vishal February 2016

is there any simple way to write code in R to get swimmer plot?

I tried below code but it gives error.

library(ggplot2)
library(reshape2)
library(dplyr)
library(grid)

set.seed(33)

dat = data.frame(Subject = 1:10, 
                 Months = sample(4:20, 10, replace=TRUE),
                 Treated=sample(0:1, 10, replace=TRUE),
                 Stage = sample(1:4, 10, replace=TRUE),
                 Continued=sample(0:1, 10, replace=TRUE))

dat = dat %>%
  group_by(Subject) %>%
  mutate(Complete=sample(c(4:(max(Months)-1),NA), 1,                        prob=c(rep(1, length(4:(max(Months)-1))),5), replace=TRUE),
         Partial=sample(c(4:(max(Months)-1),NA), 1, 
                        prob=c(rep(1, length(4:(max(Months)-1))),5), replace=TRUE),
         Durable=sample(c(-0.5,NA), 1, replace=TRUE))

# Order Subjects by Months
dat$Subject = factor(dat$Subject, levels=dat$Subject[order(dat$Months)])

# Melt part of data frame for adding points to bars
dat.m = melt(dat %>% select(Subject, Months, Complete, Partial, Durable),
             id.var=c("Subject","Months"))

ggplot(dat, aes(Subject, Months)) +
  geom_bar(stat="identity", aes(fill=factor(Stage)), width=0.7) +
  geom_point(data=dat.m, 
             aes(Subject, value, colour=variable, shape=variable), size=4) +
  geom_segment(data=dat %>% filter(Continued==1), 
             aes(x=Subject, xend=Subject, y=Months + 0.1, yend=Months + 1), 
             pch=15, size=0.8, arrow=arrow(type="closed", length=unit(0.1,"in"))) +
  coord_flip() +
  scale_fill_manual(values=hcl(seq(15,375,length.out=5)[1:4],100,70)) +
  scale_colour_manual(values=c(hcl(seq(15,375,length.out=3)[1:2],100,40),"black")) +
  scale_y_continuous(limits=c(-1,20), breaks=0:20) +
  labs(fill="Disease Stage", colour="", shape="", 
       x="Subject Recevied Study Drug") +
  theme_bw() +
  theme(panel.grid.minor=element_blank(),
        panel.grid.major=element_blank(),
        axis.text.y=element_blank(),
        axis.ticks.y=element_blank())

It gives error as unkn

Answers


Mist February 2016

Not quite sure, but if you remove pch=15, size=0.8, it looks great!

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Asked in February 2016
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