How to get percentages on the y axes in an alluvial or sankey plot?

Question

I realized this graph using ggplot2 and I'd like to change y axes to percentages, from 0% to 100% with breaks every 10. I know I can use:

+ scale_y_continuous(label=percent, breaks = seq(0,1,.1))

but I still get a problem because, turning into percentages, R interpret 30000 as 30000%, so if a limit to 100% I don't get anything in my graph. How can I manage it?

I have a dataset like this:

ID time value
1   1   B with G available
2   1   Generic
3   1   B with G available
4   1   Generic
5   1   B with G available
6   1   Generic
7   1   Generic
8   1   Generic
9   1   B with G available
10  1   B with G available
11  1   Generic
12  1   B with G available
13  1   B with G available
14  1   B with G available
15  1   Generic
16  1   B with G available
17  1   B with G available
18  1   B with G available
19  1   B with G available
20  1   B with G available
1   2   B with G available
2   2   Generic
3   2   B with G available
4   2   Generic
5   2   B with G available
6   2   Generic
7   2   Generic
8   2   Generic
9   2   B with G available
10  2   B with G available
11  2   Generic
12  2   B with G available
13  2   B with G available
14  2   B with G available
15  2   Generic
16  2   B with G available
17  2   switch
18  2   B with G available
19  2   B with G available
20  2   switch

which is reproducible with this code:

PIPPO <- data.frame("ID"=rep(c(1:20),2), "time"=c(rep(1,20),rep(2,20)), "value"=c("B","G","B","G","B",rep("G",3),rep("B",2),"G",rep("B",3),"G",rep("B",6),"G","B","G","B",rep("G",3),rep("B",2),"G",rep("B",3),"G","B","switch",rep("B",2),"switch"))

so I don't have a variable for y axes I can manage.

Here my code and the plot I obtained

ggplot(PIPPO, 
       aes(x = time, stratum = value, alluvium = ID,
           fill = value, label = value)) +
  scale_fill_brewer(type = "qual" , palette = "Set3") +
  geom_flow(stat = "flow", knot.pos = 1/4, aes.flow = "forward",
            color = "gray") + 
  geom_stratum() +
  theme(legend.position = "bottom") 

Could anyone help me?

What I get on real data using

scale_y_continuous(label = scales::percent_format(scale = 100 / n_id))

is this:

with 84% as the maximum value (and not 100%). How can i get the y-axes up to 100% and broken every 10% ?

Here what I get with

scale_y_continuous(breaks = scales::pretty_breaks(10), label = scales::percent_format(scale = 100 / n_id))

I get this weird values every 14%.

Answer 1

Using the scale argument in percent_format this can be achieved like so:

PIPPO <- data.frame("ID"=rep(c(1:20),2), "time"=c(rep(1,20),rep(2,20)), "value"=c("B","G","B","G","B",rep("G",3),rep("B",2),"G",rep("B",3),"G",rep("B",6),"G","B","G","B",rep("G",3),rep("B",2),"G",rep("B",3),"G","B","switch",rep("B",2),"switch"))

library(ggplot2)
library(ggalluvial)

n_id <- length(unique(PIPPO$ID))

ggplot(PIPPO, 
       aes(x = time, stratum = value, alluvium = ID,
           fill = value, label = value)) +
  scale_fill_brewer(type = "qual" , palette = "Set3") +
  scale_y_continuous(label = scales::percent_format(scale = 100 / n_id)) +
  geom_flow(stat = "flow", knot.pos = 1/4, aes.flow = "forward", color = "gray",) + 
  geom_stratum() +
  theme(legend.position = "bottom") 

^{Created on 2020-05-19 by the reprex package (v0.3.0)}

Answer 2

Simply normalising your y-values seems to do the trick:

library(ggplot2)

ggplot(mtcars, aes(x = cyl, y = mpg/max(mpg))) +
  geom_point() +
  scale_y_continuous(label = scales::label_percent())

^{Created on 2020-05-19 by the reprex package (v0.3.0)}

Answer 3

I assume You will need to create a new column of the percentages, by taking the total number of rows, and then dividing each "value" in your column by the total to get what percentage it represents.