id))+
facet_wrap(~protocol)+
geom_hline(yintercept = 10, col = "red", size = 1.5)+
coord_cartesian(xlim = c(50,100))+
theme_bw()+
labs(x = "Time (hours)", y = "Percentage Pore", title = title)+
theme(plot.title = element_text(hjust = 0.5))
}
# original configuration-----------------------------------------------------
setwd("D:/these/Second_project/QSP/modeling_work/VT_simeoni/article_QSPVP/data/Lindner_article")
protocols <- list( unique = tibble(cmt = "Bcl2", time = 0, amt = 0),
apog = tibble(cmt = "ApoG2", time = 50, amt = 2000),
ABT737 = tibble(cmt = "ABT737", time = 50, amt = 2000),
synergy = tibble(cmt = c("ABT737","ApoG2"), time = 50, amt = 2000))
VP_df <- crossing(Bcl20 = seq(0,900,100),
Bclxl0 = seq(0,900,100),
Mcl10 = c(0,50,100,150) ,#* seq(0.6,1.4,0.2),
BIM0 = seq(0,900,100),
PUMA0 =seq(0,900,100),
NOXA0 = seq(0,900,200),
BAXc0 = 500,
BAK0 = 500)
# Step1: Die anyways ------------------------------------------------------
# Step 1: remove those who die anyway
ApoptoWODrug <- VP_proj_creator$new(sourcefile = "D:/these/Second_project/QSP/modeling_work/VT_simeoni/1_user_inputs/1_config_Lindner_origin.r")
ApoptoWODrug$protocols <- protocols
ApoptoWODrug$set_targets(manual = tribble(~protocol, ~time, ~cmt, ~ min, ~max,
"unique",100,"TimeAbove", 1E-1, Inf
))
ApoptoWODrug$add_VP(VP_df, fillatend = F, reducefilteratend = F, use_green_filter = T, keep = "Pore", time_compteur = T, keepRedFiltaftDis = T)
saveRDS(ApoptoWODrug, "ApoptoWODrug")
VP_df %>%
left_join(ApoptoWODrug$poolVP %>% select(-simul)) %>%
filter(is.na(id)) %>%
select(1:8) -> VP_df2
# Step2: Dead Both drugs ------------------------------------------------------
BothDead <- VP_proj_creator$new(sourcefile = "D:/these/Second_project/QSP/modeling_work/VT_simeoni/1_user_inputs/1_config_Lindner_origin.r")
BothDead$protocols <- protocols
targetsBothDead <- tribble(~protocol, ~time, ~cmt, ~ min, ~max,
"unique",100,"TimeAbove", -Inf, 1E-1,
"apog",100,"TimeAbove", 1E-1, Inf,
"ABT737",100,"TimeAbove", 1E-1, Inf
)
BothDeadFull <- BothDead$clone(deep = T)
BothDead$set_targets(manual = targetsBothDead %>% slice(-1))
BothDeadFull$set_targets(manual = targetsBothDead)
BothDead$add_VP(VP_df2, fillatend = F, reducefilteratend = F, use_green_filter = T, keep = "Pore", time_compteur = T, keepRedFiltaftDis = T)
if(nrow(BothDead$poolVP) >1) saveRDS(BothDead, "BothDead")
# BothDead <- readRDS("BothDead")
BothDead$add_VP(VP_df2, fillatend = F, reducefilteratend = F, use_green_filter = T, keep = "Pore", time_compteur = T, keepRedFiltaftDis = T)
if(nrow(BothDead$poolVP) >1) saveRDS(BothDead, "BothDead")
BothDeadFull$add_VP(VP_df, fillatend = F, reducefilteratend = F, use_green_filter = T, keep = "Pore", time_compteur = T, keepRedFiltaftDis = T)
if(nrow(BothDeadFull$poolVP) >1) saveRDS(BothDeadFull, "BothDeadFull")
plotLindner(obj = BothDead)
PrevRej <-
BothDead$VP_rejected %>%
filter(!is.na(id)) %>%
rename(TimeAbove = value) %>%
select(time, protocol, TimeAbove, !!!BothDead$param)
PrevAcc <- BothDead$poolVP %>%
unnest() %>%
filter(time == 100) %>%
select(time, protocol, TimeAbove, !!!BothDead$param)
Previous <- PrevAcc %>%
bind_rows(
PrevRej
) %>%
rowid_to_column("id")
saveRDS(Previous, "previousBothdead")
BothDead$timeTrack$poolVP_compteur$nsimul %>% sum() # why not equal? Oh, because the one accepted for a proto but not the other...
