Creating a timeline in ggplot

Question

Edited below with complete and functioning code:

I am trying to create a timeline similar to the one this code creates from the Timeline package, however, the options are not very flexible. For example, I would like to create space between each bar so they are not touching. Also, I am wondering if there is a way to add the "End_Status" column to the graph so that it it is obvious that the data stops there because the animal died. Any help is greatly appreciated.

Example dataset:

df <- data.frame(id = c(rep(1201, 10), rep(1202, 14), rep(1203, 6),     rep(1204, 22)),
             date = c(seq(1,5,1), seq(5,7,1), seq(7,8,1), seq(2,5,1), seq(7,9,1), seq(11,17,1), seq(1,8,1), seq(8,12, 1), seq(12,26,1 )),
             schedule = as.factor(c(rep(1, 5,), rep(2, 3), rep(3, 6), 
                                 rep (1, 3), rep (2, 2), rep(3, 5),
                                 rep(1,8), rep(2, 5), rep(1,3), rep(3, 12))),
             status = c(rep("", 9), "Mort", rep("", 41), "Mort"))

Code to get the output table I am interested in:

library("data.table")
library(plyr)
library(dplyr)

df<-as.data.table(df)
z <- df[, unique(id)]
################
value_change_first <- function(x,a) { for(i in 1:length(x[,schedule])) {
ifelse(x[a,schedule] == x[a+1,schedule], 
       x <- x[-(a+1)], 
       a <- a+1)}
return(x)
}

value_change_second <- function(x,a) { 
for(i in 1:length(x[,schedule])) {
ifelse(x[a,schedule] == x[a+1,schedule], 
       x <- x[-(a)], 
       a <- a+1)}
return(x)
}

#################
output_1 <- c()

for(i in 1:length(z)){
ids <- df[df$id==z[i],]
out<-value_change_first(ids,1)
output_1<-as.data.frame(rbind(output_1, out))}

#################
output_2 <- c()

for(i in 1:length(z)){
ids <- df[df$id==z[i],]
out<-value_change_second(ids,1)
output_2<-as.data.frame(rbind(output_2, out))}

################
output_1$End_Date <- output_2$date
output_1$End_Status <- output_2$status
names(output_1)[names(output_1)=="date"] <- "Start_Date"

output <- output_1[c(1:2, 5, 3, 6)]

From here I can use the Timeline Package to get something close to what I want:

require(timeline)
tl <- timeline(output, 
           label.col=names(output)[4],
           text.color= NA,
           group.col=names(output)[1],
           start.col=names(output)[2],
           end.col = names(output)[3])
tl + theme_bw() + theme(panel.grid.major = element_blank(), panel.grid.minor    = element_blank())

My question is how to build something similar in ggplot. Furthermore, I want to specifically add the "Mort" message at a given date by individual from the output dataframe.

I ended up getting this to work like I want:

### creating a end status column that includes mortalities and failures
output$End_Status_Date<-NA
for(i in 1:nrow(output)){
if(output$End_Status[i] == "Mort"){
output$End_Status_Date[i]=as.character(output$End_Date)[i] 
}
}

for(i in 1:nrow(output)){
if(output$End_Status[i] == "Failure"){
output$End_Status_Date[i]=as.character(output$End_Date)[i] 
}
}

### data structuring
output$id<-as.factor(output$id)
output$End_Status_Date<-as.numeric(output$End_Status_Date)
output$End_Status[output$End_Status == ""] <- NA
output$End_Status<-as.character(output$End_Status)
output$End_Status<-as.factor(output$End_Status)

library(ggplot2)

g2 <- ggplot() +
geom_segment(data=output, aes(x=Start_Date, xend=End_Date, y=id, yend=id,    color=schedule), linetype=1, size=2) +
geom_point(data=subset(output, is.na(End_Status)==FALSE), 
         mapping=aes(x=End_Status_Date, y=id, shape=End_Status,   fill=End_Status), size=4)+
scale_colour_manual(values=c("blue4", "chartreuse4", "darkmagenta"))+
scale_fill_manual(values=c("white", "red"))+ 
scale_shape_manual(values=c(21,24))+ 
xlab("Time")+
ylab("Individuals")+
theme_bw() + theme(panel.grid.minor = element_blank(), panel.grid.major =   element_blank())

g2

Can you show what you've tried using ggplot?

Nancy
– Nancy

2017-01-20 02:43:41 +00:00
Commented Jan 20, 2017 at 2:43 — Nancy
– Nancy, Commented Jan 20, 2017 at 2:43
Edited original post with final product.

Michel Kohl
– Michel Kohl

2017-01-20 22:50:38 +00:00
Commented Jan 20, 2017 at 22:50 — Michel Kohl
– Michel Kohl, Commented Jan 20, 2017 at 22:50

Nancy · Accepted Answer · 2017-01-20 03:02:13Z

3

You did most of the work already. The key here is just to use geom_rect and take advantage of your y-axis labels to set the ymin and ymax values.

ggplot(output, aes(xmin = Start_Date, xmax = End_Date, 
                   ymin = as.numeric(id) - 1, ymax = as.numeric(id), 
                   fill = schedule)) + 
  geom_rect() +
  geom_text(aes(x = End_Date, y = id, label = End_Status))

edited Jan 20, 2017 at 3:02

answered Jan 20, 2017 at 2:56

Nancy

4,1395 gold badges35 silver badges53 bronze badges

Sign up to request clarification or add additional context in comments.

3 Comments

Nancy Over a year ago

Excellent. If this answer helped you, please accept it as correct :)

Michel Kohl Over a year ago

Edited original post with final product

vpipkt Over a year ago

In my case the id was a factor. It was useful to put y=id in the main aes. This handled the right vertical axis labels.

Collectives™ on Stack Overflow

Creating a timeline in ggplot

1 Answer 1

3 Comments

Your Answer

Hot Network Questions

Collectives™ on Stack Overflow

1 Answer 1

3 Comments

Your Answer

Sign up or log in

Post as a guest

Related