Re: SweeD / OmegaPlus visualisation script

264 views
Skip to first unread message

Pavlos Pavlidis

unread,
Jul 17, 2013, 5:09:54 AM7/17/13
to Davis, Brian, omeg...@googlegroups.com
Hi Brian,

I send you two scripts:

Here is the R script (bio.lmu.de/~pavlidis/data_analysis.tar.gz).

It is mainly used for the classification of a genomic region as either neutral or selected.

2. This is probably what you need. It's the R script taht we used in SweeD paper for figure 4 (http://mbe.oxfordjournals.org/content/early/2013/07/11/molbev.mst112.full.pdf+html)

bio.lmu.de/~pavlidis/combine_figure_omega_sweed.tar.gz
Please note that there is a comment "###### UP TO HERE TO PLOT ##############"

After this comment the code is annotating the genes that is detecting as positively selected. Perhaps this is not interesting for you.

kind regards
pavlos



On Tue, Jul 16, 2013 at 10:29 PM, Davis, Brian <BDa...@cvm.tamu.edu> wrote:
Hello Pavlos,

I posted on the Google groups page yesterday about a simple visualization method, and you mentioned that you just use R.  If you have a simple script to input both of these outputs into R for comparative visualization, I'd very much like to use them.

Thanks again for making such great software!
-Brian



--

Pavlos Pavlidis, PhD

Foundation for Research and Technology - Hellas
Institute of Molecular Biology and Biotechnology
Νikolaou Plastira 100, Vassilika Vouton
GR - 711 10, Heraklion, Crete, Greece

Yu Cao

unread,
May 19, 2020, 6:06:14 AM5/19/20
to OmegaPlus
Hi Pavlos,
I am using SweeD and OmegaPlus to detect selective sweep in my whole genome data within walnut, now I had got the report file that contains the likelihood value and a-parameter for each CLR position, and I am about to visualize the result to get outlier point. 
By browsing posts in the google group, I got to know you had written some R scripts of visualization, I am glad to use them but I failed to download them from this server (the error says: You don't have permission to access this resource). And my try to download scripts from your official web was also failed (the error says: You don't have permission to access /exelixis/resource/download/data/SweeD_DATA_SCRIPTS.tar.bz2 on this server). I wonder if you could send me these great scripts, my email address is <caoy...@mail.bnu.edu.cn>.

Thanks very much in advance, I am looking forward to citing you.

-------------------------------------

Yu Cao

Institute of Ecology

Beijing Normal University

Beijing 100875

China


在 2013年7月17日星期三 UTC+8下午5:09:54，pavlos写道：

Nikolaos Alachiotis

unread,
May 20, 2020, 9:41:26 AM5/20/20
to OmegaPlus
You are probably referring to the scripts that detect and plot common outliers, right?
If yes, this functionality is now integrated in RAiSD: https://github.com/alachins/raisd

The default operation (described here:
) is to plot common outliers between RAiSD and SweeD or OmegaPlus but you can provide the
SweeD and OmegaPlus reports instead and get the respective report and plot.
(The plot will still read "RAiSD" but the data shown will be those obtained from the provided reports.)

--
You received this message because you are subscribed to the Google Groups "OmegaPlus" group.
To unsubscribe from this group and stop receiving emails from it, send an email to omegaplus+...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/omegaplus/5896dac2-d01d-4410-bff0-92f0b8dc2aa2%40googlegroups.com.


--
Nikolaos Alachiotis

Yu Cao

unread,
May 22, 2020, 10:23:28 AM5/22/20
to OmegaPlus
Thank you for your nice reply, I'll try to plot common outliers using RAiSD~

Best wishes, thanks again~

在 2020年5月20日星期三 UTC+8下午9:41:26，N.Alachiotis写道：
To unsubscribe from this group and stop receiving emails from it, send an email to omeg...@googlegroups.com.


--
Nikolaos Alachiotis

Message has been deleted

Nikolaos Alachiotis

unread,
Jun 30, 2020, 3:53:30 AM6/30/20
to OmegaPlus
Hello, this is a copy-paste from a previous post:

You are probably referring to the scripts that detect and plot common outliers, right?
If yes, this functionality is now integrated in RAiSD: https://github.com/alachins/raisd

The default operation (described here:
) is to plot common outliers between RAiSD and SweeD or OmegaPlus but you can provide the
SweeD and OmegaPlus reports instead and get the respective report and plot.
(The plot will still read "RAiSD" but the data shown will be those obtained from the provided reports.)

On Tue, Jun 30, 2020 at 10:47 AM Manasa K.G. <manas...@gmail.com> wrote:
Hi Pavlos,

Am using SweeD for selective Sweep using Rice Data, I come across about the R script for plotting and annotation in one of the post but it's forbidden now/for me, could you please help me to get through this. 

--
You received this message because you are subscribed to the Google Groups "OmegaPlus" group.
To unsubscribe from this group and stop receiving emails from it, send an email to omegaplus+...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/omegaplus/8a9feff3-6067-49ef-8517-1309e356c459o%40googlegroups.com.


--
Nikolaos Alachiotis

Message has been deleted

N.Alachiotis

unread,
Jun 30, 2020, 6:17:45 AM6/30/20
to OmegaPlus
What I am trying to say is that we do not have access to those scripts on those servers anymore.

Part of that functionality, including more flexibility for common outliers, has been reimplemented in RAiSD and can be used for SweeD/OmegaPlus/RAiSD and any combination thereof.

You can also check the following scripts as well, in case they fit your purpose:





On Tuesday, June 30, 2020 at 12:56:15 PM UTC+3, Manasa K.G. wrote:
That's what am referring to,
The script mention in it is forbidden from accesses.
Am asking how to retrieve or accesses to it.. 
please read my post completely  
To unsubscribe from this group and stop receiving emails from it, send an email to omeg...@googlegroups.com.


--
Nikolaos Alachiotis

Reply all
Reply to author
Forward
Message has been deleted
0 new messages