Change type of line in legend (ggplot2) in figure with geom

t <- c(1,1,2,2,3,4,4,5,5,6,6,6,6,7,8,8,8,8,9,10,10,11,11,11,12,12,13,15,16,17,17,19,
       20,22,22,23,23,25,32,32,34,35)
status <-c(1,1,1,1,1,1,1,1,1,1,1,1,0,1,1,1,1,1,0,1,0,1,0,1,1,1,1,1,1,0,1,0,0,1,1,1,1,0,0,0,0,0)
grupo <- c(1,1,1,1,1,1,1,1,1,0,0,0,0,0,1,1,1,1,0,0,0,1,0,1,1,1,0,1,0,0,1,0,0,0,1,1,0,0,0,0,0,0)
sex <- c(1,1,1,1,1,1,1,1,0,0,1,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,1,0,0,0,1,1,0,1,1,1,1,1,1,1)
data<- data.frame(t,status,grupo, sex)

# Fit a Cox model 
library(survival)
fit <- coxph(Surv(t,status) ~ grupo sex, data=data, method='breslow')

# Predict Survival
datosnuevos <- data.frame(grupo=c(0,0,1,1), sex=c(0,1,0,1))  
curva <- survfit(fit, newdata = datosnuevos, conf.type = "log-log")
df<- data.frame(time=curva$time, TtoFemale=curva$surv[,1], TtoMale=curva$surv[,2],
                PboFemale=curva$surv[,3], PboMale=curva$surv[,4])

# log minus log (survival)
library(ggplot2)
ggplot() 
  geom_step(aes(time, log(-log(TtoFemale)), col='TTo0_Female0'), lty=2, data=df) 
  geom_step(aes(time, log(-log(TtoMale)), col='TTo0_Male1'),lty=2, data=df) 
  geom_step(aes(time, log(-log(PboFemale)), col='Pbo1_Female0'), data=df) 
  geom_step(aes(time, log(-log(PboMale)), col='Pbo1_Male1'), data=df) 
  labs(color= 'TRT-Sex', x = "time", y = "log(-log Survival)", title = "") 
  scale_color_manual(name = "TRT-Sex", values = c("TTo0_Female0" = "pink", "TTo0_Male1" = "blue",
                    "Pbo1_Female0" = "pink", "Pbo1_Male1" = "blue")) 
  theme_classic() 
  theme(legend.position = "right", legend.direction = "vertical")  
  theme(legend.title = element_text(family = "Courier", color = "black", size = 12,  face = 1)) 
  theme(legend.text = element_text (size = 10))  
  scale_linetype_manual(name = "TRT-Sex", values=c(2,2,1,1))

How can I modify the two first lines in the legend (must be 'dotted line') I have tried it with -- scale_linetype_manual(name = "TRT-Sex", values=c(2,2,1,1)) --- but It doesn't work... Thanks

CodePudding user response：

This type of problems generally has to do with reshaping the data. The format should be the long format and the data is in wide format. See this post on how to reshape the data from wide to long format.
Then only one call to geom_step will plot all 4 lines and the legend automatically draws the lines with the same type as the graph since it inherits the linetype aesthetic.

library(ggplot2)

df |>
  tidyr::pivot_longer(cols = -time, names_to = "TRT-Sex") |> 
  ggplot(aes(time, log(-log(value))))  
  geom_step(aes(color = `TRT-Sex`, linetype = `TRT-Sex`), size = 1)  
  labs(color = "TRT-Sex", x = "time", y = "log(-log Survival)", title = "") 
  scale_color_manual(name = "TRT-Sex", 
                     values = c(TtoFemale = "pink", TtoMale = "blue",
                                PboFemale = "pink", PboMale = "blue"))  
  scale_linetype_manual(name = "TRT-Sex", 
                        values = c(TtoFemale = "dashed", TtoMale = "dashed",
                                   PboFemale = "solid", PboMale = "solid"))  
  theme_classic(base_size = 16)  
  theme(legend.position = "right", legend.direction = "vertical",
        #legend.title = element_text(family = "Courier", color = "black", size = 12,  face = 1),
        legend.text = element_text (size = 10),
        legend.key.width = unit(2, "line"))

^{Created on 2022-10-10 with reprex v2.0.2}

CodePudding user response：

You can use

guides(color = guide_legend(override.aes = list(linetype = c(2,2,1,1))))

t <- c(1,1,2,2,3,4,4,5,5,6,6,6,6,7,8,8,8,8,9,10,10,11,11,11,12,12,13,15,16,17,17,19,
       20,22,22,23,23,25,32,32,34,35)
status <-c(1,1,1,1,1,1,1,1,1,1,1,1,0,1,1,1,1,1,0,1,0,1,0,1,1,1,1,1,1,0,1,0,0,1,1,1,1,0,0,0,0,0)
grupo <- c(1,1,1,1,1,1,1,1,1,0,0,0,0,0,1,1,1,1,0,0,0,1,0,1,1,1,0,1,0,0,1,0,0,0,1,1,0,0,0,0,0,0)
sex <- c(1,1,1,1,1,1,1,1,0,0,1,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,1,0,0,0,1,1,0,1,1,1,1,1,1,1)
data<- data.frame(t,status,grupo, sex)

# Fit a Cox model 
library(survival)

fit <- coxph(Surv(t,status) ~ grupo sex, data=data, method='breslow')

# Predict Survival
datosnuevos <- data.frame(grupo=c(0,0,1,1), sex=c(0,1,0,1))  
curva <- survfit(fit, newdata = datosnuevos, conf.type = "log-log")
df<- data.frame(time=curva$time, TtoFemale=curva$surv[,1], TtoMale=curva$surv[,2],
                PboFemale=curva$surv[,3], PboMale=curva$surv[,4])

# log minus log (survival)
library(ggplot2)

ggplot() 
  geom_step(aes(time, log(-log(TtoFemale)), col='TTo0_Female0'), lty=2, data=df) 
  geom_step(aes(time, log(-log(TtoMale)), col='TTo0_Male1'),lty=2, data=df) 
  geom_step(aes(time, log(-log(PboFemale)), col='Pbo1_Female0'), data=df) 
  geom_step(aes(time, log(-log(PboMale)), col='Pbo1_Male1'), data=df) 
  labs(color= 'TRT-Sex', x = "time", y = "log(-log Survival)", title = "") 
  scale_color_manual(name = "TRT-Sex", values = c("TTo0_Female0" = "pink", 
                                                  "TTo0_Male1" = "blue",
                                                  "Pbo1_Female0" = "pink", 
                                                  "Pbo1_Male1" = "blue")) 
  
  scale_linetype_manual(name = "TRT-Sex", values=c(2,2,1,1)) 
  #new
  guides(color = guide_legend(override.aes = list(linetype = c(2,2,1,1)))) 
  #
  theme_classic() 
  theme(legend.position = "right", 
        legend.direction = "vertical",
        legend.title = element_text(family = "Courier", color = "black", size = 12,  face = 1),
        legend.text = element_text (size = 10))

^{Created on 2022-10-10 by the reprex package (v2.0.1)}