# Step 3 Only ApoG ------------------------------------------------------------------
apoG <- VP_proj_creator$new(sourcefile = "D:/these/Second_project/QSP/modeling_work/VT_simeoni/1_user_inputs/1_config_Lindner_origin.r")
apoG$protocols <- protocols
apoGFull <- apoG$clone()
protoApoG <- tribble(~protocol, ~time, ~cmt, ~ min, ~max,
"unique",100,"TimeAbove", -Inf, 1E-1,
"apog",100,"TimeAbove", 1E-1, Inf,
"ABT737",100,"TimeAbove", -Inf, 1E-1
)
apoG$set_targets(manual = protoApoG %>% slice(-1))
apoGNoPrev <- apoG$clone(deep = T)
apoGFull$set_targets(manual = protoApoG%>% slice(-1))
apoG$add_VP(VP_df2, fillatend = F, reducefilteratend = F, use_green_filter = T, keep = "Pore",
time_compteur = T, keepRedFiltaftDis = T, PreviousResults = Previous)
apoGNoPrev$add_VP(VP_df2, fillatend = F, reducefilteratend = F, use_green_filter = T, keep = "Pore",
time_compteur = T, keepRedFiltaftDis = T)
if(nrow(apoG$poolVP) > 1 ) saveRDS(apoG, "apoG")
if(nrow(apoGNoPrev$poolVP) > 1 ) saveRDS(apoGNoPrev, "apoGNoPrev")
apoGFull$add_VP(VP_df, fillatend = F, reducefilteratend = F, use_green_filter = T, keep = "Pore",
time_compteur = T, keepRedFiltaftDis = T)
if(nrow(apoGFull$poolVP) > 1 ) saveRDS(apoGFull, "apoGFull")
apoGFull$timeTrack$tTOTAL/60
PrevRej <-
apoG$VP_rejected %>%
filter(!is.na(id)) %>%
rename(TimeAbove = value) %>%
select(time, protocol, TimeAbove, !!!NeverDead$param)
PrevAcc <- apoG$poolVP %>%
unnest() %>%
filter(time == 100) %>%
select(time, protocol, TimeAbove, !!!NeverDead$param)
Previous <- bind_rows(readRDS( "previousBothdead"), PrevAcc, PrevRej) %>%
distinct()
saveRDS(Previous, "previousPostApoG")
# Step 4 Only ABT737 ------------------------------------------------------------------
ABT737 <- VP_proj_creator$new(sourcefile = "D:/these/Second_project/QSP/modeling_work/VT_simeoni/1_user_inputs/1_config_Lindner_origin.r")
ABT737$protocols <- protocols
ABT737Full <- ABT737$clone(deep = T)
ABT737targets <- tribble(~protocol, ~time, ~cmt, ~ min, ~max,
"unique",100,"TimeAbove", -Inf, 1E-1,
"apog",100,"TimeAbove", -Inf, 1E-1,
"ABT737",100,"TimeAbove", 1E-1, Inf
)
ABT737$set_targets(manual = ABT737targets %>% slice(-1) )
ABT737NoPrev <- ABT737$clone(deep = T)
ABT737Full$set_targets(manual = ABT737targets %>% slice(-1))
ABT737$add_VP(VP_df2, fillatend = F, reducefilteratend = F, use_green_filter = T, keep = "Pore",
time_compteur = T, keepRedFiltaftDis = T, PreviousResults = Previous)
if(nrow(ABT737$poolVP) >1) saveRDS(ABT737, "ABT737")
ABT737NoPrev$add_VP(VP_df2, fillatend = F, reducefilteratend = F, use_green_filter = T, keep = "Pore",
time_compteur = T, keepRedFiltaftDis = T)
if(nrow(ABT737NoPrev$poolVP) >1) saveRDS(ABT737NoPrev, "ABT737NoPrev")
ABT737Full$add_VP(VP_df, fillatend = F, reducefilteratend = F, use_green_filter = T, keep = "Pore",
time_compteur = T, keepRedFiltaftDis = T)
