Thanks, Jeff. I tried this previously by using a header in my data file
(and 'header=TRUE'), but for some reason, that did not seem to work.
Creating a 'names' vector as you suggested did solve the problem, though.
Thank you!
Loren
2015-03-24 23:19 GMT-04:00 Jeff Newmiller <jdnew...@dcn.davis.ca.us>:
> You MUST put all data you plan to refer to into a data frame when using
> ggplot. There are a couple of ways you could do this... the easiest is to
> put a header line in the data file with column names. Or, you can assign a
> vector of new names to the names of the data frame.
>
> names( hetshoms ) <- c( "chrom", "start.pos", "end.pos", "hets",
> "het_stat", "homs", "hom_stat", "indiv" )
> ---------------------------------------------------------------------------
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>
> On March 24, 2015 3:40:11 PM PDT, Loren <sacke...@colorado.edu> wrote:
> >Hello all,
> >
> >I am having a perplexing problem trying to use facet_wrap in ggplot,
> >with
> >both my real dataset and a simplified dummy dataset. I am trying to
> >plot
> >heterozygosity across the genome for multiple individuals, with each
> >chromosome shown separately.
> >
> >My dummy data:
> >chr1 123000 124000 2 0.00002 26 0.00026 indiv1
> >chr1 124000 125000 3 0.00003 12 0.00012 indiv1
> >chr1 125000 126000 1 0.00001 6 0.00006 indiv1
> >chr1 126000 126000 2 0.00002 14 0.00014 indiv1
> >chr2 123000 124000 6 0.00006 20 0.00020 indiv1
> >chr2 124000 125000 0 0.00000 12 0.00012 indiv1
> >chr1 123000 124000 2 0.00002 26 0.00026 indiv2
> >chr1 124000 125000 3 0.00003 12 0.00012 indiv2
> >chr1 125000 126000 1 0.00001 6 0.00006 indiv2
> >chr1 126000 126000 2 0.00002 14 0.00014 indiv2
> >chr2 123000 124000 6 0.00006 20 0.00020 indiv2
> >chr2 124000 125000 0 0.00000 12 0.00012 indiv2
> >
> >My code to read in the data:
> >hetshoms <- read.table("fakedata.txt", header=F)
> >
> >chrom <- hetshoms$V1
> >start.pos <- hetshoms$V2
> >end.pos <- hetshoms$V3
> >hets <- hetshoms$V4
> >het_stat <- hetshoms$V5
> >homs <- hetshoms$V6
> >hom_stat <- hetshoms$V7
> >indiv <- hetshoms$V8
> >
> >HetRatio <- hets/(hets+homs)
> >
> >When I try to plot the chromosomes separately in qplot, it works fine:
> >testplot <- qplot(start.pos, HetRatio, facets = chrom ~ .,
> >colour=chrom)
> >
> >But when I try an analogous thing in ggplot, it does not work.
> >The first part works fine:
> >testplot <- ggplot(hetshoms, aes(x=start.pos, y=HetRatio)) +
> >geom_point(aes(color=chrom, alpha=1/4))
> >
> >but when I try to add the facet_wrap:
> >testplot + facet_wrap(~chrom)
> >
> >This produces the following error (and no plot)
> >"Error en layout_base(data, vars, drop = drop) :
> > At least one layer must contain all variables used for facetting"
> >
> >I have tried adding an (as.formula(paste)) and directly calling
> >hetshoms$V1
> >but neither solves the problem.
> >
> >Can anyone please point out where I have gone wrong and how to fix my
> >code?
> >
> >Much appreciated,
> >Loren
> >
> >
> >
> >
> >
> >
> >--
> >View this message in context:
> >
> http://r.789695.n4.nabble.com/facets-work-in-qplot-but-facet-wrap-produces-an-error-in-ggplot-tp4705058.html
> >Sent from the R help mailing list archive at Nabble.com.
> >
> >______________________________________________
> >R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> >https://stat.ethz.ch/mailman/listinfo/r-help
> >PLEASE do read the posting guide
> >http://www.R-project.org/posting-guide.html
> >and provide commented, minimal, self-contained, reproducible code.
>
>
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