I tried the code in the answer in this previous thread, ggplot2 and a Stacked Bar Chart with Negative Values.
dat <- read.table(text = " Division Year OperatingIncome
1 A 2012 11460
2 B 2012 7431
3 C 2012 -8121
4 D 2012 15719
5 E 2012 364
6 A 2011 12211
7 B 2011 6290
8 C 2011 -2657
9 D 2011 14657
10 E 2011 1257
11 A 2010 12895
12 B 2010 5381
13 C 2010 -2408
14 D 2010 11849
15 E 2010 517",header = TRUE,sep = "",row.names = 1)
dat1 <- subset(dat,OperatingIncome >= 0)
dat2 <- subset(dat,OperatingIncome < 0)
plot <- ggplot() +
geom_bar(data = dat1, aes(x=Year, y=OperatingIncome, fill=Division),stat = "identity") +
geom_bar(data = dat2, aes(x=Year, y=OperatingIncome, fill=Division),stat = "identity") +
scale_fill_brewer(type = "seq", palette = 1)
ggplotly(plot)
Here is what I'm getting:

If I run plot(plot) then it works fine:

How do I fix the issue in Plotly?
For future readers
Nowadays, plotly (I am using 4.8.0) supports stacked barcharts with negative values. In the layout you have to set barmode=relative. Moreover, you can also use the ggplotly functionality posted in the question.
plot_ly(dat, y=~OperatingIncome, x=~Year, type='bar', name=~Division, color =~Division,
colors='Blues', marker=list(line=list(width=1, color='lightgray'))) %>%
layout(barmode = 'relative')
Will return:

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