if(nrow(ABT737Full$poolVP) >1) saveRDS(ABT737Full, "ABT737Full")
ABT737Full$timeTrack$tTOTAL / 60
plotLindner(obj = ABT737)
# saveRDS(ABT737, "ABT737")
# Sum to verify
# Cmopute last df ---------------------------------------------------------
BothDead <- readRDS("BothDead")
OnlyApoG <- readRDS( "apoG")
onlyABT737 <- readRDS("ABT737")
ResistantsMono <- VP_df2 %>%
left_join(BothDead$poolVP) %>%
filter(is.na(protocol)) %>%
select(1:8) %>%
left_join(OnlyApoG$poolVP) %>%
filter(is.na(protocol)) %>%
select(1:8) %>%
left_join(onlyABT737$poolVP) %>%
filter(is.na(protocol)) %>%
select(1:8)
saveRDS(ResistantsMono, "ResistantsMono")
# Step 6 Synergy ------------------------------------------------------------------
synergy <- VP_proj_creator$new(sourcefile = "D:/these/Second_project/QSP/modeling_work/VT_simeoni/1_user_inputs/1_config_Lindner_origin.r")
synergy$protocols <- protocols
synergyFull <- synergy$clone(deep = T)
protocolSynergy <- tribble(~protocol, ~time, ~cmt, ~ min, ~max,
"unique",100,"TimeAbove", -Inf, 1E-1,
"apog",100,"TimeAbove", -Inf, 1E-1,
"ABT737",100,"TimeAbove", -Inf, 1E-1,
"synergy",100,"TimeAbove", 1E-1, Inf
)
synergy$set_targets(manual = protocolSynergy %>% slice(-1))
synergyFull$set_targets(manual = protocolSynergy %>% slice(-1))
synergy$add_VP(ResistantsMono, fillatend = F, reducefilteratend = F, use_green_filter = T, keep = "Pore",
time_compteur = T, keepRedFiltaftDis = T)
if(nrow(synergy$poolVP) >1) saveRDS(synergy, "synergy")
synergyFull$add_VP(VP_df, fillatend = F, reducefilteratend = F, use_green_filter = T, keep = "Pore",
time_compteur = T, keepRedFiltaftDis = T)
if(nrow(synergyFull$poolVP) >1) saveRDS(synergyFull, "synergy")
synergy$timeTrack$tTOTAL / 60
synergyFull$timeTrack$tTOTAL / 60
# Step7: Single treatment therapy failure ------------------------------------------------------
NeverDead <- VP_proj_creator$new(sourcefile = "D:/these/Second_project/QSP/modeling_work/VT_simeoni/1_user_inputs/1_config_Lindner_origin.r")
NeverDead$protocols <- protocols
NeverDeadFull <- NeverDead$clone(deep = T)
ProtNeverDead <- tribble(~protocol, ~time, ~cmt, ~ min, ~max,
"unique",100,"TimeAbove", -Inf, 1E-1,
"apog",100,"TimeAbove", -Inf, 1E-1,
"ABT737",100,"TimeAbove", -Inf, 1E-1
)
NeverDead$set_targets(manual = ProtNeverDead %>% slice(-1) )
NeverDeadFull$set_targets(manual = ProtNeverDead %>% slice(-1) )
#
NeverDead$add_VP(VP_df2, fillatend = F, reducefilteratend = F, use_green_filter = T, keep = "Pore",
time_compteur = T, keepRedFiltaftDis = T, PreviousResults = Previous)
# NeverDead$add_VP(VP_df2, fillatend = F, reducefilteratend = F, use_green_filter = T, keep = "Pore",
# time_compteur = T, keepRedFiltaftDis = T)
NeverDeadFull$add_VP(VP_df, fillatend = F, reducefilteratend = F, use_green_filter = T, keep = "Pore",
time_compteur = T, keepRedFiltaftDis = T)
