CODEWITHSUNDEEP
rpdfggplot2
Winawer
Winawer

Reputation: 711

R ggplot: geom_tile lines in pdf output

I'm constructing a plot that uses geom_tile and then outputting it to .pdf (using pdf("filename",...)). However, when I do, the .pdf result has tiny lines (striations, as one person put it) running through it. I've attached an image showing the problem. Minimal example

Googling let to this thread, but the only real advice in there was to try passing size=0 to geom_tile, which I did with no effect. Any suggestions on how I can fix these? I'd like to use this as a figure in a paper, but it's not going to work like this.

Minimal code:

require(ggplot2)
require(scales)
require(reshape)

volcano3d <- melt(volcano) 
names(volcano3d) <- c("x", "y", "z") 
 v <- ggplot(volcano3d, aes(x, y, z = z)) 

pdf("mew.pdf")
print(v + geom_tile(aes(fill=z)) + stat_contour(size=2) + scale_fill_gradient("z"))

Upvotes: 11

Views: 4729

Answers (4)

mdsumner
mdsumner

Reputation: 29487

In the interests of skinning this cat, and going into waaay too much detail, this code decomposes the R image into a mesh of quads (as used by rgl), and then shows the difference between a raster plot and a "tile" or "rect" plot. 

library(raster)
im <- raster::raster(volcano)
## this is the image in rgl corner-vertex form
msh <- quadmesh::quadmesh(im)

## manual labour for colour scaling
dif <- diff(range(values(im)))
mn <- min(values(im))
scl <- function(x) (x - mn)/dif

This the the traditional R 'image', which draws a little tile or 'rect()' for every pixel. 

list_image <- list(x = xFromCol(im), y = rev(yFromRow(im)), z = t(as.matrix(im)[nrow(im):1, ]))
image(list_image)

It's slow, and though it calls the source of 'rect()' under the hood, we can't also set the border colour. Use 'useRaster = TRUE' to use 'rasterImage' for more efficient drawing time, control over interpolation, and ultimately - file size.

Now let's plot the image again, but by explicitly calling rect for every pixel. ('quadmesh' probably not the easiest way to demonstrate, it's just fresh in my mind). 

## worker function to plot rect from vertex index
rectfun <- function(x, vb, ...) rect(vb[1, x[1]], vb[2,x[1]], vb[1,x[3]], vb[2,x[3]], ...)

## draw just the borders on the original, traditional image
apply(msh$ib, 2, rectfun, msh$vb, border = "white")

Now try again with 'rect'. 

## redraw the entire image, with rect calls 
##(not efficient, but essentially the same as what image does with useRaster = FALSE)
cols <- heat.colors(12)
## just to clear the plot, and maintain the plot space
image(im, col = "black")  
for (i in seq(ncol(msh$ib))) {
  rectfun(msh$ib[,i], msh$vb, col = cols[scl(im[i]) * (length(cols)-1) + 1], border = "dodgerblue")
}

Upvotes: 0

Dieter Menne
Dieter Menne

Reputation: 10215

I cannot reproduce the problem on my computer (Windows 7), but I remember it was a problem discussed on the list for certain configurations. Brian Ripley (if I remember) recommended 

CairoPDF("mew.pdf") # Package Cairo

to get around this

Upvotes: 0

Andrie
Andrie

Reputation: 179428

This happens because the default colour of the tiles in geom_tile seems to be white.

To fix this, you need to map the colour to z in the same way as fill.

print(v + 
  geom_tile(aes(fill=z, colour=z), size=1) + 
  stat_contour(size=2) + 
  scale_fill_gradient("z")
)

enter image description here

Upvotes: 20

kohske
kohske

Reputation: 66852

Try to use geom_raster:

pdf("mew.pdf")
print(v + geom_raster(aes(fill=z)) + stat_contour(size=2) + scale_fill_gradient("z"))
dev.off()

good quality in my environment.

enter image description here

Upvotes: 8

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