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

[Jeff Newmiller]

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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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.
>
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