No subject
Mon Mar 12 08:12:10 EDT 2012
continuous, you see, no gaps.
ii) I tried to gave all of the entries, located in the same chromosome, the
same IDs. This method did solve the problem, i.e. the boxes are fixed on
the same line. However, as you told in the last email, this led to a
problem, the performance became poor, and the gbrowse couldn't display the
curves sometimes, if there were lots of boxes which had the same IDs.
So I think the best way would be, can we find a way to display them on the
same line, while no limitation of their IDs?
iii) The reason that there is no title of some tracks, is not very clear.
However, when I changed the 'key' with some other words, the title can be
normally displayed. So this has not been a problem now.
Thanks very much for your patience.
Regards
Jiantao
2012/4/27 Scott Cain <scott at scottcain.net>
> Jiantao,
>
> Please always respond to the mailing list too (reply-all).
>
> No, you absolutely should not try to group these features by ID. That
> will result in the database loader putting all of the features
> together into one gigantic object in the database, and your
> performance will be very poor (GBrowse may stop rendering those tracks
> altogether). I'll try to reproduce your problem now.
>
> Scott
>
>
> On Tue, Apr 24, 2012 at 12:23 PM, Jiantao Yu <joelyu.2003 at googlemail.com>
> wrote:
> > Hi Scott,
> >
> > I still got the picture like the attahed file, although I changed
> > group_on=subject. Do you think I need to add 'ID=1' for all of the
> entries
> > in .gff3 file, in order to let them displayed on the single line?
> >
> > GBrowse may group entries according to their IDs? However, when I did
> this,
> > I can't get the specific balloon for each position/block in the picture,
> you
> > see, I just got a very general description in the balloon, such as this
> > position is from 1..30Mbp, which is not what I want to get.
> >
> > Thanks a lot.
> >
> >
> > Jiantao
> >
> > 2012/4/24 Scott Cain <scott at scottcain.net>
> >>
> >> Hi Jiantao,
> >>
> >> "subject" should work for your data. Did you try panning or zooming
> >> to another location to make sure GBrowse wasn't using a cached image
> >> (just reloading isn't enough)?
> >>
> >> Scott
> >>
> >>
> >> On Tue, Apr 24, 2012 at 11:44 AM, Jiantao Yu <
> joelyu.2003 at googlemail.com>
> >> wrote:
> >> > Hi Scott,
> >> >
> >> > Really thanks for you quick reply. I tried to change group-on in the
> >> > config
> >> > file into
> >> > group_on = display_name or
> >> > group_on =subject
> >> >
> >> > However, it seems no effect. I have attached the .gff3 and .conf
> files,
> >> > and
> >> > the configure script for the .gff3 data starts at the line of No.1365.
> >> >
> >> > Could you please have a look at them? Thanks very much.
> >> >
> >> > Best regards
> >> > Jiantao
> >> >
> >> >
> >> > 2012/4/24 Scott Cain <scott at scottcain.net>
> >> >>
> >> >> 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
> >> >
> >> >
> >>
> >>
> >>
> >> --
> >> ------------------------------------------------------------------------
> >> Scott Cain, Ph. D. scott at scottcain
> >> dot net
> >> GMOD Coordinator (http://gmod.org/) 216-392-3087
> >> Ontario Institute for Cancer Research
> >
> >
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D. scott at scottcain
> dot net
> GMOD Coordinator (http://gmod.org/) 216-392-3087
> Ontario Institute for Cancer Research
>
--f46d043c093ea9bb2804beab6148
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable
<div class=3D"gmail_extra">Hi Scott,<br><br>Thanks for reply. I found some =
answers for the three questions:<br>i) The reason that the boxes are displa=
yed in hierarchy, I think, would be the boxes are too close. For example, i=
f the start and end positions are like this:<br>
<br>1=A0=A0=A0 10 =A0=A0 0.8=A0=A0=A0 .=A0=A0=A0 .=A0=A0=A0 <br>11 =A0=A0 2=
0 =A0=A0 0.7 =A0=A0 .=A0=A0=A0 .=A0=A0=A0 <br>21 =A0=A0 30 =A0=A0 0.7 =A0=
=A0 .=A0=A0=A0 .=A0=A0=A0 <br>...<br><br>They would probably be in hierarch=
y when I zoom in. However, if I changed the positions like this (+ or - 4):=
<br>
<br>4=A0=A0=A0 7 =A0=A0 0.8=A0=A0=A0 .=A0=A0=A0 .=A0=A0=A0 <br>
14 =A0=A0 17 =A0=A0 0.7 =A0=A0 .=A0=A0=A0 .=A0=A0=A0 <br>
