Escalier plot

The Escalier plot is a graphical display of each individual’s assigned dose level and follow-up duration over trial enrollment. The y-axis is patient ID, and the x-axis is the time of enrollment. For each patient, the line represents the time from the patient’s enrollment to the time of their last-follow-up. The dose level information is displayed as text at the start of each line and also by color. DLT is denoted as a cross. Patient’s evaluability is displayed by the line type of each patient.

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

Escalier 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"

# `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
data <- data[order(data[, var_Therapy_Start_Date]), ]
data$ID <- 1:nrow(data)
###### Escalier plot ###### 
escalier_plot <- ggplot(data) +
  geom_point(aes(x = get(var_Therapy_Start_Date), y = ID, colour = get(var_Dose_Level)), 
             size = 1, 
             pch = ".") +
  geom_point(aes(x = get(var_Last_Assessment_Date), y = ID, shape = get(var_DLT), colour = get(var_Dose_Level)), 
             size = 1) +
  geom_segment(aes(x = get(var_Therapy_Start_Date), y = ID, 
                   xend = get(var_Last_Assessment_Date), yend = ID, 
                   linetype = factor(get(var_Evaluable)),
                   colour = get(var_Dose_Level)), 
               size = 1) +
  geom_text(aes(x = get(var_Therapy_Start_Date), y = ID, label = paste('d',get(var_Dose_Level))), 
            nudge_y = 0.5, size = 2) +
  scale_shape_manual(values=c("1" = 4, "0" = NA), 
                     labels = c("1" = "DLT", "0" = "")) +
  scale_linetype_manual(values=c("1" = 1, "0" = 3), 
                        labels = c("1" = "Evaluable", "0" = "Non Evaluable")) +
  scale_y_continuous(breaks = seq(min(data$ID), max(data$ID), by = 1)) + 
  scale_colour_manual(values=c("#1d4f91", "#FF9800", "#228848", '#AE2573', '#D14124')) +
  scale_x_date(
    name = "Treatment date",
    date_breaks = "3 months", date_labels = "%b \n %Y")+
  labs(shape = "",
       linetype = "",
       color = "Dose Level",
       x = "Date of the Enrollment",
       y = "Patient ID") + 
  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)) +
  guides(linetype = guide_legend(order=3),
         shape = guide_legend(order=2),
         colours = guide_legend(order=1))

escalier_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.