DLT plot

The DLT plot is a graphical display of each individual’s assigned dose level over trial enrollment time. The y-axis is dose level, and the x-axis is the time of enrollment. The points in the graph represent the dose level assigned to each patient at their date of enrollment. The points will automatically jitter to avoid overlapping when enrollment dates are close to each other. The color of the point indicates if the patient had a dose limiting toxicity (DLT).

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 




#Head of dataset
knitr::kable(head(data,8), align = "l")
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




Contact

This document is a work of the statistics team in the Biostatistics and Medical Information Department at Saint-Louis Hospital in Paris (SBIM).
Based on The R Graph Gallery by Yan Holtz.