Add a custom element with lines to a ggplot object?-CodePudding

I've made a Kaplan Meier plot using ggplot2 that denotes the disease-free survival (in %) between 3 groups of patients: those unexposed to a risk factor (No exposure), exposed to risk factor 1 (Exposure 1), or those exposed to risk factor 2 (Exposure 2). The data and plot look as follows:

# Load packages
library(tidyverse)
library(magrittr)

# Get data.
data <- 
structure(list(time = c(15.4661190965092, 14.2340862422998, 14.8501026694045, 
9.94934976043806, 4.5119780971937, 7.76454483230664, 12.3121149897331, 
11.7344284736482, 15.6030116358658, 11.9123887748118, 13.9493497604381, 
3.09377138945927, 9.97672826830938, 6.24229979466119, 11.0362765229295, 
12.3805612594114, 9.28405201916495, 3.75633127994524, 6.88021902806297, 
14.2614647501711, 1.95208761122519, 13.3744010951403, 10.4804928131417, 
12.1149897330595, 11.668720054757, 11.211498973306, 5.50855578370979, 
7.61396303901437, 0.939082819986311, 7.0362765229295, 12.911704312115, 
16.0574948665298, 5.34702258726899, 13.3032169746749, 5.637234770705, 
15.0800821355236, 14.1601642710472, 12.7638603696099, 15.6796714579055, 
6.07802874743327, 15.2142368240931, 11.8001368925394, 2.92676249144422, 
10.5051334702259, 10.072553045859, 15.9479808350445, 4.84052019164956, 
4.36960985626283, 12.7775496235455, 15.0280629705681, 13.8891170431211, 
2.2258726899384, 8.90622861054073, 14.7433264887064, 4.61875427789186, 
2.81998631074606, 11.0225872689938, 7.67145790554415, 13.9958932238193, 
9.27310061601643, 15.4496919917864, 11.8986995208761, 11.9972621492129, 
13.7604380561259, 2.8993839835729, 5.82614647501711, 8.0684462696783, 
13.4455852156057, 3.06091718001369, 10.9869952087611, 13.1471594798083, 
14.1273100616016, 13.7577002053388, 6.88021902806297, 11.7973990417522, 
10.3819301848049, 5.47843942505133, 14.2477754962355, 6.94045174537988, 
9.94387405886379, 4.54483230663929, 8.18891170431212, 13.7960301163587, 
8.27104722792608, 14.2422997946612, 14.5325119780972, 14.3655030800821, 
14.072553045859, 3.64681724845996, 6.3791923340178, 10.5434633812457, 
11.378507871321, 14.9322381930185, 14.0123203285421, 2.48323066392882, 
14.8583162217659, 9.88364134154689, 12.145106091718, 15.5838466803559, 
2.80082135523614, 12.9007529089665, 3.50718685831622, 13.3771389459274, 
10.5379876796715, 15.2525667351129, 16.2299794661191, 16.1779603011636, 
8.2217659137577, 15.315537303217, 11.7289527720739, 10.9568788501027, 
13.2676249144422, 7.32375085557837, 11.6112251882272, 5.66735112936345, 
15.7782340862423, 10.113620807666, 9.5523613963039, 1.83983572895277, 
13.5003422313484, 9.6208076659822, 13.9575633127995, 10.9377138945927, 
3.63860369609856, 10.4284736481862, 10.9678302532512, 13.4209445585216, 
15.233401779603, 4.70088980150582, 12.4024640657084, 14.6830937713895, 
13.2977412731006, 0.717316906228611, 12.9691991786448, 7.9315537303217, 
15.6386036960986, 5.82340862422998, 1.0321697467488, 9.89459274469541, 
15.0280629705681, 13.4483230663929, 10.6639288158795, 3.39493497604381, 
12.3203285420945, 4.47364818617385, 14.839151266256, 14.2669404517454, 
6.12183436002738, 13.2101300479124, 3.39493497604381, 15.9671457905544, 
15.9479808350445, 11.9753593429158, 5.46475017111567, 15.9425051334702, 
7.35934291581109, 5.87268993839836, 9.12525667351129, 15.2717316906229, 
6.80082135523614, 14.8583162217659, 12.974674880219, 14.6967830253251, 
13.5797399041752, 11.1321013004791, 3.87679671457906, 14.8336755646817, 
12.5585215605749, 15.6988364134155, 7.60574948665298, 3.40041067761807, 
15.9288158795346, 14.9733059548255, 15.066392881588, 10.2067077344285, 
13.223819301848, 5.34976043805613, 12.0766598220397, 10.9787816563997, 
11.9123887748118, 11.0581793292266, 14.5763175906913, 14.0533880903491, 
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14.6776180698152, 15.4086242299795, 10.4421629021218, 6.7378507871321, 
13.9466119096509, 4.22724161533196, 13.7960301163587, 15.7399041752225, 
10.92128678987, 10.425735797399, 11.772758384668, 7.86036960985626, 
2.16837782340862), surv = c(78.895930965634, 82.939817991606, 
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89.2078379065114, 84.5274669486008, 90.2944085152522, 98.1562293390666, 
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"Exposure 1", "Exposure 1", "Exposure 3", "Exposure 2", "Exposure 3", 
"Exposure 3", "Exposure 3", "Exposure 3", "Exposure 1", "Exposure 1", 
"Exposure 1", "Exposure 1", "Exposure 1", "Exposure 1", "Exposure 1", 
"Exposure 1", "Exposure 1", "Exposure 3", "Exposure 2", "Exposure 1", 
"Exposure 1", "Exposure 2", "Exposure 1", "Exposure 2", "Exposure 1", 
"Exposure 3", "Exposure 2", "Exposure 1", "Exposure 1", "Exposure 1", 
"Exposure 3", "Exposure 2", "Exposure 3", "Exposure 1", "Exposure 1", 
"Exposure 1", "Exposure 2", "Exposure 2", "Exposure 2", "Exposure 2", 
"Exposure 1", "Exposure 3", "Exposure 1", "Exposure 2", "Exposure 1", 
"Exposure 2", "Exposure 1", "Exposure 1", "Exposure 2", "Exposure 1", 
"Exposure 1", "Exposure 1", "Exposure 3", "Exposure 3", "Exposure 1", 
"Exposure 3", "Exposure 2", "Exposure 1", "Exposure 3", "Exposure 1", 
"Exposure 3", "Exposure 3", "Exposure 1", "Exposure 3", "Exposure 1", 
"Exposure 2", "Exposure 3", "Exposure 3", "Exposure 2", "Exposure 1", 
"Exposure 1", "Exposure 1", "Exposure 1", "Exposure 3", "Exposure 2", 
"Exposure 2", "Exposure 3", "Exposure 1", "Exposure 2", "Exposure 3", 
"Exposure 3", "Exposure 1", "Exposure 1", "Exposure 2", "Exposure 2", 
"Exposure 3", "Exposure 3", "Exposure 2", "Exposure 3", "Exposure 3", 
"Exposure 2", "Exposure 1", "Exposure 1", "Exposure 2", "Exposure 3", 
"Exposure 1", "Exposure 1", "Exposure 1", "Exposure 1", "Exposure 3", 
"Exposure 1", "Exposure 1", "Exposure 1", "Exposure 2", "Exposure 1", 
"Exposure 3", "Exposure 2", "Exposure 1", "Exposure 3", "Exposure 1", 
"Exposure 2", "Exposure 3", "Exposure 1", "Exposure 2", "Exposure 1", 
"Exposure 1", "Exposure 1", "Exposure 2", "Exposure 1", "Exposure 1", 
"Exposure 2", "Exposure 2", "Exposure 3", "Exposure 3", "Exposure 1", 
"Exposure 1", "Exposure 1", "Exposure 3", "Exposure 3", "Exposure 1", 
"Exposure 1", "Exposure 1", "Exposure 1", "Exposure 2", "Exposure 2", 
"Exposure 1", "Exposure 3", "Exposure 1", "Exposure 3")), class = "data.frame", row.names = c(NA, 
-200L))

