gomwuPlot visualization issue

[deleod]

Hi,

I am having issues visualizing the hierarchical clustering tree on my plots. I tried playing around with some of the parameters with no luck. For both my MF and BP plots, I am just getting unconnected horizontal lines instead of a clustered tree image.

I attached one here as an example, not sure what the issue is. Any advice would be appreciated!
eyes_MF_Rplot.pdf

[z0on]

Hmmm. I’ve seen this before but don’t quite recall how this was solved... try adjusting treeHeight parameter in gomwuPlot, and/or plotting directly to pdf. iPhone. Apologies for brevity

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On Sep 18, 2019, at 11:10 AM, deleod ***@***.***> wrote: Hi, I am having issues visualizing the hierarchical clustering tree on my plots. I tried playing around with some of the parameters with no luck. For both my MF and BP plots, I am just getting unconnected horizontal lines instead of a clustered tree image. I attached one here as an example, not sure what the issue is. Any advice would be appreciated! eyes_MF_Rplot.pdf — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

[deleod]

Thanks, I tired the treeHeight parameter with no luck. Any advice on how to plot directly to pdf? On Wed, Sep 18, 2019, 1:03 PM Mikhail V Matz <notifications@github.com> wrote:

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Hmmm. I’ve seen this before but don’t quite recall how this was solved... try adjusting treeHeight parameter in gomwuPlot, and/or plotting directly to pdf. iPhone. Apologies for brevity > On Sep 18, 2019, at 11:10 AM, deleod ***@***.***> wrote: > > Hi, > > I am having issues visualizing the hierarchical clustering tree on my plots. I tried playing around with some of the parameters with no luck. For both my MF and BP plots, I am just getting unconnected horizontal lines instead of a clustered tree image. > > I attached one here as an example, not sure what the issue is. Any advice would be appreciated! > eyes_MF_Rplot.pdf > > — > You are receiving this because you are subscribed to this thread. > Reply to this email directly, view it on GitHub, or mute the thread. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#5?email_source=notifications&email_token=AIT7WWDWTWR3XGRGXQSAYS3QKJNMXA5CNFSM4IYA4PUKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD7AYGXI#issuecomment-532775773>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AIT7WWF4CSFD2YOKOGT5EE3QKJNMXANCNFSM4IYA4PUA> .

[z0on]

pdf(“myplot.pdf”, height=10,width=10) gomwuPlot(…) dev.off() (adjust height and width depending on how it comes out)

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On Sep 18, 2019, at 1:52 PM, deleod ***@***.***> wrote: Thanks, I tired the treeHeight parameter with no luck. Any advice on how to plot directly to pdf? On Wed, Sep 18, 2019, 1:03 PM Mikhail V Matz ***@***.*** ***@***.***>> wrote: > Hmmm. I’ve seen this before but don’t quite recall how this was solved... > try adjusting treeHeight parameter in gomwuPlot, and/or plotting directly > to pdf. > > iPhone. Apologies for brevity > > > On Sep 18, 2019, at 11:10 AM, deleod ***@***.*** ***@***.***>> wrote: > > > > Hi, > > > > I am having issues visualizing the hierarchical clustering tree on my > plots. I tried playing around with some of the parameters with no luck. For > both my MF and BP plots, I am just getting unconnected horizontal lines > instead of a clustered tree image. > > > > I attached one here as an example, not sure what the issue is. Any > advice would be appreciated! > > eyes_MF_Rplot.pdf > > > > — > > You are receiving this because you are subscribed to this thread. > > Reply to this email directly, view it on GitHub, or mute the thread. > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub > <#5?email_source=notifications&email_token=AIT7WWDWTWR3XGRGXQSAYS3QKJNMXA5CNFSM4IYA4PUKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD7AYGXI#issuecomment-532775773 <#5?email_source=notifications&email_token=AIT7WWDWTWR3XGRGXQSAYS3QKJNMXA5CNFSM4IYA4PUKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD7AYGXI#issuecomment-532775773>>, > or mute the thread > <https://github.com/notifications/unsubscribe-auth/AIT7WWF4CSFD2YOKOGT5EE3QKJNMXANCNFSM4IYA4PUA <https://github.com/notifications/unsubscribe-auth/AIT7WWF4CSFD2YOKOGT5EE3QKJNMXANCNFSM4IYA4PUA>> > . > — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#5?email_source=notifications&email_token=ABZUHGC4FJOQXIAP2QW4W4DQKJ2H7A5CNFSM4IYA4PUKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD7BCVKY#issuecomment-532818603>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABZUHGANNDGSZD3UUUFXUIDQKJ2H7ANCNFSM4IYA4PUA>.

