Question

Gviz: Plot only exons?

2

Entering edit mode

stianlagstad ▴ 90

@stianlagstad-9723

Last seen 5.7 years ago

Is there an easy way to plot only exons, not introns? Consider:

gr <- GenomicRanges::GRanges(17, IRanges(start = c(5,20,30,50), end = c(10,25,40,60)))
mcols(gr)$transcript <- "test"
tr <- Gviz::GeneRegionTrack(gr)
Gviz::plotTracks(tr)

Which plots this:

How could I plot this without the introns? With the exons "smacked together", so to speak? I was imagining something like this:

Gviz::plotTracks(
  tr,
  ranges = gr
)

gviz • 3.0k views

ADD COMMENT • link 9.6 years ago stianlagstad ▴ 90

1

Entering edit mode

florian.hahne@novartis.com ★ 1.6k

@florianhahnenovartiscom-3784

Last seen 7.2 years ago

Switzerland

That is not possible since it would essentially imply a non-continuous x axis. One of the fundamental concepts of Gviz is that every track shares the same x axis of genomic coordinates. You are asking for a plot along transcript coordinates.

ADD COMMENT • link 9.6 years ago florian.hahne@novartis.com ★ 1.6k

0

Entering edit mode

florian.hahne@novartis.com ★ 1.6k

@florianhahnenovartiscom-3784

Last seen 7.2 years ago

Switzerland

Please take a look at section 4.5 in the vignette. The parameter you want to look at is called collapseTranscripts.

Florian

ADD COMMENT • link 9.6 years ago florian.hahne@novartis.com ★ 1.6k

0

Entering edit mode

I'm sorry, I mean "smacked together" horizontally, not vertically. As if there were no spaces in between the exons in my example plot. Is that possible? Maybe this can help explain: drawing.

My end goal is a plot of the transcript (but only exons) with coverage, using GeneRegionTrack and AlignmentsTrack.

ADD REPLY • link 9.6 years ago stianlagstad ▴ 90

score 1 · Accepted Answer · 2016-04-02

1

Entering edit mode

stianlagstad ▴ 90

@stianlagstad-9723

Last seen 5.7 years ago

For others that might be interested, I solved this by shifting all exons to the left. A full example:

gr <- GenomicRanges::GRanges(17, IRanges(start = c(5,20,30,50), end = c(10,25,40,60)))
mcols(gr)$transcript <- "test"
tr <- Gviz::GeneRegionTrack(gr)
Gviz::plotTracks(tr)

This produces the plot in my original question:

Now let's remove spaces between exons:

# Move the first exon down to position 1, and then remove the spaces between all the others. Effectively pushing all exons to the leftmost edge.
for (i in 1:length(gr)) {
  if (i == 1) {
    gr[i] <- IRanges::shift(gr[i], shift = 1-start(gr[i]))
  } else {
    shiftDownBy <- -(start(gr[i])-end(gr[i-1]))+1
    gr[i] <- IRanges::shift(gr[i], shift = shiftDownBy)
  }
}

tr <- Gviz::GeneRegionTrack(gr)
Gviz::plotTracks(tr)

This produces the following plot:

ADD COMMENT • link 9.6 years ago stianlagstad ▴ 90

0

Entering edit mode

Hey, I just want to comment a convenient way to do this, for anyone who might look at it. It can be done with:

exon <- exonsBy(TxDb.Hsapiens.UCSC.hg19.knownGene, 'tx')[42]
exon_mapped <- GenomicFeatures::mapToTranscripts(exon[[1]],exon)

And this is just the intended transformation of the exons.

exon

GRangesList object of length 1:
$42 
GRanges object with 13 ranges and 3 metadata columns:
       seqnames           ranges strand |   exon_id   exon_name exon_rank
          <Rle>        <IRanges>  <Rle> | <integer> <character> <integer>
   [1]     chr1 [861302, 861393]      + |        36        <NA>         1
   [2]     chr1 [865535, 865716]      + |        37        <NA>         2
   [3]     chr1 [866419, 866469]      + |        38        <NA>         3
   [4]     chr1 [871152, 871276]      + |        39        <NA>         4
   [5]     chr1 [874420, 874509]      + |        42        <NA>         5
   ...      ...              ...    ... .       ...         ...       ...
   [9]     chr1 [877790, 877868]      + |        51        <NA>         9
  [10]     chr1 [877939, 878438]      + |        53        <NA>        10
  [11]     chr1 [878633, 878757]      + |        54        <NA>        11
  [12]     chr1 [879078, 879188]      + |        55        <NA>        12
  [13]     chr1 [879288, 879961]      + |        58        <NA>        13

-------
seqinfo: 93 sequences (1 circular) from hg19 genome

exon_mapped

GRanges object with 13 ranges and 2 metadata columns:
       seqnames       ranges strand |     xHits transcriptsHits
          <Rle>    <IRanges>  <Rle> | <integer>       <integer>
   [1]       42   [  1,  92]      + |         1               1
   [2]       42   [ 93, 274]      + |         2               1
   [3]       42   [275, 325]      + |         3               1
   [4]       42   [326, 450]      + |         4               1
   [5]       42   [451, 540]      + |         5               1
   ...      ...          ...    ... .       ...             ...
   [9]       42 [ 930, 1008]      + |         9               1
  [10]       42 [1009, 1508]      + |        10               1
  [11]       42 [1509, 1633]      + |        11               1
  [12]       42 [1634, 1744]      + |        12               1
  [13]       42 [1745, 2418]      + |        13               1
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths

ADD REPLY • link 9.2 years ago Marlin ▴ 20