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%.

score 2 · Accepted Answer · answered May 19 '20 at 14:11

2

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)}

answered May 19 '20 at 14:11

stefan

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6
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Thanks. What I'd like to obtain is the y-axes broken every 10% till 100%. How could I do it? – jeff May 21 '20 at 08:31
In this case you have to set the breaks. Try `scale_y_continuous(breaks = scales::pretty_breaks(10), label = scales::percent_format(scale = 100 / n_id))`. – stefan May 21 '20 at 08:43
I'll edit my question adding what I get using 'break'. – jeff May 21 '20 at 08:49
1

Hi @SabrinaG. What's clear is that something weird happens with the normalization. Seems to be the case that `n_id` is slightly larger the the number of obs used in the plot. (???) But this is tricky to solve without having a look at the real data. To get nice breaks you could try setting the breaks via `breaks = seq(0, n_id, length.out = 11)`. However, this is probably (or quite suzre) no solution to the problem. – stefan May 21 '20 at 09:30
With absolute values on the y-axes I had the following: 10.000, 20.000 and 30.000. When I changed the y-axes into percentages I got: 28%, 56% and 84%, given that the total number of observations is 35.514. And when I use 'breaks' it keep on plotting those percentages, adding others in between. And I don't understand why. Thanks anyway – jeff May 21 '20 at 10:16
Thanks @stefan! Your last advice solved the situation. – jeff May 21 '20 at 10:25
You are welcome @SabrinaG.. If you want do me a favor: Mark the question as answered. Besides giving me some credit it shows others with a similar problem that the solution worked and removes the question from the queue of questions still waiting for an answer. – stefan May 21 '20 at 11:11
Sorry @stefan, how may I mark the question as answered and give you some credit? I'm sorry for asking but I'm quite new! Thanks again – jeff May 22 '20 at 10:08
Hi @SabrinaG. No problem. Everything is fine. Look at https://stackoverflow.com/help/someone-answers on how to mark a question as answered. Thanks for your reply. – stefan May 23 '20 at 07:54

score 0 · Answer 2 · answered May 19 '20 at 14:04

0

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.

answered May 19 '20 at 14:04

Daniel_j_iii

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score 0 · Answer 3 · answered May 19 '20 at 14:05

0

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)}

answered May 19 '20 at 14:05

MSR

2,731
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How to get percentages on the y axes in an alluvial or sankey plot?

3 Answers3