[deleod]

Thanks, still having the same issue though when plotting directly to pdf. Not sure what the issue is. On Thu, Sep 19, 2019 at 2:10 PM Mikhail V Matz <notifications@github.com> wrote:

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pdf(“myplot.pdf”, height=10,width=10) gomwuPlot(…) dev.off() (adjust height and width depending on how it comes out) > On Sep 18, 2019, at 1:52 PM, deleod ***@***.***> wrote: > > Thanks, I tired the treeHeight parameter with no luck. Any advice on how to > plot directly to pdf? > > On Wed, Sep 18, 2019, 1:03 PM Mikhail V Matz ***@***.*** ***@***.***>> > wrote: > > > Hmmm. I’ve seen this before but don’t quite recall how this was solved... > > try adjusting treeHeight parameter in gomwuPlot, and/or plotting directly > > to pdf. > > > > iPhone. Apologies for brevity > > > > > On Sep 18, 2019, at 11:10 AM, deleod ***@***.*** ***@***.***>> wrote: > > > > > > Hi, > > > > > > I am having issues visualizing the hierarchical clustering tree on my > > plots. I tried playing around with some of the parameters with no luck. For > > both my MF and BP plots, I am just getting unconnected horizontal lines > > instead of a clustered tree image. > > > > > > I attached one here as an example, not sure what the issue is. Any > > advice would be appreciated! > > > eyes_MF_Rplot.pdf > > > > > > — > > > You are receiving this because you are subscribed to this thread. > > > Reply to this email directly, view it on GitHub, or mute the thread. > > > > — > > You are receiving this because you authored the thread. > > Reply to this email directly, view it on GitHub > > < #5?email_source=notifications&email_token=AIT7WWDWTWR3XGRGXQSAYS3QKJNMXA5CNFSM4IYA4PUKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD7AYGXI#issuecomment-532775773 < #5?email_source=notifications&email_token=AIT7WWDWTWR3XGRGXQSAYS3QKJNMXA5CNFSM4IYA4PUKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD7AYGXI#issuecomment-532775773 >>, > > or mute the thread > > < https://github.com/notifications/unsubscribe-auth/AIT7WWF4CSFD2YOKOGT5EE3QKJNMXANCNFSM4IYA4PUA < https://github.com/notifications/unsubscribe-auth/AIT7WWF4CSFD2YOKOGT5EE3QKJNMXANCNFSM4IYA4PUA >> > > . > > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub < #5?email_source=notifications&email_token=ABZUHGC4FJOQXIAP2QW4W4DQKJ2H7A5CNFSM4IYA4PUKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD7BCVKY#issuecomment-532818603>, or mute the thread < https://github.com/notifications/unsubscribe-auth/ABZUHGANNDGSZD3UUUFXUIDQKJ2H7ANCNFSM4IYA4PUA >. > — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#5?email_source=notifications&email_token=AIT7WWCD3W5RGICFF53CTS3QKO6CTA5CNFSM4IYA4PUKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD7ELF6Y#issuecomment-533246715>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AIT7WWD5F3ACDAQCU3KQIDDQKO6CTANCNFSM4IYA4PUA> .

