Unexpected error message
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Dennis Murphy
Jan 11, 2010, 9:16:20 AM1/11/10
to ggp...@googlegroups.com
Hi:
While responding to a post on R-help this morning, I used plyr and ggplot2 to do the bulk of the
work, but I kept getting an error message on each plot even though it rendered correctly on the
graphics device.
Here's the input data set I used, in dput form :)
> dput(spikelets2)
structure(list(cn = structure(c(4L, 3L, 5L, 2L, 3L, 6L, 5L, 6L,
4L, 2L, 1L, 1L, 3L, 2L, 1L, 6L, 5L, 2L, 5L, 1L, 4L, 4L, 3L, 6L
), .Label = c("Boomer", "Hereford", "Kranich", "Lans", "Loyal",
"Oakley"), class = "factor"), spl01 = c(1.8, 0.6, 1.1, 0.6, 0.3,
0.5, 1.6, 0.5, 1.4, 1.2, 0.3, 0.2, 0.3, 0.5, 0.3, 0.5, 0.9, 0.7,
0.7, 0.7, 1.9, 1.1, 0.5, 0.1), spl02 = c(3.1, 2.4, 2.7, 2.3,
2.5, 2.1, 3.3, 2.1, 3, 2.7, 2.5, 1.9, 1.1, 2.1, 0.8, 2.7, 2.6,
2.9, 2.3, 2, 3, 2.6, 1.3, 2), spl03 = c(3.5, 3.4, 3.6, 3.3, 3.6,
3.2, 3.9, 3.2, 3.3, 3.6, 3.1, 3, 2.9, 3.1, 2.8, 3.4, 3.6, 3.6,
3.5, 3.3, 3.7, 3.3, 2.9, 3.1), spl04 = c(3.8, 4.2, 3.7, 3.6,
4, 3.4, 4.2, 3.6, 3.8, 3.8, 3.8, 3.4, 3.5, 3.6, 3, 3.8, 3.8,
4, 3.7, 3.5, 3.8, 3.7, 3.8, 3.5), spl05 = c(3.8, 4.5, 4.1, 3.9,
4.4, 3.8, 4.3, 4, 3.9, 4, 3.9, 3.7, 3.9, 3.7, 3.6, 4, 3.8, 4,
3.9, 3.9, 3.9, 4.1, 3.8, 4.1), spl06 = c(4.1, 4.7, 4.4, 4, 4.5,
4.4, 4.4, 4, 4.3, 4, 4.4, 3.9, 4.3, 3.9, 3.7, 3.9, 4.4, 3.9,
3.8, 3.7, 4, 4, 4.3, 3.9), spl07 = c(4.2, 4.9, 4.4, 4.2, 4.3,
4.3, 4.4, 4.1, 4, 4.1, 4.1, 3.9, 4.4, 4, 3.8, 4.2, 4.2, 4, 4.2,
4, 3.9, 4.2, 4.3, 4.1), spl08 = c(4.3, 4.9, 4.6, 4.1, 4.8, 4.3,
4.6, 4.4, 4.3, 4.2, 4.2, 4, 4.4, 3.8, 4, 4.5, 4.4, 4, 4.1, 3.9,
4.3, 4.2, 4.4, 4.2), spl09 = c(4.4, 4.8, 4.3, 4.1, 4.7, 4.3,
4.6, 4.4, 4.3, 4.1, 4.3, 4, 4, 4, 3.8, 4.3, 4.2, 4, 4.1, 3.8,
4.1, 4.2, 4.4, 4.2), spl10 = c(4.5, 4.7, 4.5, 3.9, 4.6, 4.2,
4.5, 4.2, 4.3, 4.1, 4, 4, 4.2, 3.8, 3.5, 4.4, 3.9, 3.9, 4.1,
4, 4.1, 4, 4, 4.2), spl11 = c(4.2, 4.4, 4.3, 3.9, 4.4, 4.2, 4.3,
4.1, 4, 3.9, 4.2, 3.8, 4.2, 3.6, 3.3, 4, 3.8, 3.8, 4, 3.7, 4.1,
4.1, 4.3, 4.1), spl12 = c(4.1, 4.1, 4.1, 3.6, 4.3, 3.9, 4.3,
3.8, 4.1, 3.6, 4, 3.8, 4, 3.6, 3.2, 4, 4, 3.7, 4, 3.8, 3.8, 4.1,
3.9, 4), spl13 = c(3.9, 4.1, 3.8, 3.4, 4.1, 3.8, 4.2, 3.8, 4,
3.8, 3.8, 3.6, 3.9, 3.1, 3.2, 3.9, 3.4, 3, 3.4, 3.5, 3.8, 3.8,
3.6, 3.9), spl14 = c(3.8, 3.9, 3.7, 3.2, 4, 3.6, 4, 4, 4, 3.3,
3.7, 3.4, 3.8, 3, 2.9, 3.9, 3.7, 3, 3.6, 3.4, 3.9, 3.6, 3.4,
3.8)), .Names = c("cn", "spl01", "spl02", "spl03", "spl04", "spl05",
"spl06", "spl07", "spl08", "spl09", "spl10", "spl11", "spl12",
"spl13", "spl14"), row.names = c(1L, 2L, 3L, 6L, 7L, 8L, 9L,
11L, 13L, 14L, 15L, 17L, 21L, 22L, 24L, 25L, 26L, 28L, 30L, 31L,
33L, 34L, 35L, 36L), class = "data.frame")
Here's the code I used:
library(ggplot2)
spikes.long <- melt(spikelets2, id = 'cn')
# Pull out the numeric part of the var names
spikes.long$loc <- as.numeric(substring(spikes.long$variable, 4))
# Poster wanted to separate 'side', where odd was one side and even the other
spikes.long$side <- factor(2 - spikes.long$loc %% 2)
