Error in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : polygon edge not found (new)

Question

I know that the title of this question is a duplicate of this Question and this Question but the solutions over there don't work for me and the error message is (slightly) different:

Error in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  : 
polygon edge not found

(note the missing part about the missing font)

I tried all suggestions that I found (updating / reinstalling all loaded graphic packages, ggplot2, GGally, and scales, reinitialising the Fonts on Mac OSX by starting in safe mode, moving the Fonts from /Fonts/ (Disabled) back into /Fonts...) but none of it resolved the problem.

The error seems to occure when I plot a ggplot graph with

scale_y_continuous(label=scientific_10)

where scientific_10 is defined as

scientific_10 <- function(x) {
parse(text = gsub("e", " %*% 10^", scientific_format()(x)))
}

Therefore the I suspect that the scales library has something to do with it.

The most puzzling is that the error only occurs each so-and-so many times, maybe each 3rd or 5th time i try to plot the same graph...

> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.9.5 (Mavericks)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] gridExtra_2.0.0 scales_0.3.0    broom_0.4.0     tidyr_0.3.1             ggplot2_1.0.1   GGally_0.5.0    dplyr_0.4.3    

loaded via a namespace (and not attached):
 [1] Rcpp_0.11.5      magrittr_1.5     MASS_7.3-43      mnormt_1.5-1         munsell_0.4.2    colorspace_1.2-6 lattice_0.20-33  R6_2.0.1        
 [9] stringr_0.6.2    plyr_1.8.1       tools_3.2.2      parallel_3.2.2       grid_3.2.2       gtable_0.1.2     nlme_3.1-121     psych_1.5.8     
[17] DBI_0.3.1        htmltools_0.2.6  lazyeval_0.1.10  yaml_2.1.13      assertthat_0.1   digest_0.6.8     reshape2_1.4.1   rmarkdown_0.8.1 
[25] labeling_0.3     reshape_0.8.5    proto_0.3-10    

traceback()
35: grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y, 
    resolveHJust(x$just, x$hjust), resolveVJust(x$just, x$vjust), 
    x$rot, 0)
34: widthDetails.text(x)
33: widthDetails(x)
32: (function (x) 
{
    widthDetails(x)
})(list(label = expression(5 %*% 10^+5, 7.5 %*% 10^+5, 1 %*% 
    10^+6, 1.25 %*% 10^+6, 1.5 %*% 10^+6), x = 1, y =   c(0.0777214770341215, 
0.291044141334423, 0.504366805634725, 0.717689469935027, 0.931012134235329
), just = "centre", hjust = 1, vjust = 0.5, rot = 0, check.overlap = FALSE, 
    name = "axis.text.y.text.8056", gp = list(fontsize = 9.6, 
        col = "black", fontfamily = "", lineheight = 0.9, font = 1L), 
    vp = NULL))
31: grid.Call.graphics(L_setviewport, vp, TRUE)
30: push.vp.viewport(X[[i]], ...)

score 3 · Answer 1 · answered Jul 18 '17 at 20:48

I solved it by installing the library extrafont, installing a set of specific fonts and forcing ggplot to use only these fonts:

    require(extrafont)
    # need only do this once!
    font_import(pattern="[A/a]rial", prompt=FALSE)
    require(ggplot2)
    # extending the help file example
    df <- data.frame(gp = factor(rep(letters[1:3], each = 10)), y = rnorm(30))
    ds <- plyr::ddply(df, "gp", plyr::summarise, mean = mean(y), sd = sd(y))
    plotobj <- ggplot(df, aes(gp, y)) +
      geom_point() +
      geom_point(data = ds, aes(y = mean), colour = 'red', size = 3) + 
      theme(text=element_text(size=16, family="Arial"))
    print(plotobj)

Joost Keuskamp · Answer 2 · 2016-08-14T12:56:56.100

1

I experienced the same issue when trying to plot ggplot/grid output to the graph window in Rstudio. However, plotting to an external graphing device seems to work fine.

The external device of choice depends on your system, but the script below, paraphrased from this blog, works for most systems:

a = switch(tolower(Sys.info()["sysname"]),
               "darwin"  = "quartz",
               "linux"   = "x11",
               "windows" = "windows")
options("device" = a)
graphics.off()
rm(a)

and to switch back to using the Rstudio plot window:

options("device"="RStudioGD")
graphics.off()

Note that by switching, you lose any existing plots.

edited Aug 14 '16 at 12:56

answered Aug 14 '16 at 08:05

Joost Keuskamp

125
1
9

Links to potential solutions are always welcome but please add essential parts here in case link gets removed. – Nikolay Mihaylov Aug 14 '16 at 08:13
1

Added the required code so that the answer is now self-containg – Joost Keuskamp Aug 14 '16 at 13:01

score 0 · Answer 3 · answered Sep 13 '16 at 14:03

A lot of solutions for this particular error direct you to look under the hood of your computer but this error can also be caused by a scripting error in which R expects to match elements from two data structures but cannot.

For me the error was caused by calling a fairly complex graphing function (see below) that read an ordered character vector as well as a matrix whose row names were supposed to each match a value in the ordered character vector. The problem was that some of my values contained dashes in them and R's read.table() function translated those dashes to periods (Ex: "HLA-DOA" became "HLA.DOA").

