Data

We build the following dataset:

# Library
library(tidyverse)

# Creation of dataset
data <- data.frame(
  c(1,1,2,2,3,3,3,3,3,3,3,3,3,3,3,3,5,5,6,6,7,7,15,15,17,17,19,19,20,20,21,21,21,22,22,24,24,25,25,25,25,25,25,25,25),
  c(45,56,28,28,79,72,67,75,77,77,75,71,74,74,71,72,69,79,27,28,15,21,43,43,27,32,32.6,38,131,142,27,26,31,90,109,83,71,166,45,46,46,44,46,48,47),
  c("PD","PD","PD","PD","PD","PD","PD","PD","PD","PD","PD","PD","PD","PD","PD","PD","PD","PD","SD","SD","PD","PD","PD","PD","SD","SD","SD","SD","PD","PD","SD","SD","SD","PD","PD","PD","PD","PR","PR","PR","PR","PR","PR","PR","PR"),
  c(0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0,0,1,1,1,1,0,0,0,0,1,1,0,0,0,0,0,1,1,0,0,0,0,0,0,0,0),
  c(0,9,0,9,0,9,18,27,36,45,54,63,72,81,90,99,0,9,0,9,0,9,0,9,0,9,0,9,0,9,0,9,18,0,9,0,9,0,9,18,27,36,45,54,63)
)

colnames(data) <- c("ID","sum","RECIST","lesion","week") 

# Add change from baseline variable
data1 <- data %>%
  group_by(ID) %>%
  arrange(ID, week) %>%
  mutate(changebsl = 100*(sum - first(sum))/(first(sum)))  %>%
  ungroup() %>%
  mutate(changebsl = replace(changebsl, changebsl == "NaN", 0))

data format :

A data frame with 45 observations on the following 5 variables :
ID : ID of each participant patient, which will be used as a unique identifier
sum : The variable you want to plot, and it must be a numeric variable
RECIST : This variable is a group identifier (the color of the plot)
lesion: The variable to annotate particular patients, and it must be binary
week : The time of each visit, which can be measured by day, month, and year

#Head of dataset
knitr::kable(head(data1,8), align = "l")

ID	sum	RECIST	lesion	week	changebsl
1	45	PD	0	0	0.000000
1	56	PD	0	9	24.444444
2	28	PD	1	0	0.000000
2	28	PD	1	9	0.000000
3	79	PD	1	0	0.000000
3	72	PD	1	9	-8.860760
3	67	PD	1	18	-15.189873
3	75	PD	1	27	-5.063291

Function

For this spider plot, we will use the package ggplot2 and its functions.

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.

SBIM