# remove the unnecessary variable term...
spikes.long$variable <- NULL
# Scatterplot by cultivar (cn), coded by color:
p <- qplot(loc, value, data = spikes.long, group = cn,
colour = side)
p + facet_grid(cn ~ .)
# Paired boxplots by side for each cultivar:
q <- ggplot(spikes.long, aes(side, value))
q + geom_boxplot() + facet_grid(~ cn)
# Scatterplot with smooths for each cultivar:
ggplot(spikes.long, aes(loc, value, colour = cn)) +
geom_point() + geom_smooth(se = FALSE)
In each of the three plots, I got the error message:
Error in recordGraphics(drawGTree(x), list(x = x), getNamespace("grid")) :
invalid graphics state
yet all three graphs rendered in the graphics device as expected. As this may
be a possible buglet, I thought I'd report it here.
> sessionInfo()
R version 2.10.1 Patched (2010-01-01 r50884)
i386-pc-mingw32
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] grid stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] ggplot2_0.8.5 digest_0.4.2 reshape_0.8.3 plyr_0.1.9
[5] proto_0.3-8 lattice_0.17-26
loaded via a namespace (and not attached):
[1] tools_2.10.1
Dennis
While responding to a post on R-help this morning, I used plyr and ggplot2 to do the bulk of the
work, but I kept getting an error message on each plot even though it rendered correctly on the
graphics device.
Here's the input data set I used, in dput form :)
> dput(spikelets2)
structure(list(cn = structure(c(4L, 3L, 5L, 2L, 3L, 6L, 5L, 6L,
4L, 2L, 1L, 1L, 3L, 2L, 1L, 6L, 5L, 2L, 5L, 1L, 4L, 4L, 3L, 6L
), .Label = c("Boomer", "Hereford", "Kranich", "Lans", "Loyal",
"Oakley"), class = "factor"), spl01 = c(1.8, 0.6, 1.1, 0.6, 0.3,
0.5, 1.6, 0.5, 1.4, 1.2, 0.3, 0.2, 0.3, 0.5, 0.3, 0.5, 0.9, 0.7,
0.7, 0.7, 1.9, 1.1, 0.5, 0.1), spl02 = c(3.1, 2.4, 2.7, 2.3,
2.5, 2.1, 3.3, 2.1, 3, 2.7, 2.5, 1.9, 1.1, 2.1, 0.8, 2.7, 2.6,
2.9, 2.3, 2, 3, 2.6, 1.3, 2), spl03 = c(3.5, 3.4, 3.6, 3.3, 3.6,
3.2, 3.9, 3.2, 3.3, 3.6, 3.1, 3, 2.9, 3.1, 2.8, 3.4, 3.6, 3.6,
3.5, 3.3, 3.7, 3.3, 2.9, 3.1), spl04 = c(3.8, 4.2, 3.7, 3.6,
4, 3.4, 4.2, 3.6, 3.8, 3.8, 3.8, 3.4, 3.5, 3.6, 3, 3.8, 3.8,
4, 3.7, 3.5, 3.8, 3.7, 3.8, 3.5), spl05 = c(3.8, 4.5, 4.1, 3.9,
4.4, 3.8, 4.3, 4, 3.9, 4, 3.9, 3.7, 3.9, 3.7, 3.6, 4, 3.8, 4,
3.9, 3.9, 3.9, 4.1, 3.8, 4.1), spl06 = c(4.1, 4.7, 4.4, 4, 4.5,
4.4, 4.4, 4, 4.3, 4, 4.4, 3.9, 4.3, 3.9, 3.7, 3.9, 4.4, 3.9,
3.8, 3.7, 4, 4, 4.3, 3.9), spl07 = c(4.2, 4.9, 4.4, 4.2, 4.3,
4.3, 4.4, 4.1, 4, 4.1, 4.1, 3.9, 4.4, 4, 3.8, 4.2, 4.2, 4, 4.2,
4, 3.9, 4.2, 4.3, 4.1), spl08 = c(4.3, 4.9, 4.6, 4.1, 4.8, 4.3,
4.6, 4.4, 4.3, 4.2, 4.2, 4, 4.4, 3.8, 4, 4.5, 4.4, 4, 4.1, 3.9,
4.3, 4.2, 4.4, 4.2), spl09 = c(4.4, 4.8, 4.3, 4.1, 4.7, 4.3,
