Question

ggbio - change transcript label sizes

0

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Kevin Blighe ★ 4.0k

@kevin

Last seen 26 days ago

Republic of Ireland

It seems next to impossible to change the size of the geom_text() labels with autoplot() in ggbio. For example, take the reproducible code:

require(ggbio)
require(GenomicRanges)
require(Mus.musculus)

p <- autoplot(
  Mus.musculus, # OrganismDb class
  which = GRanges("chr12", IRanges(116052334, 116929233)),
  columns = c("SYMBOL"),
  gap.geom = 'chevron')
p

The label sizes are too small. So, I figured that something like this would work:

p + geom_text(size = 16)

However, that doesn't change the size.

I also tried (before running autoplot()) to set defaults for geom_text(), but that neither works:

update_geom_defaults("text", list(colour = "black", size = 20))

I also tried to create a custom function and specify label.text.cex, but it neither works:

theme_tracks_custom <- function (bg = "#fffedb", alpha = 1, ...) {
  res <- theme_clear(grid.x.major = FALSE, ...)
  attr(res, "track.plot.color") <- sapply(bg, scales::alpha, alpha)
  attr(res, "track.bg.color") <- bg
  attr(res, "label.text.color") <- "white"
  attr(res, "label.bg.fill") <- "#a52a2a"
  attr(res, 'label.text.cex') <- 3
  res
}
p + theme_tracks_custom()

All of the autoplots that I have seen via Google Images have these small labels; so, I figured that nobody else neither found a way to change them.

One issue is that the global text size attribute for ggplot2's theme() is not carried through to geom_text(), which has its own text size attribute.

In the ideal situation, autoplot() would permit the user to specify the label size that is then passed to geom_text(), and also permit that check.overlap could be TRUE or FALSE

Kevin

ggbio annotation • 1.8k views

ADD COMMENT • link updated 2.6 years ago by chrisclarkson100 ▴ 50 • written 5.3 years ago by Kevin Blighe ★ 4.0k

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Personally I firstly got the gene locacations from a file that I had locally:

        gene_data=read.table('ensembl_genes.v87.grch37.txt',sep='\t',header=T,stringsAsFactors=F)
        gene_data=gene_data[gene_data$gene_name==gene_of_interest,]

and then I used the geom_alignment() command where I was able to specify label.size

        library(TxDb.Hsapiens.UCSC.hg19.knownGene)
        data(genesymbol, package = "biovizBase")
        wh=GRanges(paste0('chr',gene_data$chr_name), IRanges(gene_data$start_pos, gene_data$end_pos))
        from=findOverlaps(genesymbol,wh)@from
        p.txdb=ggplot()+geom_alignment(txdb,which= wh, names.expr =genesymbol$symbol[from],cds.rect.h = 0.1,label.size=5)

ADD REPLY • link 2.6 years ago chrisclarkson100 ▴ 50

score 1 · Answer 1 · 2019-08-24

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Michael Lawrence ★ 11k

@michael-lawrence-3846

Last seen 3.0 years ago

United States

The forthcoming version 1.33.2 supports a labels.size= argument for this purpose. Btw, you can always pass additional arguments that get passed down to different layers. Passing size= is problematic, because it also affects the lines. But you can pass check_overlap= without issues.