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## ----setup, include=FALSE-----------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.width = 7
)
## ---- warning=FALSE, message=FALSE--------------------------------------------
library(xgxr)
library(ggplot2)
library(dplyr)
library(tidyr)
# flag for labeling figures as draft
status <- "DRAFT"
# ggplot settings
xgx_theme_set()
## ---- warning=FALSE, message=FALSE--------------------------------------------
pkpd_data <- case1_pkpd %>%
arrange(DOSE) %>%
subset(,-IPRED) %>%
mutate(TRTACT_low2high = factor(TRTACT, levels = unique(TRTACT)),
TRTACT_high2low = factor(TRTACT, levels = rev(unique(TRTACT))),
DAY_label = paste("Day", PROFDAY),
DAY_label = ifelse(DAY_label == "Day 0","Baseline",DAY_label))
LOQ = 0.05 #ng/ml
dose_max = as.numeric(max(pkpd_data$DOSE))
pk_data <- pkpd_data %>%
filter(CMT == 2) %>%
mutate(LIDVNORM = LIDV / as.numeric(DOSE))
pk_data_cycle1 <- pk_data %>%
filter(CYCLE == 1)
pd_data <- pkpd_data %>%
filter(CMT == 3)
pd_data_baseline_day85 <- pkpd_data %>%
filter(CMT == 3,
DAY_label %in% c("Baseline", "Day 85"))
pk_vs_pd_data <- pkpd_data %>%
filter(!is.na(LIDV)) %>%
subset(,-c(EVENTU,NAME)) %>%
spread(CMT,LIDV) %>%
rename(Concentration = `2`, Response = `3`)
NCA <- pk_data_cycle1 %>%
group_by(ID, DOSE) %>%
filter(!is.na(LIDV)) %>%
summarize(AUC_last = caTools::trapz(TIME, LIDV),
Cmax = max(LIDV)) %>%
tidyr::gather(PARAM,VALUE,-c(ID, DOSE)) %>%
ungroup() %>%
mutate(VALUE_NORM = VALUE / DOSE)
AUC_last <- NCA %>%
filter(PARAM == "AUC_last") %>%
rename(AUC_last = VALUE) %>%
subset(,-c(DOSE,PARAM,VALUE_NORM))
pk_vs_pd_data_day85 <- pk_vs_pd_data %>%
filter(DAY_label == "Day 85",
!is.na(Concentration),
!is.na(Response)) %>%
left_join(AUC_last)
time_units_dataset <- "hours"
time_units_plot <- "days"
trtact_label <- "Dose"
dose_label <- "Dose (mg)"
conc_label <- "Concentration (ng/ml)"
auc_label <- "AUCtau (h.(ng/ml))"
concnorm_label <- "Normalized Concentration (ng/ml)/mg"
sex_label <- "Sex"
w100_label <- "WEIGHTB>100"
pd_label <- "FEV1 (mL)"
cens_label <- "Censored"
## ---- echo=TRUE, warning=FALSE, message=FALSE, fig.height=3-------------------
ggplot(data = pk_data_cycle1, aes(x = NOMTIME,
y = LIDV,
group = DOSE,
color = TRTACT_high2low)) +
xgx_geom_ci(conf_level = 0.95) +
xgx_scale_y_log10() +
xgx_scale_x_time_units(units_dataset = time_units_dataset, units_plot = time_units_plot) +
labs(y = conc_label, color = trtact_label) +
xgx_annotate_status(status)
## ---- echo=TRUE, warning=FALSE, message=FALSE, fig.height=3-------------------
ggplot(data = pk_data_cycle1, aes(x = TIME, y = LIDV)) +
geom_line(aes(group = ID), color = "grey50", size = 1, alpha = 0.3) +
geom_point(aes(color = factor(CENS), shape = factor(CENS))) +
scale_shape_manual(values = c(1, 8)) +
scale_color_manual(values = c("grey50", "red")) +
xgx_geom_ci(aes(x = NOMTIME, color = NULL, group = NULL, shape = NULL), conf_level = 0.95) +
xgx_scale_y_log10() +
xgx_scale_x_time_units(units_dataset = time_units_dataset, units_plot = time_units_plot) +
labs(y = conc_label, color = trtact_label) +
theme(legend.position = "none") +
facet_grid(.~TRTACT_low2high) +
xgx_annotate_status(status)
## ---- echo=TRUE, warning=FALSE, message=FALSE, fig.height=3-------------------
ggplot(data = pk_data_cycle1,
aes(x = NOMTIME,
y = LIDVNORM,
group = DOSE,
color = TRTACT_high2low)) +
xgx_geom_ci(conf_level = 0.95, alpha = 0.5, position = position_dodge(1)) +
xgx_scale_y_log10() +
xgx_scale_x_time_units(units_dataset = time_units_dataset, units_plot = time_units_plot) +
labs(y = concnorm_label, color = trtact_label) +