I was using the ComplexHeatmap package with a call like this:

oncoPrint(mat, 
      get_type = function(x) strsplit(x, ";")[[1]],
      alter_fun_list = alter_fun_list, 
      col = col, 
      row_order = my_order,
      column_title = "OncoPrint",
      heatmap_legend_param = list(title = "Alternations", at = c("AMP", "HOMDEL", "MUT"), labels = c("Amplification", "Deep deletion", "Mutation"))
)

In this call:

mat was a matrix that had dashes swapped out for periods
my_order was a character vector containing the same values as the row names of matexcept the dashes remained
every other argument is essential to the call but irrelevant to this post

To help R find this elusive "polygon edge", I just edited my character vector with:

row_order <- gsub("\\.", "-", row_order)

If you've tried re-installing packages, restarting your computer and re-enabling fonts - maybe check and see if you've got some faulty character matching going on in your call.

score 0 · Answer 4 · answered Feb 22 '17 at 10:08

0

i tried to set the font of aes,returned the error info

the added words:

p <- p + theme(text = element_text(family = "宋体"))

when i tried to remove the setting,it's ok then.

answered Feb 22 '17 at 10:08

mlhu

1

For me too, but I really need that font family. Did you solve that problem with another way? – Ênio Rodrigues Feb 09 '19 at 20:20

score 0 · Answer 5 · answered Aug 25 '17 at 12:49

Actually, I have the same problem on my MAC and couldn't solve it on a regular base... Since it also happens like every 5th or 10th execution I decided to wrap the whole ggplot command into a trycatch call and execute it until it doesn't fail...

The code would looks like this

error_appeared <- FALSE
  repeat{
    tryCatch({ # we put everything into a try catch block, because sometimes we get an error
      gscat <- 
        ggplot() # my ggplot command which sometimes fail

      ggsave('file.pdf', gscat, width=8,height=8)
      plot(gscat)
    },
    error=function(e) {
      print('redo the ratioscatterplot.')
      error_appeared <- TRUE
    }
    )
    if(!error_appeared){
      break
    }
  }

Actually I figured out, only the drawing/plotting of the figure gives problems! Saving always works.

Maybe this is helping someone, since I couldn't find a solution which actually solves the whole thing!

Additional:
If somebody wants to play with the problem on a "reproducible example" the code below throws an average of 2 errors out of 20 within the loop.

library(scales)
library(ggplot2)
df <- data.frame(
    log2.Ratio.H.L.normalized.rev = c(2.53861265542646, 0.402176424979483, 0.438931541934545, 0.639695233399582, 0.230203013366421, 
                                      2.88223218956399, 1.23051046036618, 2.56554843533357, 0.265436896049098, 
                                      1.32866415755805, -0.92108963514092, 0.0976107966264223, -0.43048946484291, 
                                      -0.558665259531966, 4.13183638727079, 0.904580434921318, -0.0733780789564803, 
                                      -0.621932351219966, 1.48594198341242, -0.365611185917855, 1.21088754922081, 
                                      -2.3717583289898, 2.95160644380282, 3.71446534016249), 
    Intensity = c(5951600000, 2.4433e+10, 1.1659e+10, 2273600000, 6.852e+10, 9.8746e+10, 5701600000, 
                  1758500000, 987180000, 3.4167e+11, 1.5718e+10, 6.8888e+10, 5.5936e+10, 
                  8702900000, 1093500000, 4426200000, 1.3681e+11, 7.773e+09, 5860400000, 
                  1.2861e+12, 2017900000, 2061300000, 240520000, 1382700000), 
    my_label = c("RPL18", 
                 "hCG_2024613", "NOL7", "PRPF4B", "HIST1H2BC", "XRCC1", "C9orf30", 
                 "CABIN1", "MGC3731", "XRCC6", "RPL23", "RPL27", "RPL17", "RPL32", 
                 "XPC", "RPL15", "GNL3", "RPL29", "JOSD3", "PARP1", "DNAPTP6", 
                 "ORC2L", "NCL", "TARDBP"))

unlink("figures", recursive=TRUE)
if(!dir.exists('figures')) dir.create('figures')
for(i in 1:20) {
  error_appeared <- FALSE
  repeat{
    tryCatch({ # we put everything into a try catch block, because sometimes we get an error
      gscat <-
        ggplot(df, aes_string("log2.Ratio.H.L.normalized.rev", 'Intensity')) +
        geom_point(data=df[abs(df[["log2.Ratio.H.L.normalized.rev"]]) < 1,],
                   color='black', alpha=.3, na.rm=TRUE) +
        scale_y_log10(labels = scales::trans_format("log10", scales::math_format()))

      ggsave(file.path('figures', paste0('intensity_scatter_', i, '.pdf')),
             gscat, width=8, height=8)
      plot(gscat)
    },
    error=function(e) {
      # print(e)
      print(sprintf('%s redo the ratioscatterplot.', i))
      error_appeared <- TRUE
    }
    )
    if(!error_appeared){
      break
    }
  }
}

Error in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : polygon edge not found (new)

5 Answers5

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