if(nrow(NeverDead$poolVP) >1) saveRDS(NeverDead, "NeverDead")
if(nrow(NeverDeadFull$poolVP) >1) saveRDS(NeverDead, "NeverDeadFull")
NeverDeadFull$timeTrack$tTOTAL/60
plotLindner(obj = NeverDead)
# Step7: Combination treatment failure ------------------------------------------------------
CombinationResist <- VP_proj_creator$new(sourcefile = "D:/these/Second_project/QSP/modeling_work/VT_simeoni/1_user_inputs/1_config_Lindner_origin.r")
CombinationResist$protocols <- protocols
protocolCombinationResist <- tribble(~protocol, ~time, ~cmt, ~ min, ~max,
"unique",100,"TimeAbove", -Inf, 1E-1,
"apog",100,"TimeAbove", -Inf, 1E-1,
"ABT737",100,"TimeAbove", -Inf, 1E-1,
"synergy",100,"TimeAbove", -Inf, 1E-1
)
CombinationResist$set_targets(manual =protocolCombinationResist %>% slice(4))
#
CombinationResist$add_VP(VP_df, fillatend = F, reducefilteratend = F, use_green_filter = T, keep = "Pore",
time_compteur = T, keepRedFiltaftDis = T)
saveRDS(CombinationResist, "CombinationResist")
# NeverDead$add_VP(VP_df2, fillatend = F, reducefilteratend = F, use_green_filter = T, keep = "Pore",
# time_compteur = T, keepRedFiltaftDis = T)
# Final Plot supplement-------------------------------------------------------------------
ApoptoWODrug <- readRDS("ApoptoWODrug")
ABT737 <- readRDS("ABT737")
apoG <- readRDS("apoG")
BothDead <- readRDS("BothDead")
Synergy <- readRDS("Synergy")
CombinationResist <- readRDS("CombinationResist")
nsim <- 100
set.seed(23)
# plotLindner(NeverDead, npatient = nsim, title = paste0("Both ineffective drugs (", nrow(NeverDead$poolVP)/2," VPs)")),
cowplot::plot_grid(
plotLindner(ApoptoWODrug, npatient = nsim, title = paste0("Spontaneous Apoptosis (", length(unique(ApoptoWODrug$poolVP$id))," VPs)")),
plotLindner(BothDead, npatient = nsim, title = paste0("Both effective drugs (", length(unique(BothDead$poolVP$id))," VPs)")),
plotLindner(apoG, npatient = nsim, title = paste0("Effective ApoG2 only (",length(unique(apoG$poolVP$id)) ," VPs)")) ,
plotLindner(ABT737, npatient = nsim, title = paste0("Effective ABT-373 only (", length(unique(ABT737$poolVP$id))," VPs)")),
plotLindner(Synergy, npatient = nsim, title = paste0("Effective combination only (", length(unique(Synergy$poolVP$id)) ," VPs)")),
plotLindner(CombinationResist, npatient = nsim, title = paste0("Combination resistance (", length(unique(CombinationResist$poolVP$id)) ," VPs)")),
labels = letters
) -> finaloutput
# Save 300 dip for article
them <- theme(plot.title = element_text(hjust = 0.5))
tiff(width = 3500, height = 2300,filename = "D:/these/Second_project/QSP/modeling_work/VT_simeoni/article_QSPVP/figures_300_dpi/figS9.tiff", res = 300)
finaloutput
dev.off()
shell.exec( "D:/these/Second_project/QSP/modeling_work/VT_simeoni/article_QSPVP/figures_300_dpi/figS9.tiff")
Thibaudpmx/QSPVP documentation built on Nov. 14, 2022, 7:07 p.m.