xgx_annotate_status(status)
## ---- echo=TRUE, warning=FALSE, message=FALSE, fig.height=3-------------------
ggplot(data = NCA, aes(x = DOSE, y = VALUE_NORM)) +
geom_boxplot(aes(group = DOSE)) +
geom_smooth(method = "lm", color = "black") +
facet_wrap(~PARAM, scales = "free_y") +
labs(x = dose_label) +
theme(axis.title.y = element_blank()) +
xgx_annotate_status(status)
## ---- echo=TRUE, warning=FALSE, message=FALSE, fig.height=3-------------------
ggplot(data = NCA[!NCA$DOSE == 3 & !NCA$DOSE == 10 , ],
aes(x = DOSE, y = VALUE_NORM)) +
geom_boxplot(aes(group = DOSE)) +
geom_smooth(method = "lm", color = "black") +
facet_wrap(~PARAM, scales = "free_y") +
labs(x = dose_label) +
theme(axis.title.y = element_blank()) +
xgx_annotate_status(status)
## ---- echo=TRUE, warning=FALSE, message=FALSE, fig.height=3-------------------
ggplot(data = pk_data_cycle1, aes(x = NOMTIME,
y = LIDV,
group = WEIGHTB > 100,
color = WEIGHTB > 100)) +
xgx_geom_ci(conf_level = 0.95) +
xgx_scale_y_log10() +
xgx_scale_x_time_units(units_dataset = time_units_dataset, units_plot = time_units_plot) +
facet_grid(.~DOSE) +
labs(y = conc_label, color = w100_label) +
xgx_annotate_status(status)
## ---- echo=TRUE, warning=FALSE, message=FALSE, fig.height=3-------------------
ggplot(data = pd_data, aes(x = NOMTIME,
y = LIDV,
group = DOSE,
color = TRTACT_high2low)) +
xgx_geom_ci(conf_level = 0.95) +
xgx_scale_y_log10() +
xgx_scale_x_time_units(units_dataset = time_units_dataset, units_plot = time_units_plot) +
labs(y = pd_label, color = trtact_label) +
xgx_annotate_status(status)
## ---- echo=TRUE, warning=FALSE, message=FALSE, fig.height=3-------------------
ggplot(data = pd_data, aes(x = NOMTIME, y = LIDV, group = ID)) +
geom_line(alpha = 0.5) +
geom_point(alpha = 0.5) +
xgx_scale_y_log10() +
xgx_scale_x_time_units(units_dataset = time_units_dataset, units_plot = time_units_plot) +
facet_grid(~TRTACT_low2high) +
labs(y = pd_label, color = trtact_label) +
xgx_annotate_status(status)
## ---- echo=TRUE, warning=FALSE, message=FALSE, fig.height=3-------------------
ggplot(data = pd_data_baseline_day85, aes(x = DOSE,
y = LIDV,
group = DOSE)) +
xgx_geom_ci(conf_level = 0.95) +
facet_grid(~DAY_label) +
labs(x = dose_label, y = pd_label, color = trtact_label) +
xgx_annotate_status(status)
## ---- echo=TRUE, warning=FALSE, message=FALSE, fig.height=3-------------------
ggplot(data = pd_data, aes(x = DOSE, y = LIDV, group = DOSE)) +
xgx_geom_ci(conf_level = 0.95) +
facet_grid(~DAY_label) +
labs(x = dose_label, y = pd_label, color = trtact_label) +
xgx_annotate_status(status)
## ---- echo=TRUE, warning=FALSE, message=FALSE, fig.height=3-------------------
ggplot(data = pd_data_baseline_day85, aes(x = DOSE,
y = LIDV,
group = WEIGHTB > 100,
color = WEIGHTB > 100)) +
xgx_geom_ci(conf_level = .95) +
facet_grid(~DAY_label) +
labs(x = dose_label, y = pd_label, color = w100_label) +
xgx_annotate_status(status)
## ---- echo=TRUE, warning=FALSE, message=FALSE, fig.height=3-------------------
g = ggplot(data = pk_vs_pd_data_day85, aes(x = Concentration, y = Response)) +
geom_point(aes(color = TRTACT_high2low, shape = factor(CENS))) +
geom_smooth(color="black",shape=NULL) +
xgx_scale_x_log10() +
labs(x = conc_label, y = pd_label, color = trtact_label, shape = cens_label) +
xgx_annotate_status(status)
print(g)
## ---- echo=TRUE, warning=FALSE, message=FALSE, fig.height=3-------------------
gAUC = g +
aes(x = AUC_last) +
xlab(auc_label)
print(gAUC)
## -----------------------------------------------------------------------------
sessionInfo()
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