Data
We build the following dataset:
# Libraries
library(ggplot2)
# Creation of dataset
data <- data.frame(
Evaluable=c(1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0,1),
Therapy_Start_Date=c("2014-11-05", "2014-11-24", "2014-12-17", "2015-01-21", "2015-03-08",
"2015-04-12", "2015-05-03", "2015-08-08", "2015-08-24", "2016-01-12",
"2016-02-02", "2016-02-22", "2016-03-09", "2016-03-28", "2016-06-06",
"2016-07-10", "2016-10-10", "2017-03-27", "2017-04-26", "2017-07-11",
"2017-07-27", "2017-08-15", "2017-09-10", "2017-09-27"),
Dose_Level=c("2", "2", "3", "4", "4", "4", "5", "4", "4", "4", "4", "3",
"4", "4", "3", "3", "3", "3", "3", "3", "3", "3", "3", "3"),
Last_Assessment_Date=c("2014-12-29", "2015-01-19", "2015-02-10", "2015-03-10", "2015-04-19",
"2015-06-10", "2015-05-24", "2015-10-03", "2015-09-14", "2016-03-08",
"2016-02-21", "2016-04-12", "2016-03-23", "2016-05-23", "2016-07-21",
"2016-07-25", "2016-10-24", "2017-05-24", "2017-06-07", "2017-07-25",
"2017-07-27", "2017-09-25", "2017-11-07", "2017-10-24"),
DLT=c("0", "0", "0", "0", "0", "0", "1", "0", "0", "0", "1", "1",
"0", "0", "0", "1", "0", "0", "1", "1", "0", "1", "0", "1")
)
data$Dose_Level <- factor(data$Dose_Level, c(2, 3, 4, 5))
data$Therapy_Start_Date <- as.Date(data$Therapy_Start_Date)
data$Last_Assessment_Date <- as.Date(data$Last_Assessment_Date)
data <- data[order(data[, "Therapy_Start_Date"]), ]
data$ID <- 1:nrow(data)data format:
A data frame with 24 observations on the following 6 variables:
ID A distinct number or character for each patient. ID
order should correspond to the entry time of the patient. Start from 1
to the last patient
Evaluable The evaluable variable
should indicate whether or not the patient is evaluable in the trial. It
should be 0 or 1 (1 = Evaluable) for each entry
Therapy_Start_Date This variable gives the start date of
treatment
Dose_Level The dose level variable can be a
numeric or character variable indicating the dose level each patient has
been assigned
Last_Assessment_Date This variable gives
the last date of treatment
DLT The toxicity variable
should indicate whether or not a patient experienced a dose-limiting
toxicity (DLT). It should be 0 or 1 (1 = DLT) for each entry
| Evaluable | Therapy_Start_Date | Dose_Level | Last_Assessment_Date | DLT | ID |
|---|---|---|---|---|---|
| 1 | 2014-11-05 | 2 | 2014-12-29 | 0 | 1 |
| 1 | 2014-11-24 | 2 | 2015-01-19 | 0 | 2 |
| 1 | 2014-12-17 | 3 | 2015-02-10 | 0 | 3 |
| 1 | 2015-01-21 | 4 | 2015-03-10 | 0 | 4 |
| 1 | 2015-03-08 | 4 | 2015-04-19 | 0 | 5 |
| 1 | 2015-04-12 | 4 | 2015-06-10 | 0 | 6 |
| 1 | 2015-05-03 | 5 | 2015-05-24 | 1 | 7 |
| 1 | 2015-08-08 | 4 | 2015-10-03 | 0 | 8 |
DLT plot using ggplot2
###### Parameters to be defined ######
# Sys.setlocale("LC_TIME", "fr_CA.UTF-8")
Sys.setlocale("LC_TIME", "en_US.UTF-8")
var_DLT <- "DLT"
var_Therapy_Start_Date <- "Therapy_Start_Date"
var_Last_Assessment_Date <- "Last_Assessment_Date"
var_Dose_Level <- "Dose_Level"
var_Evaluable <- "Evaluable"###### DLT plot ######
dlt_plot <- ggplot(data, aes(x=get(var_Therapy_Start_Date), y=factor(get(var_Dose_Level)), colour=factor(get(var_DLT)))) +
geom_point(size = 2) +
scale_x_date(
name = "Treatment date",
date_breaks = "2 months", date_labels = "%b \n %Y")+
labs(color = "", shape="", y="Assigned dose level") +
scale_color_manual(values = c("0" = "#1d4f91", "1" = "#D14124"), labels = c("Non-DLT", "DLT")) +
theme_light() +
theme(
panel.grid.major.y = element_blank(),
panel.grid.minor.y = element_blank(),
panel.grid.minor.x = element_blank(),
axis.title.x = element_text(size = 9),
# axis.text.x = element_text(size = 7, angle=45, hjust=1),
axis.title.y = element_text(size = 9),
axis.text.y = element_text(size = 9),
legend.title = element_blank(),
legend.text = element_text(size=9))
dlt_plot