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## ---------------------------
## Script name: Figure R article
##
## Purpose of script: production of figure 7
##c
## Author: Thibaud Derippe
##
## Date Created: 2022-04-18 (trial codes previously in "eval_performance" file)
##
## Under GPL-3 License
## Email: thibaud.derippe@gmail.com
## GitHub: https://github.com/Thibaudpmx/PaSM
## ---------------------------
##
##
##
##
##
## ---------------------------
library(PaSM)
plotLindner <- function(obj, npatient = 2000, title = ""){
obj$poolVP %>%
arrange(id) %>%
mutate(test = map_lgl(simul, ~class(.x)[[1]] == "tbl_df")) %>%
filter(test) %>%
mutate(protocol = case_when(protocol == "ABT737" ~ "ABT-737",
protocol == "apog" ~ "ApoG2",
protocol == "synergy" ~ "Combination",
T~ protocol))-> temp
temp <- temp %>% left_join(temp %>%
group_by(id) %>%
tally )
idtosample <- temp$id[temp$n == max(temp$n)] %>% unique
temp %>%
filter(id%in% sample(idtosample, min(npatient, length(idtosample))) ) %>%
# slice(1:(min(npatient * obj$targets$protocol %>% unique %>% length(), nrow(temp)))) %>%
unnest(simul) %>%
mutate(protocol = if_else(protocol == "unique", "No Drug" , protocol)) %>%
ggplot()+
geom_line(aes(time, Pore, group = id))+
facet_wrap(~protocol)+
geom_hline(yintercept = 10, col = "red", size = 1.5)+
coord_cartesian(xlim = c(50,100))+
theme_bw()+
labs(x = "Time (hours)", y = "Percentage Pore", title = title)+
theme(plot.title = element_text(hjust = 0.5))
}
# original configuration-----------------------------------------------------
setwd("D:/these/Second_project/QSP/modeling_work/VT_simeoni/article_QSPVP/data/Lindner_article")
protocols <- list( unique = tibble(cmt = "Bcl2", time = 0, amt = 0),
apog = tibble(cmt = "ApoG2", time = 50, amt = 2000),
ABT737 = tibble(cmt = "ABT737", time = 50, amt = 2000),
synergy = tibble(cmt = c("ABT737","ApoG2"), time = 50, amt = 2000))
VP_df <- crossing(Bcl20 = seq(0,900,100),
Bclxl0 = seq(0,900,100),
Mcl10 = c(0,50,100,150) ,#* seq(0.6,1.4,0.2),
BIM0 = seq(0,900,100),
PUMA0 =seq(0,900,100),
NOXA0 = seq(0,900,200),
BAXc0 = 500,
BAK0 = 500)
# Step1: Die anyways ------------------------------------------------------
# Step 1: remove those who die anyway
ApoptoWODrug <- VP_proj_creator$new(sourcefile = "D:/these/Second_project/QSP/modeling_work/VT_simeoni/1_user_inputs/1_config_Lindner_origin.r")
ApoptoWODrug$protocols <- protocols
ApoptoWODrug$set_targets(manual = tribble(~protocol, ~time, ~cmt, ~ min, ~max,
"unique",100,"TimeAbove", 1E-1, Inf
))
ApoptoWODrug$add_VP(VP_df, fillatend = F, reducefilteratend = F, use_green_filter = T, keep = "Pore", time_compteur = T, keepRedFiltaftDis = T)
saveRDS(ApoptoWODrug, "ApoptoWODrug")
VP_df %>%
left_join(ApoptoWODrug$poolVP %>% select(-simul)) %>%
filter(is.na(id)) %>%
select(1:8) -> VP_df2
# Step2: Dead Both drugs ------------------------------------------------------
BothDead <- VP_proj_creator$new(sourcefile = "D:/these/Second_project/QSP/modeling_work/VT_simeoni/1_user_inputs/1_config_Lindner_origin.r")
BothDead$protocols <- protocols
targetsBothDead <- tribble(~protocol, ~time, ~cmt, ~ min, ~max,
"unique",100,"TimeAbove", -Inf, 1E-1,
"apog",100,"TimeAbove", 1E-1, Inf,
"ABT737",100,"TimeAbove", 1E-1, Inf
)
BothDeadFull <- BothDead$clone(deep = T)
BothDead$set_targets(manual = targetsBothDead %>% slice(-1))
BothDeadFull$set_targets(manual = targetsBothDead)
BothDead$add_VP(VP_df2, fillatend = F, reducefilteratend = F, use_green_filter = T, keep = "Pore", time_compteur = T, keepRedFiltaftDis = T)
if(nrow(BothDead$poolVP) >1) saveRDS(BothDead, "BothDead")
# BothDead <- readRDS("BothDead")
BothDead$add_VP(VP_df2, fillatend = F, reducefilteratend = F, use_green_filter = T, keep = "Pore", time_compteur = T, keepRedFiltaftDis = T)
if(nrow(BothDead$poolVP) >1) saveRDS(BothDead, "BothDead")
BothDeadFull$add_VP(VP_df, fillatend = F, reducefilteratend = F, use_green_filter = T, keep = "Pore", time_compteur = T, keepRedFiltaftDis = T)
if(nrow(BothDeadFull$poolVP) >1) saveRDS(BothDeadFull, "BothDeadFull")
plotLindner(obj = BothDead)
PrevRej <-
BothDead$VP_rejected %>%
filter(!is.na(id)) %>%
rename(TimeAbove = value) %>%
select(time, protocol, TimeAbove, !!!BothDead$param)
PrevAcc <- BothDead$poolVP %>%
unnest() %>%
filter(time == 100) %>%
select(time, protocol, TimeAbove, !!!BothDead$param)
Previous <- PrevAcc %>%
bind_rows(
PrevRej
) %>%
rowid_to_column("id")
saveRDS(Previous, "previousBothdead")
BothDead$timeTrack$poolVP_compteur$nsimul %>% sum() # why not equal? Oh, because the one accepted for a proto but not the other...