24 =A0=A0 27 =A0=A0 0.7 =A0=A0 .=A0=A0=A0 .=A0=A0=A0 <br><br>They would be =
on the same line. However, in the case of my data, it is hard to determine =
what values should be added or subtracted. For example, I used 30 as the va=
lue, it wasn't enough, I mean, 30 is not enough to ensure all of the bo=
xes are on the same line for every scale of zooming in or zooming out. <br>
<br>From another point, I really hope the width of boxes are still kept con=
tinuous, you see, no gaps.<br><br>ii) I tried to gave all of the entries, l=
ocated in the same chromosome, the same IDs. This method did solve the prob=
lem, i.e. the boxes are fixed on the same line. However, as you told in the=
last email, this led to a problem, the performance became poor, and the gb=
rowse couldn't display the curves sometimes, if there were lots of boxe=
s which had the same IDs.<br>
<br>So I think the best way would be, can we find a way to display them on =
the same line, while no limitation of their IDs?<br><br>iii) The reason tha=
t there is no title of some tracks, is not very clear. However, when I chan=
ged the 'key' with some other words, the title can be normally disp=
layed. So this has not been a problem now.<br>
<br>Thanks very much for your patience.<br><br>Regards<br>Jiantao<br><br><b=
r><div class=3D"gmail_quote">2012/4/27 Scott Cain <span dir=3D"ltr"><<a =
href=3D"mailto:scott at scottcain.net" target=3D"_blank">scott at scottcain.net</=
a>></span><br>
<blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1p=
x #ccc solid;padding-left:1ex">Jiantao,<br>
<br>
Please always respond to the mailing list too (reply-all).<br>
<br>
No, you absolutely should not try to group these features by ID. =A0That<br=
>
will result in the database loader putting all of the features<br>
together into one gigantic object in the database, and your<br>
performance will be very poor (GBrowse may stop rendering those tracks<br>
altogether). =A0I'll try to reproduce your problem now.<br>
<span class=3D"HOEnZb"><font color=3D"#888888"><br>
Scott<br>
</font></span><div class=3D"HOEnZb"><div class=3D"h5"><br>
<br>
On Tue, Apr 24, 2012 at 12:23 PM, Jiantao Yu <<a href=3D"mailto:joelyu.2=
003 at googlemail.com">joelyu.2003 at googlemail.com</a>> wrote:<br>
> Hi Scott,<br>
><br>
> I still got the picture like the attahed file, although I changed<br>
> group_on=3Dsubject. Do you think I need to add 'ID=3D1' for al=
l of the entries<br>
> in .gff3 file, in order to let them displayed on the single line?<br>
><br>
> GBrowse may group entries according to their IDs? However, when I did =
this,<br>
> I can't get the specific balloon for each position/block in the pi=
cture, you<br>
> see, I just got a very general description in the balloon, such as thi=
s<br>
> position is from 1..30Mbp, which is not what I want to get.<br>
><br>
> Thanks a lot.<br>
><br>
><br>
> Jiantao<br>
><br>
> 2012/4/24 Scott Cain <<a href=3D"mailto:scott at scottcain.net">scott@=
scottcain.net</a>><br>
>><br>
>> Hi Jiantao,<br>
>><br>
>> "subject" should work for your data. =A0Did you try pann=
ing or zooming<br>
>> to another location to make sure GBrowse wasn't using a cached=
image<br>
>> (just reloading isn't enough)?<br>
>><br>
>> Scott<br>
>><br>
>><br>
>> On Tue, Apr 24, 2012 at 11:44 AM, Jiantao Yu <<a href=3D"mailto=
:joelyu.2003 at googlemail.com">joelyu.2003 at googlemail.com</a>><br>
>> wrote:<br>
>> > Hi Scott,<br>
>> ><br>
>> > Really thanks for you quick reply. I tried to change group-on=
in the<br>
>> > config<br>
>> > file into<br>
>> > group_on =3D display_name=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=
=A0=A0=A0=A0=A0=A0=A0 or<br>
>> > group_on =3Dsubject<br>
>> ><br>
>> > However, it seems no effect. I have attached the .gff3 and .c=
onf files,<br>
>> > and<br>
>> > the configure script for the .gff3 data starts at the line of=
No.1365.<br>
>> ><br>
>> > Could you please have a look at them? Thanks very much.<br>
>> ><br>
>> > Best regards<br>
>> > Jiantao<br>
>> ><br>
>> ><br>
>> > 2012/4/24 Scott Cain <<a href=3D"mailto:scott at scottcain.ne=
t">scott at scottcain.net</a>><br>
>> >><br>
>> >> Hello Jiantao,<br>
>> >><br>
>> >> What you are seeing is almost always a result of the conf=
ig and the<br>
>> >> data not matching. =A0I think your "group_on" s=
