[R] Help required with png graphic production as text has shadows?

Wed Apr 14 00:39:27 CEST 2010

Hi Greg

Thank you, the wmf version looks much better in Word and prints out lovely. The file size is very large for the volcano plots, but the other graphs are smaller than the png ones.  I wasn't resizing the png's but I think word was definitely changing them.  I only have six volcano plots so hopefully word will manage when I convert them all.

Thanks again
Alice

-----Original Message-----
From: Greg Snow [mailto:Greg.Snow at imail.org]
Sent: Wednesday, 14 April 2010 1:59 a.m.
To: Alice Johnstone; r-help at R-project.org
Subject: RE: Help required with png graphic production as text has shadows?

Are you resizing the graphs at all?  This can cause the shadows/blur, it is best to create the graphs at the exact size that you will end up using them so that there is no resizing (though I would not trust word to not resize even if you tell it not to).  You may also want to try producing wmf files as they are vector based, but can be included in word and other ms products (but could suffer the same size issues as pdf).

When pdf files are much larger than png files, it is usually because you are plotting many points and there is much overplotting, if that is the case, then you may want to try some different types of plots, for example, boxplots, hexbin plots, sunflower plots, or others.

Hope this helps,

--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
greg.snow at imail.org
801.408.8111

> -----Original Message-----
> From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-
> project.org] On Behalf Of Alice Johnstone
> Sent: Monday, April 12, 2010 9:41 PM
> To: r-help at R-project.org
> Subject: [R] Help required with png graphic production as text has
> shadows?
>
> I have produced a series of graphs with the png command, however when I
> have finally printed these out the black text appears to have a colour
> shadow with blue or red on either side of the letter.
> I tried increasing my res to 1200 and this improved it somewhat, but
> the text is still not sharp and occassionally these "shadows" will
> still print.
>
> I initially thought this was an issue with the printer.. But I can
> produce a pdf image and it is sharp.  However as I have 50+ images I
> want to include in a word document the pdf files are much too large and
> was the reason I was using png.
>
> I am using an older version of R, but didn't want to upgrade as this
> may cause issues with my completed analyses and the potential changes
> to other functions.
>
> Can someone suggest what it is I have missed?
> Thank you very much.
>
> Alice Johnstone
>
> Example code:
> Png("volcano.png",units="cm",height=15,width=15,res=1200,pointsize=12)
> Volcano2(fit2.eb,coef=2,highlight=5,xlab="log fold change",ylab="log
> odds",pch=16,cex=0.5, main="Volcano Plot",xlim=c(-2,2))
> Dev.off()
>
>
> > sessionInfo()
> R version 2.8.0 (2008-10-20)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_New Zealand.1252;LC_CTYPE=English_New
> Zealand.1252;LC_MONETARY=English_New
> Zealand.1252;LC_NUMERIC=C;LC_TIME=English_New Zealand.1252
>
> attached base packages:
>  [1] grid      splines   tools     stats     graphics  grDevices utils
>  [8] datasets  methods   base
>
> other attached packages:
>  [1] affyQCReport_1.20.0       arrayQualityMetrics_1.8.1
>  [3] marray_1.20.0             beadarray_1.10.0
>  [5] hwriter_0.93              latticeExtra_0.5-4
>  [7] simpleaffy_2.18.0         affyPLM_1.18.0
>  [9] preprocessCore_1.4.0      RColorBrewer_1.0-2
> [11] vsn_3.8.0                 genefilter_1.22.0
> [13] survival_2.34-1           geneplotter_1.20.0
> [15] annotate_1.20.0           xtable_1.5-4
> [17] lattice_0.17-15           sma_0.5.15
> [19] rat2302probe_2.3.0        rat2302cdf_2.3.0
> [21] rat2302.db_2.2.5          RSQLite_0.7-1
> [23] DBI_0.2-4                 AnnotationDbi_1.4.0
> [25] MASS_7.2-44               gcrma_2.14.0
> [27] matchprobes_1.14.0        affy_1.20.0
> [29] Biobase_2.2.0             limma_2.16.2
> [31] gplots_2.6.0              gdata_2.4.2
> [33] gtools_2.5.0
>
> loaded via a namespace (and not attached):
> [1] affyio_1.10.0      KernSmooth_2.22-22
>
> P Think before you print
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