# Step 3 Only ApoG ------------------------------------------------------------------
apoG <- VP_proj_creator$new(sourcefile = "D:/these/Second_project/QSP/modeling_work/VT_simeoni/1_user_inputs/1_config_Lindner_origin.r")
apoG$protocols <- protocols
apoGFull <- apoG$clone()
protoApoG <- tribble(~protocol, ~time, ~cmt, ~ min, ~max,
"unique",100,"TimeAbove", -Inf, 1E-1,
"apog",100,"TimeAbove", 1E-1, Inf,
"ABT737",100,"TimeAbove", -Inf, 1E-1
)
apoG$set_targets(manual = protoApoG %>% slice(-1))
apoGNoPrev <- apoG$clone(deep = T)
apoGFull$set_targets(manual = protoApoG%>% slice(-1))
apoG$add_VP(VP_df2, fillatend = F, reducefilteratend = F, use_green_filter = T, keep = "Pore",
time_compteur = T, keepRedFiltaftDis = T, PreviousResults = Previous)
apoGNoPrev$add_VP(VP_df2, fillatend = F, reducefilteratend = F, use_green_filter = T, keep = "Pore",
time_compteur = T, keepRedFiltaftDis = T)
if(nrow(apoG$poolVP) > 1 ) saveRDS(apoG, "apoG")
if(nrow(apoGNoPrev$poolVP) > 1 ) saveRDS(apoGNoPrev, "apoGNoPrev")
apoGFull$add_VP(VP_df, fillatend = F, reducefilteratend = F, use_green_filter = T, keep = "Pore",
time_compteur = T, keepRedFiltaftDis = T)
if(nrow(apoGFull$poolVP) > 1 ) saveRDS(apoGFull, "apoGFull")
apoGFull$timeTrack$tTOTAL/60
PrevRej <-
apoG$VP_rejected %>%
filter(!is.na(id)) %>%
rename(TimeAbove = value) %>%
select(time, protocol, TimeAbove, !!!NeverDead$param)
PrevAcc <- apoG$poolVP %>%
unnest() %>%
filter(time == 100) %>%
select(time, protocol, TimeAbove, !!!NeverDead$param)
Previous <- bind_rows(readRDS( "previousBothdead"), PrevAcc, PrevRej) %>%
distinct()
saveRDS(Previous, "previousPostApoG")
# Step 4 Only ABT737 ------------------------------------------------------------------
ABT737 <- VP_proj_creator$new(sourcefile = "D:/these/Second_project/QSP/modeling_work/VT_simeoni/1_user_inputs/1_config_Lindner_origin.r")
ABT737$protocols <- protocols
ABT737Full <- ABT737$clone(deep = T)
ABT737targets <- tribble(~protocol, ~time, ~cmt, ~ min, ~max,
"unique",100,"TimeAbove", -Inf, 1E-1,
"apog",100,"TimeAbove", -Inf, 1E-1,
"ABT737",100,"TimeAbove", 1E-1, Inf
)
ABT737$set_targets(manual = ABT737targets %>% slice(-1) )
ABT737NoPrev <- ABT737$clone(deep = T)
ABT737Full$set_targets(manual = ABT737targets %>% slice(-1))
ABT737$add_VP(VP_df2, fillatend = F, reducefilteratend = F, use_green_filter = T, keep = "Pore",
time_compteur = T, keepRedFiltaftDis = T, PreviousResults = Previous)
if(nrow(ABT737$poolVP) >1) saveRDS(ABT737, "ABT737")
ABT737NoPrev$add_VP(VP_df2, fillatend = F, reducefilteratend = F, use_green_filter = T, keep = "Pore",
time_compteur = T, keepRedFiltaftDis = T)
if(nrow(ABT737NoPrev$poolVP) >1) saveRDS(ABT737NoPrev, "ABT737NoPrev")
ABT737Full$add_VP(VP_df, fillatend = F, reducefilteratend = F, use_green_filter = T, keep = "Pore",
time_compteur = T, keepRedFiltaftDis = T)
