ggplot2 facet_wrap plotting points, segments, text in every facet

Question

This is the same issue that has been posted here and here. However, the solutions there do not appear to be working.

I have example data here:

library("ggplot2")
library("ggrepel")

# order of the chromosomes
chrom_order <- c("chr1", "chr2", "chr3", "chr4", "chr5", 
    "chr6", "chr7", "chr8", "chr9", "chr10", "chr11", "chr12", 
    "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", 
    "chr20", "chr21", "chr22", "chrX", "chrY", "chrM")

# data frame of chromosome sizes
chrom_sizes <- structure(list(chrom = structure(c(25L, 1L, 2L, 3L, 4L, 5L, 6L, 
7L, 8L, 9L, 10L, 11L, 12L, 13L, 14L, 15L, 16L, 17L, 18L, 19L, 
20L, 21L, 22L, 23L, 24L), .Label = c("chr1", "chr2", "chr3", 
"chr4", "chr5", "chr6", "chr7", "chr8", "chr9", "chr10", "chr11", 
"chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", 
"chr19", "chr20", "chr21", "chr22", "chrX", "chrY", "chrM"), class = "factor"), 
    size = c(16571L, 249250621L, 243199373L, 198022430L, 191154276L, 
    180915260L, 171115067L, 159138663L, 146364022L, 141213431L, 
    135534747L, 135006516L, 133851895L, 115169878L, 107349540L, 
    102531392L, 90354753L, 81195210L, 78077248L, 59128983L, 63025520L, 
    48129895L, 51304566L, 155270560L, 59373566L)), .Names = c("chrom", 
"size"), row.names = c(NA, -25L), class = "data.frame")

# regions to label 
sample_cns <- structure(list(gene = c("AFF1", "ANKRD24", "ARID1A", "CDH23", 
"CDH23-AS1", "CHD5", "CTC-554D6.1", "DCC", "DOT1L", "FLT4"), 
    chromosome = structure(c(4L, 19L, 1L, 10L, 10L, 1L, 5L, 18L, 
    19L, 5L), .Label = c("chr1", "chr2", "chr3", "chr4", "chr5", 
    "chr6", "chr7", "chr8", "chr9", "chr10", "chr11", "chr12", 
    "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", 
    "chr20", "chr21", "chr22", "chrX", "chrY", "chrM"), class = "factor"), 
    start = c(87869685L, 4183350L, 27022894L, 73199588L, 73269838L, 
    6166339L, 112162804L, 49867157L, 2164183L, 180030191L), end = c(88056853L, 
    4224502L, 27107247L, 73575035L, 73270969L, 6240083L, 112179823L, 
    51057023L, 2229791L, 180076545L), log2 = c(-1.01818, -0.517649, 
    -1.14236, -0.527636, -0.527636, -1.14236, -0.438652, -0.741936, 
    -0.517649, -0.438652), depth = c(466, 155.508, 304.046, 720.821, 
    1096.83, 253.5, 871.9, 626.033, 160.42, 567.457), weight = c(17.8883, 
    17.0764, 23.296, 52.0485, 1.77117, 25.5399, 22.9053, 19.3831, 
    26.4509, 19.0353), cn = c(1L, 1L, 0L, 1L, 1L, 0L, 1L, 1L, 
    1L, 1L), probes = c(587L, 462L, 1023L, 922L, 922L, 1023L, 
    753L, 465L, 462L, 753L)), .Names = c("gene", "chromosome", 
"start", "end", "log2", "depth", "weight", "cn", "probes"), row.names = c(NA, 
10L), class = "data.frame")

# base plot
p <- ggplot(data = chrom_sizes, aes(x = chrom, y = size)) + geom_bar(stat="identity", fill="grey90") + coord_flip() +
    theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(), panel.background = element_blank(), axis.line = element_line(colour = "black")) + facet_wrap( ~ chrom, scales = "free_y")

print(p)

Which produces the desired base plot shown here:

However, I next want to annotate the plot with the entries in the sample_cns dataframe. But when I try to add them, every value gets placed in every plot:

# places labels and lines on every facet
p + geom_segment(data = sample_cns, aes(x = chromosome, xend = chromosome, y = start, yend = end, colour = cn), size=13) + 
    geom_text_repel(data = sample_cns, aes(x = chromosome, y = start, label = gene))

As per the referrenced questions, I tried passing a single-entry dataframe to add the annotations one at a time. However, this still results in the data being plotted in every facet. The same happens when I try to re-create the dataframe from scratch and pass it instead, and it happens with text, line segments, and points being passed:

# first row only; still adds to every facet
df <- sample_cns[1, ]
p + geom_segment(data = df, aes(x = chromosome, xend = chromosome, y = start, yend = end, colour = cn), size=13) + 
    geom_text_repel(data = df, aes(x = chromosome, y = start, label = gene))


# make new df from scratch
df <- data.frame(gene = "AFF1", chromosome = factor("chr4", levels = chrom_order), start = 87869685, end = 88056853, cn = 1)
p + geom_segment(data = df, aes(x = chromosome, xend = chromosome, y = start, yend = end, colour = cn), size=13) + 
    geom_text_repel(data = df, aes(x = chromosome, y = start, label = gene))

p + geom_point(data = df, aes(x = chromosome, y = start, colour = cn), size=13)

Any ideas? What am I missing? Why does this same technique work in those other code samples, but not here?

Also I am using R version 3.2.3, and ggplot2 version 2.2.1

You are faceting by a column called `chrom`, `facet_wrap( ~ chrom)`. Your data frame for the labels, `cns`, does not have a column called `chrom`, so it is part of every facet. If you want labels to appear only on certain facets, and a column called `chrom` to `cns` that show which facet each label should be in. — Gregor Thomas, Aug 22 '17 at 22:03
One other note - I'd encourage you to make *minimal* examples in the future. You'll get quicker help with more approachable questions. You did a nice job sharing reproducible data, but if you had subset your data/plots down to just 2 or 3 facets the problem is still illustrated, but it makes your question look so much shorter that it will get help more quickly. — Gregor Thomas, Aug 23 '17 at 16:01

score 3 · Accepted Answer · answered Aug 23 '17 at 15:55

You have to tell ggplot which facet each labels go in. This means the data frame containing the labels needs to have the column(s) you facet on.

You are faceting by a column called chrom, facet_wrap( ~ chrom). Your data frame for the labels, cns, does not have a column called chrom. Add a column called chrom to cns that show which facet each label should be in.

ggplot2 facet_wrap plotting points, segments, text in every facet

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