[R] facets work in qplot but facet_wrap produces an error in ggplot

[Loren Cassin Sackett]

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 <jdnewmil at 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" )
> ---------------------------------------------------------------------------
> Jeff Newmiller                        The     .....       .....  Go Live...
> DCN:<jdnewmil at dcn.davis.ca.us>        Basics: ##.#.       ##.#.  Live
> Go...
>                                       Live:   OO#.. Dead: OO#..  Playing
> Research Engineer (Solar/Batteries            O.O#.       #.O#.  with
> /Software/Embedded Controllers)               .OO#.       .OO#.  rocks...1k
> ---------------------------------------------------------------------------
> Sent from my phone. Please excuse my brevity.
>
> On March 24, 2015 3:40:11 PM PDT, Loren <sackettl at 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 at 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.
>
>

	[[alternative HTML version deleted]]