4.6, 4.4, 4.3, 4.1, 4.3, 4, 4, 4, 3.8, 4.3, 4.2, 4, 4.1, 3.8,
4.1, 4.2, 4.4, 4.2), spl10 = c(4.5, 4.7, 4.5, 3.9, 4.6, 4.2,
4.5, 4.2, 4.3, 4.1, 4, 4, 4.2, 3.8, 3.5, 4.4, 3.9, 3.9, 4.1,
4, 4.1, 4, 4, 4.2), spl11 = c(4.2, 4.4, 4.3, 3.9, 4.4, 4.2, 4.3,
4.1, 4, 3.9, 4.2, 3.8, 4.2, 3.6, 3.3, 4, 3.8, 3.8, 4, 3.7, 4.1,
4.1, 4.3, 4.1), spl12 = c(4.1, 4.1, 4.1, 3.6, 4.3, 3.9, 4.3,
3.8, 4.1, 3.6, 4, 3.8, 4, 3.6, 3.2, 4, 4, 3.7, 4, 3.8, 3.8, 4.1,
3.9, 4), spl13 = c(3.9, 4.1, 3.8, 3.4, 4.1, 3.8, 4.2, 3.8, 4,
3.8, 3.8, 3.6, 3.9, 3.1, 3.2, 3.9, 3.4, 3, 3.4, 3.5, 3.8, 3.8,
3.6, 3.9), spl14 = c(3.8, 3.9, 3.7, 3.2, 4, 3.6, 4, 4, 4, 3.3,
3.7, 3.4, 3.8, 3, 2.9, 3.9, 3.7, 3, 3.6, 3.4, 3.9, 3.6, 3.4,
3.8)), .Names = c("cn", "spl01", "spl02", "spl03", "spl04", "spl05",
"spl06", "spl07", "spl08", "spl09", "spl10", "spl11", "spl12",
"spl13", "spl14"), row.names = c(1L, 2L, 3L, 6L, 7L, 8L, 9L,
11L, 13L, 14L, 15L, 17L, 21L, 22L, 24L, 25L, 26L, 28L, 30L, 31L,
33L, 34L, 35L, 36L), class = "data.frame")
Here's the code I used:
library(ggplot2)
spikes.long <- melt(spikelets2, id = 'cn')
# Pull out the numeric part of the var names
spikes.long$loc <- as.numeric(substring(spikes.long$variable, 4))
# Poster wanted to separate 'side', where odd was one side and even the other
spikes.long$side <- factor(2 - spikes.long$loc %% 2)
# remove the unnecessary variable term...
spikes.long$variable <- NULL
# Scatterplot by cultivar (cn), coded by color:
p <- qplot(loc, value, data = spikes.long, group = cn,
colour = side)
p + facet_grid(cn ~ .)
# Paired boxplots by side for each cultivar:
q <- ggplot(spikes.long, aes(side, value))
q + geom_boxplot() + facet_grid(~ cn)
# Scatterplot with smooths for each cultivar:
ggplot(spikes.long, aes(loc, value, colour = cn)) +
geom_point() + geom_smooth(se = FALSE)
In each of the three plots, I got the error message:
Error in recordGraphics(drawGTree(x), list(x = x), getNamespace("grid")) :
invalid graphics state
yet all three graphs rendered in the graphics device as expected. As this may
be a possible buglet, I thought I'd report it here.
> sessionInfo()
R version 2.10.1 Patched (2010-01-01 r50884)
i386-pc-mingw32
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] grid stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] ggplot2_0.8.5 digest_0.4.2 reshape_0.8.3 plyr_0.1.9
[5] proto_0.3-8 lattice_0.17-26
loaded via a namespace (and not attached):
[1] tools_2.10.1
Dennis
hadley wickham
Jan 11, 2010, 9:29:44 AM1/11/10
to Dennis Murphy, ggp...@googlegroups.com
Hi Dennis,
Whenever I've encountered this error in the past, it's gone away after
I restarted R. Does that fix it for you?
Hadley
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