[Gmod-help] Can I ask a question of Gbrowse2?

[Scott Cain]

Hello Jiantao,

What you are seeing is almost always a result of the config and the
data not matching.  I think your "group_on" setting is incorrect; it
is usually something like "group_on = display_name" or "group_on =
subject".  I don't think setting it equal to the name of the feature
type does anything.  If fixing that doesn't work, you could send a
sample of the GFF to the list.  Also, there is a section of the
tutorial that came with GBrowse that covers xyplots that might help
(look for "quantitative data" in the tutorial).

Scott


On Mon, Apr 23, 2012 at 8:14 PM, Jiantao Yu <joelyu.2003 at googlemail.com> wrote:
> Dear Sir/Madam,
>
> I highly appreciate the smart of GBrowse. When I tried to display the
> quantitative data, and set up the zoom with small values, such as 40Kbp, I
> got the picture as is attached (picture1.png). However, I perfer the blocks
> to locate on the same line, rather than being hierarchical. I mean, It would
> be better if the blocks are kept as they are in the zoom of 500Kbp (all of
> the blocks are at one line, shown in the picture2.png). Could you please
> tell me how to do this? Many thanks!
>
> BTW: my configure script is like this:
>
> [methySW_MSH1_1000K]
> feature         = methySW_MSH1_1000K
> glyph           = xyplot
> graph_type      = boxes
> fgcolor         = red
> bgcolor         = red
> height          = 80
> min_score       = 0
> max_score       = 1
> scale           = none
> group_on        = methySW_MSH1_1000K
> category        = Quantitative Data
> label           = 0
> key             = Methylation Profile - MSH1_dr_vs_Col0 (Sliding
> Windows:1000K-size)
>
>
> Best wishes,
> Jiantao



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research