[BioC] Gviz output extra empty page on pdf device

[Hahne, Florian]

Hi Dan,
Thanks for the heads up. I think this issue is resolved in the latest
development version (1.7.8)
At least on the build machines in Seattle the vignette has been built
properly.
Florian

On 2/19/14 5:04 PM, "Dan Du" <tooyoung at gmail.com> wrote:

>Hi Florian and others,
>
>I have been testing some functions and parameters, and noticed something
>odd when plotting tracks on a pdf device (postscript turns out fine),
>this only happens to some recent R-devel versions (tested on three
>r-devel builds Feb.3, Feb.14 and Feb.18), apparently the build machine
>in Seattle is not yet affected, which has a devel build on Jan.15. This
>happens to the most recent devel version of Gviz 1.7.7.
>
>Here is an example, can't really figure it why,
>#########################################
># say using the 1st example of plotTracks, I will get one empty page
>before the real deal.
>#########################################
>pdf('test.Gviz.pdf')
>#postscript('test.Gviz.eps', fonts='sans') # this is ok...
>st <- c(2000000, 2070000, 2100000, 2160000)
>ed <- c(2050000, 2130000, 2150000, 2170000)
>str <- c("-", "+", "-", "-")
>gr <- c("Group1","Group2","Group1", "Group3")
>annTrack <- AnnotationTrack(start=st, end=ed, strand=str, chromosome=7,
>                            genome="hg19", feature="test", group=gr,
>                            id=paste("annTrack item", 1:4),
>                            name="annotation track foo",
>                            stacking="squish")
>ax <- GenomeAxisTrack()
>dt <- DataTrack(start=seq(min(st), max(ed), len=10), width=18000,
>data=matrix(runif(40), nrow=4), genome="hg19", chromosome=7,
>type="histogram", name="data track bar")
>## Now plot the tracks
>res <- plotTracks(list(ax, annTrack, dt))
>dev.off()
>#########################################
>
>#########################################
># while it turns out fine for a normal multipage grid viewport, say the
>viewport clipping example of viewport()
>#########################################
>pdf('test.viewport.pdf')
>clip.demo <- function(i, j, clip1, clip2) {
>  pushViewport(viewport(layout.pos.col=i,
>                         layout.pos.row=j))
>  pushViewport(viewport(width=0.6, height=0.6, clip=clip1))
>  grid.rect(gp=gpar(fill="white"))
>  grid.circle(r=0.55, gp=gpar(col="red", fill="pink"))
>  popViewport()
>  pushViewport(viewport(width=0.6, height=0.6, clip=clip2))
>  grid.polygon(x=c(0.5, 1.1, 0.6, 1.1, 0.5, -0.1, 0.4, -0.1),
>               y=c(0.6, 1.1, 0.5, -0.1, 0.4, -0.1, 0.5, 1.1),
>               gp=gpar(col="blue", fill="light blue"))
>  popViewport(2)
>}
>
>grid.newpage()
>grid.rect(gp=gpar(fill="grey"))
>pushViewport(viewport(layout=grid.layout(2, 2)))
>clip.demo(1, 1, FALSE, FALSE)
>clip.demo(1, 2, TRUE, FALSE)
>clip.demo(2, 1, FALSE, TRUE)
>clip.demo(2, 2, TRUE, TRUE)
>popViewport()
># Demonstrate turning clipping off
>grid.newpage()
>pushViewport(viewport(w=.5, h=.5, clip="on"))
>grid.rect()
>grid.circle(r=.6, gp=gpar(lwd=10))
>pushViewport(viewport(clip="inherit"))
>grid.circle(r=.6, gp=gpar(lwd=5, col="grey"))
>pushViewport(viewport(clip="off"))
>grid.circle(r=.6)
>popViewport(3)
># Demonstrate vpList, vpStack, and vpTree
>grid.newpage()
>tree <- vpTree(viewport(w=0.8, h=0.8, name="A"),
>               vpList(vpStack(viewport(x=0.1, y=0.1, w=0.5, h=0.5,
>                                       just=c("left", "bottom"),
>name="B"),
>                              viewport(x=0.1, y=0.1, w=0.5, h=0.5,
>                                       just=c("left", "bottom"),
>name="C"),
>                              viewport(x=0.1, y=0.1, w=0.5, h=0.5,
>                                       just=c("left", "bottom"),
>name="D")),
>                      viewport(x=0.5, w=0.4, h=0.9,
>                               just="left", name="E")))
>pushViewport(tree)
>for (i in LETTERS[1:5]) {
>  seekViewport(i)
>  grid.rect()
>  grid.text(current.vpTree(FALSE),
>            x=unit(1, "mm"), y=unit(1, "npc") - unit(1, "mm"),
>            just=c("left", "top"),
>            gp=gpar(fontsize=8))
>}
>dev.off()
>#########################################
>
>I found that there has been a bug fix introduced in R-devel on Feb 2, not
>sure if this is the cause. Also noticed some very recent commit (r65013)
>to r-devel, will see if this changes anything.
>
># R-devel news
>"Bug fix for pushing viewports in Œgrid¹ (reported by JJ Allaire and
>Kevin Ushey).
>NOTE for anyone poking around within the graphics engine display list
>(despite the warnings not to) that this changes what is recorded by
>Œgrid¹ on the graphics engine display list."
>
># R-devel svn log
>r64901 | murrell | 2014-01-31 00:45:44 +0100 (Fri, 31 Jan 2014) | 1 line
>Changed paths:
>   M /trunk/doc/NEWS.Rd
>   M /trunk/src/library/grid/R/grid.R
>   M /trunk/src/library/grid/R/util.R
>   M /trunk/src/library/grid/R/viewport.R
>   M /trunk/src/library/grid/inst/doc/changes.txt
>   M /trunk/src/library/grid/src/grid.c
>   M /trunk/src/library/grid/src/grid.h
>
>bug fix for pushing grid viewports (only record viewport, NOT pushedvp,
>on graphics engine display list)
>
>Best regards,
>Dan
>