Hi Vince,
Martin forwarded your message about allowing more control over the show
method. There are now 2 global options that control the number of lines
displayed in the head and tail:
showHeadLines
showTailLines
When set, these options affect GenomicRanges, GappedAlignments, Ranges
and XStringSet objects. Essentially the objects that display with a
"..." separating head and tail. Changes are in the following versions:
GenomicRanges (1.11.43)
IRanges (1.17.42)
Biostrings (2.27.14)
The default number of head/tail lines is now 5:
gr <- GRanges("chr1", IRanges(1:100, width=5))
> gr
GRanges with 100 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chr1 [1, 5] *
[2] chr1 [2, 6] *
[3] chr1 [3, 7] *
[4] chr1 [4, 8] *
[5] chr1 [5, 9] *
... ... ... ...
[96] chr1 [ 96, 100] *
[97] chr1 [ 97, 101] *
[98] chr1 [ 98, 102] *
[99] chr1 [ 99, 103] *
[100] chr1 [100, 104] *
Modify head and tail:
options("showHeadLines"=3)
options("showTailLines"=1)
> gr
GRanges with 100 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chr1 [1, 5] *
[2] chr1 [2, 6] *
[3] chr1 [3, 7] *
... ... ... ...
[100] chr1 [100, 104] *
Back to defaults:
options("showHeadLines"=NULL)
options("showTailLines"=NULL)
These options are not tied to a particular package or object type. Any
author/user can make a show method aware of these, similar to the global
option "width".
Let me know if you run into trouble or if this implementation isn't what
you were after.
Valerie
-------- Original Message --------
Subject: [biocore] show for GRanges
Date: Wed, 20 Mar 2013 07:15:35 -0400
From: Vincent Carey <st...@channing.harvard.edu>
To: <bioc...@stat.math.ethz.ch>
GenomicRanges:::makePrettyMatrixForCompactPrinting
function (x, makeNakedMat.FUN)
{
lx <- length(x)
nms <- names(x)
if (lx < 20L) {
ans <- makeNakedMat.FUN(x)
if (!is.null(nms)) {
ans_rownames <- nms
}
else if (lx == 0L) {
ans_rownames <- character(0)
}
else {
ans_rownames <- paste0("[", seq_len(lx), "]")
}
}
else {
top_idx <- 1:9
bottom_idx <- (lx - 8L):lx
...
would it be useful to have this constant (9) and its implied companion
settable by option?
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