# Make the plot:
data %>% 
  ggplot(aes(x=time, y=surv))   
  geom_line(aes(color=group), size=0.3)   
  scale_y_continuous(name="Disease-free survival (%)")  
  scale_x_continuous(name="Follow-up time (years)")  
  scale_color_manual(name="Groups", 
                     values=c("Exposure 1"="firebrick3", "Exposure 2"="#255B1D", "Exposure 3"="darkblue"), 
                     labels=c("Exposure 1 (p<.01)", "Exposure 2 (p=.02)", "Exposure 3 (p=.03)"))   
  theme_classic()   
  theme(legend.position=c(0.3, 0.3))

This produces the following plot:

In this figure the p-values denote the difference in survival between each group and the unexposed group (using Log Rank tests). Now I've also compared the survival between the two exposed groups, Exposure 1 and Exposure 2, for which the p-value was p=.01. I'd like to add this to the plot in the following manner:

I've made this (very ugly) adaptation in Paint, but I'd like to be able to do this in R. Any help?

CodePudding user response：

Perhaps the easiest thing would be to draw your own legend, so that you don't need to guess where to put the lines, and so that relative positions stay constant during plot resizing:

data %>% 
  ggplot(aes(x=time, y=surv))   
  geom_line(aes(color=group), size=0.3)   
  scale_y_continuous(name = "Disease-free survival (%)")  
  scale_x_continuous(name = "Follow-up time (years)")  
  scale_color_manual(name = "Groups", 
                     values=c("firebrick3", "#255B1D", "darkblue"))  
  geom_line(data = data.frame(time = c(3.9, 5, 3.9, 5, 3.9, 5),
                              surv = c(84, 84, 83, 83, 82, 82),
                              group = rep(paste('Exposure', 1:3), each = 2)),
            aes(color = group))  
  geom_text(data = data.frame(time = c(5.3, 5.3, 5.3, 10), 
                              surv = c(84, 83, 82, 82.5),
                              group = c("No Exposure", "Exposure 1 (p = 0.02)",
                                        "Exposure 2 (p = 0.03)", "p = 0.01")),
            aes(label = group), hjust = 0, size = 3.2)  
  geom_path(data = data.frame(time = c(9, 9.5, 9.5, 9), 
                              surv = c(82, 82, 83, 83)))  
  annotate('text', x = 3.8, y = 85.2, label = "Groups", hjust = 0, size = 4)  
  theme_classic()   
  theme(legend.position = 'none')