empty first page in pdf output

[ChristofferFlensburg]

Hi and thanks for a great package! I always link this package on twitter whenever I see a venn diagram with too many sets, as do many others.

For the (minor) issue I want to output a pdf, but it keeps producing an empty first page and the actual plot on the second page. For example

pdf('upsetExample.pdf', width=10, height=7)
example(upset)
dev.off()

produces the attached file on my system. upsetExample.pdf

I'm not experienced with ggplot, so not sure if this is a ggplot thing or an upset thing, sorry. It's not hard to manually delete the empty page, but I'd like to to automate over many files and then it becomes a bit annoying.

Thanks, and all the best, /Christoffer

[JakeConway]

I believe setting the onefile parameter of pdf() to FALSE will fix this

[ChristofferFlensburg]

Thanks Jake.

It does indeed solve the issue with the empty first page, but it doesn't allow you to output multipage pdf. In my case I only wanted a single page, so it works around my issue, thanks!

The example code still produces a pdf with only the last plot as opposed to the desired 3 pages.

pdf('upsetExample.pdf', width=10, height=7, onefile=F)
example(upset)
dev.off()

upsetExample.pdf

So umm, feel free to close this unless you want to fix the multipage thing. I got what I needed, thanks.

[alanocallaghan]

The reason for this, I believe, is that the upset plot functions (in UpSet.plot.R) contain calls to gridExtra:::grid.newpage(). This leads to blank pages being inserted. These calls should be removed, since they also prevent the user from (eg) inserting an upset plot as part of a larger grid object.

In fact, I think that the upset function should merely return the grid objects, and a separate function should handle the plotting...

[mcbg]

The onefile = FALSE solution doesn't work when you're using CairoPDF from the Cairo package.

[reesese]

So has a true solution to this been found? I want to be able to use onefile=TRUE and not have that pesky blank first page. This issue is bigger than just an upset one. It has to do with using pdf to save multipage plots.

[ChristofferFlensburg]

I haven't had this issue in base plotting. After a quick google, it seems like an issue with ggplot and pdf(): https://github.com/wilkelab/cowplot/issues/24

According to Claus Wilke in that thread, ggsave() replaces pdf() for this situation.

[vidaletal]

All suggested options worked for on global .env, once I used within my own function the only thing that worked was (maybe because of .env):

png(plot_filepath)
  print({
    plot_upset<-upset(fromExpression(upset_expression))
    homer_upset
  })
  dev.off()

Hope it helps others as well

[jdblischak]

My UpSet plot wasn't displayed in my Sweave document because of the first blank page. I wasn't sure how to use the onefile = FALSE trick in this context. Fortunately a workaround was merged in PR #101. You can now set the argument newpage = FALSE when printing an upset object.

Below is a reproducible example. The plot displays with newpage = FALSE, but if you change it to newpage = TRUE (the default), it disappears from the output PDF.

\documentclass{article}

\begin{document}
\SweaveOpts{concordance=TRUE}

<<upset, fig=TRUE>>=
library(UpSetR)
movies <- read.csv(system.file("extdata", "movies.csv", package = "UpSetR"),
                   header = TRUE, sep = ";")
upsetPlot <- upset(movies, nsets = 7, nintersects = 30, mb.ratio = c(0.5, 0.5),
                   order.by = c("freq", "degree"), decreasing = c(TRUE,FALSE))
print(upsetPlot, newpage = FALSE)
@

\end{document}