facets work in qplot but facet_wrap produces an error in ggplot

Question

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))

but when I try to add the facet_wrap:

testplot + facet_wrap(~chrom)

This produces the following error

"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)) to facet_wrap() and directly calling hetshoms$V1 but neither solves the problem.

I would appreciate any suggestions for how to correct my code.

Answer 1

To replicate qplot output we need facet_grid(chrom~.)

#data
hetshoms <- read.table(text="
                       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
                       ",header=FALSE)
#calculate HetRatio
colnames(hetshoms) <- c("chrom","start.pos","end.pos","hets","hets_stat","homs","homs_stat","indiv")
hetshoms$HetRatio <- hetshoms$hets/(hetshoms$hets+hetshoms$homs)

#plot
ggplot(hetshoms, aes(x=start.pos, y=HetRatio)) + 
  geom_point(aes(color=chrom)) +
  facet_grid(chrom~.)