etting is incorrect; it<br>
>> >> is usually something like "group_on =3D display_name=
" or "group_on =3D<br>
>> >> subject". =A0I don't think setting it equal to t=
he name of the feature<br>
>> >> type does anything. =A0If fixing that doesn't work, y=
ou could send a<br>
>> >> sample of the GFF to the list. =A0Also, there is a sectio=
n of the<br>
>> >> tutorial that came with GBrowse that covers xyplots that =
might help<br>
>> >> (look for "quantitative data" in the tutorial).=
<br>
>> >><br>
>> >> Scott<br>
>> >><br>
>> >><br>
>> >> On Mon, Apr 23, 2012 at 8:14 PM, Jiantao Yu<br>
>> >> <<a href=3D"mailto:joelyu.2003 at googlemail.com">joelyu.=
2003 at googlemail.com</a>><br>
>> >> wrote:<br>
>> >> > Dear Sir/Madam,<br>
>> >> ><br>
>> >> > I highly appreciate the smart of GBrowse. When I tri=
ed to display the<br>
>> >> > quantitative data, and set up the zoom with small va=
lues, such as<br>
>> >> > 40Kbp,<br>
>> >> > I<br>
>> >> > got the picture as is attached (picture1.png). Howev=
er, I perfer the<br>
>> >> > blocks<br>
>> >> > to locate on the same line, rather than being hierar=
chical. I mean,<br>
>> >> > It<br>
>> >> > would<br>
>> >> > be better if the blocks are kept as they are in the =
zoom of 500Kbp<br>
>> >> > (all<br>
>> >> > of<br>
>> >> > the blocks are at one line, shown in the picture2.pn=
g). Could you<br>
>> >> > please<br>
>> >> > tell me how to do this? Many thanks!<br>
>> >> ><br>
>> >> > BTW: my configure script is like this:<br>
>> >> ><br>
>> >> > [methySW_MSH1_1000K]<br>
>> >> > feature=A0=A0=A0=A0=A0=A0=A0=A0 =3D methySW_MSH1_100=
0K<br>
>> >> > glyph=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 =3D xyplot<br>
>> >> > graph_type=A0=A0=A0=A0=A0 =3D boxes<br>
>> >> > fgcolor=A0=A0=A0=A0=A0=A0=A0=A0 =3D red<br>
>> >> > bgcolor=A0=A0=A0=A0=A0=A0=A0=A0 =3D red<br>
>> >> > height=A0=A0=A0=A0=A0=A0=A0=A0=A0 =3D 80<br>
>> >> > min_score=A0=A0=A0=A0=A0=A0 =3D 0<br>
>> >> > max_score=A0=A0=A0=A0=A0=A0 =3D 1<br>
>> >> > scale=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 =3D none<br>
>> >> > group_on=A0=A0=A0=A0=A0=A0=A0 =3D methySW_MSH1_1000K=
<br>
>> >> > category=A0=A0=A0=A0=A0=A0=A0 =3D Quantitative Data<=
br>
>> >> > label=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 =3D 0<br>
>> >> > key=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 =3D Methylat=
ion Profile - MSH1_dr_vs_Col0 (Sliding<br>
>> >> > Windows:1000K-size)<br>
>> >> ><br>
>> >> ><br>
>> >> > Best wishes,<br>
>> >> > Jiantao<br>
>> >><br>
>> >><br>
>> >><br>
>> >> --<br>
>> >><br>
>> >> ---------------------------------------------------------=
---------------<br>
>> >> Scott Cain, Ph. D.=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0=
=A0 =A0 =A0 =A0 =A0 =A0 =A0=A0 scott at scottcain<br>
>> >> dot net<br>
>> >> GMOD Coordinator (<a href=3D"http://gmod.org/" target=3D"=
_blank">http://gmod.org/</a>)=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0=A0 <a =
href=3D"tel:216-392-3087" value=3D"+12163923087">216-392-3087</a><br>
>> >> Ontario Institute for Cancer Research<br>
>> ><br>
>> ><br>
>><br>
>><br>
>><br>
>> --<br>
>> ------------------------------------------------------------------=
------<br>
>> Scott Cain, Ph. D.=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =
=A0 =A0 =A0 =A0 =A0=A0 scott at scottcain<br>
>> dot net<br>
>> GMOD Coordinator (<a href=3D"http://gmod.org/" target=3D"_blank">h=
ttp://gmod.org/</a>)=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0=A0 <a href=3D"t=
el:216-392-3087" value=3D"+12163923087">216-392-3087</a><br>
>> Ontario Institute for Cancer Research<br>
><br>
><br>
<br>
<br>
<br>
--<br>
------------------------------------------------------------------------<br=
>
Scott Cain, Ph. D.=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =
=A0 =A0 =A0=A0 scott at scottcain dot net<br>
GMOD Coordinator (<a href=3D"http://gmod.org/" target=3D"_blank">http://gmo=
d.org/</a>)=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0=A0 <a href=3D"tel:216-39=
2-3087" value=3D"+12163923087">216-392-3087</a><br>
Ontario Institute for Cancer Research<br>
</div></div></blockquote></div><br></div>
--f46d043c093ea9bb2804beab6148--
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