if(nrow(ABT737Full$poolVP) >1) saveRDS(ABT737Full, "ABT737Full")
ABT737Full$timeTrack$tTOTAL / 60
plotLindner(obj = ABT737)
# saveRDS(ABT737, "ABT737")
# Sum to verify
# Cmopute last df ---------------------------------------------------------
BothDead <- readRDS("BothDead")
OnlyApoG <- readRDS( "apoG")
onlyABT737 <- readRDS("ABT737")
ResistantsMono <- VP_df2 %>%
left_join(BothDead$poolVP) %>%
filter(is.na(protocol)) %>%
select(1:8) %>%
left_join(OnlyApoG$poolVP) %>%
filter(is.na(protocol)) %>%
select(1:8) %>%
left_join(onlyABT737$poolVP) %>%
filter(is.na(protocol)) %>%
select(1:8)
saveRDS(ResistantsMono, "ResistantsMono")
# Step 6 Synergy ------------------------------------------------------------------
synergy <- VP_proj_creator$new(sourcefile = "D:/these/Second_project/QSP/modeling_work/VT_simeoni/1_user_inputs/1_config_Lindner_origin.r")
synergy$protocols <- protocols
synergyFull <- synergy$clone(deep = T)
protocolSynergy <- tribble(~protocol, ~time, ~cmt, ~ min, ~max,
"unique",100,"TimeAbove", -Inf, 1E-1,
"apog",100,"TimeAbove", -Inf, 1E-1,
"ABT737",100,"TimeAbove", -Inf, 1E-1,
"synergy",100,"TimeAbove", 1E-1, Inf
)
synergy$set_targets(manual = protocolSynergy %>% slice(-1))
synergyFull$set_targets(manual = protocolSynergy %>% slice(-1))
synergy$add_VP(ResistantsMono, fillatend = F, reducefilteratend = F, use_green_filter = T, keep = "Pore",
time_compteur = T, keepRedFiltaftDis = T)
if(nrow(synergy$poolVP) >1) saveRDS(synergy, "synergy")
synergyFull$add_VP(VP_df, fillatend = F, reducefilteratend = F, use_green_filter = T, keep = "Pore",
time_compteur = T, keepRedFiltaftDis = T)
if(nrow(synergyFull$poolVP) >1) saveRDS(synergyFull, "synergy")
synergy$timeTrack$tTOTAL / 60
synergyFull$timeTrack$tTOTAL / 60
# Step7: Single treatment therapy failure ------------------------------------------------------
NeverDead <- VP_proj_creator$new(sourcefile = "D:/these/Second_project/QSP/modeling_work/VT_simeoni/1_user_inputs/1_config_Lindner_origin.r")
NeverDead$protocols <- protocols
NeverDeadFull <- NeverDead$clone(deep = T)
ProtNeverDead <- tribble(~protocol, ~time, ~cmt, ~ min, ~max,
"unique",100,"TimeAbove", -Inf, 1E-1,
"apog",100,"TimeAbove", -Inf, 1E-1,
"ABT737",100,"TimeAbove", -Inf, 1E-1
)
NeverDead$set_targets(manual = ProtNeverDead %>% slice(-1) )
NeverDeadFull$set_targets(manual = ProtNeverDead %>% slice(-1) )
#
NeverDead$add_VP(VP_df2, fillatend = F, reducefilteratend = F, use_green_filter = T, keep = "Pore",
time_compteur = T, keepRedFiltaftDis = T, PreviousResults = Previous)
# NeverDead$add_VP(VP_df2, fillatend = F, reducefilteratend = F, use_green_filter = T, keep = "Pore",
# time_compteur = T, keepRedFiltaftDis = T)
NeverDeadFull$add_VP(VP_df, fillatend = F, reducefilteratend = F, use_green_filter = T, keep = "Pore",
time_compteur = T, keepRedFiltaftDis = T)
