i think this is what i was hoping for, thanks

On Wed, Mar 27, 2013 at 4:21 PM, Valerie Obenchain <vobencha@fhcrc.org>wrote:

> 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 <stvjc@channing.harvard.edu>
> To: <biocore@stat.math.ethz.ch>
>
>  GenomicRanges:::**makePrettyMatrixForCompactPrin**ting
>>
> 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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>
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>
>
>
>

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