if(nrow(NeverDead$poolVP) >1) saveRDS(NeverDead, "NeverDead")
if(nrow(NeverDeadFull$poolVP) >1) saveRDS(NeverDead, "NeverDeadFull")
NeverDeadFull$timeTrack$tTOTAL/60
plotLindner(obj = NeverDead)
# Step7: Combination treatment failure ------------------------------------------------------
CombinationResist <- VP_proj_creator$new(sourcefile = "D:/these/Second_project/QSP/modeling_work/VT_simeoni/1_user_inputs/1_config_Lindner_origin.r")
CombinationResist$protocols <- protocols
protocolCombinationResist <- tribble(~protocol, ~time, ~cmt, ~ min, ~max,
"unique",100,"TimeAbove", -Inf, 1E-1,
"apog",100,"TimeAbove", -Inf, 1E-1,
"ABT737",100,"TimeAbove", -Inf, 1E-1,
"synergy",100,"TimeAbove", -Inf, 1E-1
)
CombinationResist$set_targets(manual =protocolCombinationResist %>% slice(4))
#
CombinationResist$add_VP(VP_df, fillatend = F, reducefilteratend = F, use_green_filter = T, keep = "Pore",
time_compteur = T, keepRedFiltaftDis = T)
saveRDS(CombinationResist, "CombinationResist")
# NeverDead$add_VP(VP_df2, fillatend = F, reducefilteratend = F, use_green_filter = T, keep = "Pore",
# time_compteur = T, keepRedFiltaftDis = T)
# Final Plot supplement-------------------------------------------------------------------
ApoptoWODrug <- readRDS("ApoptoWODrug")
ABT737 <- readRDS("ABT737")
apoG <- readRDS("apoG")
BothDead <- readRDS("BothDead")
Synergy <- readRDS("Synergy")
CombinationResist <- readRDS("CombinationResist")
nsim <- 100
set.seed(23)
# plotLindner(NeverDead, npatient = nsim, title = paste0("Both ineffective drugs (", nrow(NeverDead$poolVP)/2," VPs)")),
cowplot::plot_grid(
plotLindner(ApoptoWODrug, npatient = nsim, title = paste0("Spontaneous Apoptosis (", length(unique(ApoptoWODrug$poolVP$id))," VPs)")),
plotLindner(BothDead, npatient = nsim, title = paste0("Both effective drugs (", length(unique(BothDead$poolVP$id))," VPs)")),
plotLindner(apoG, npatient = nsim, title = paste0("Effective ApoG2 only (",length(unique(apoG$poolVP$id)) ," VPs)")) ,
plotLindner(ABT737, npatient = nsim, title = paste0("Effective ABT-373 only (", length(unique(ABT737$poolVP$id))," VPs)")),
plotLindner(Synergy, npatient = nsim, title = paste0("Effective combination only (", length(unique(Synergy$poolVP$id)) ," VPs)")),
plotLindner(CombinationResist, npatient = nsim, title = paste0("Combination resistance (", length(unique(CombinationResist$poolVP$id)) ," VPs)")),
labels = letters
) -> finaloutput
# Save 300 dip for article
them <- theme(plot.title = element_text(hjust = 0.5))
tiff(width = 3500, height = 2300,filename = "D:/these/Second_project/QSP/modeling_work/VT_simeoni/article_QSPVP/figures_300_dpi/figS9.tiff", res = 300)
finaloutput
dev.off()
shell.exec( "D:/these/Second_project/QSP/modeling_work/VT_simeoni/article_QSPVP/figures_300_dpi/figS9.tiff")
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