[z0on]

does it happen with any GO division, BP, MF and CC?

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On Sep 19, 2019, at 1:18 PM, deleod ***@***.***> wrote: Thanks, still having the same issue though when plotting directly to pdf. Not sure what the issue is. On Thu, Sep 19, 2019 at 2:10 PM Mikhail V Matz ***@***.*** ***@***.***>> wrote: > pdf(“myplot.pdf”, height=10,width=10) > gomwuPlot(…) > dev.off() > > (adjust height and width depending on how it comes out) > > > On Sep 18, 2019, at 1:52 PM, deleod ***@***.*** ***@***.***>> wrote: > > > > Thanks, I tired the treeHeight parameter with no luck. Any advice on how > to > > plot directly to pdf? > > > > On Wed, Sep 18, 2019, 1:03 PM Mikhail V Matz ***@***.*** ***@***.***> > ***@***.*** ***@***.***>>> > > wrote: > > > > > Hmmm. I’ve seen this before but don’t quite recall how this was > solved... > > > try adjusting treeHeight parameter in gomwuPlot, and/or plotting > directly > > > to pdf. > > > > > > iPhone. Apologies for brevity > > > > > > > On Sep 18, 2019, at 11:10 AM, deleod ***@***.*** ***@***.***> > ***@***.*** ***@***.***>>> wrote: > > > > > > > > Hi, > > > > > > > > I am having issues visualizing the hierarchical clustering tree on my > > > plots. I tried playing around with some of the parameters with no > luck. For > > > both my MF and BP plots, I am just getting unconnected horizontal lines > > > instead of a clustered tree image. > > > > > > > > I attached one here as an example, not sure what the issue is. Any > > > advice would be appreciated! > > > > eyes_MF_Rplot.pdf > > > > > > > > — > > > > You are receiving this because you are subscribed to this thread. > > > > Reply to this email directly, view it on GitHub, or mute the thread. > > > > > > — > > > You are receiving this because you authored the thread. > > > Reply to this email directly, view it on GitHub > > > < > #5?email_source=notifications&email_token=AIT7WWDWTWR3XGRGXQSAYS3QKJNMXA5CNFSM4IYA4PUKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD7AYGXI#issuecomment-532775773 <#5?email_source=notifications&email_token=AIT7WWDWTWR3XGRGXQSAYS3QKJNMXA5CNFSM4IYA4PUKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD7AYGXI#issuecomment-532775773> > < > #5?email_source=notifications&email_token=AIT7WWDWTWR3XGRGXQSAYS3QKJNMXA5CNFSM4IYA4PUKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD7AYGXI#issuecomment-532775773 <#5?email_source=notifications&email_token=AIT7WWDWTWR3XGRGXQSAYS3QKJNMXA5CNFSM4IYA4PUKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD7AYGXI#issuecomment-532775773> > >>, > > > or mute the thread > > > < > https://github.com/notifications/unsubscribe-auth/AIT7WWF4CSFD2YOKOGT5EE3QKJNMXANCNFSM4IYA4PUA <https://github.com/notifications/unsubscribe-auth/AIT7WWF4CSFD2YOKOGT5EE3QKJNMXANCNFSM4IYA4PUA> > < > https://github.com/notifications/unsubscribe-auth/AIT7WWF4CSFD2YOKOGT5EE3QKJNMXANCNFSM4IYA4PUA <https://github.com/notifications/unsubscribe-auth/AIT7WWF4CSFD2YOKOGT5EE3QKJNMXANCNFSM4IYA4PUA> > >> > > > . > > > > > — > > You are receiving this because you commented. > > Reply to this email directly, view it on GitHub < > #5?email_source=notifications&email_token=ABZUHGC4FJOQXIAP2QW4W4DQKJ2H7A5CNFSM4IYA4PUKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD7BCVKY#issuecomment-532818603 <#5?email_source=notifications&email_token=ABZUHGC4FJOQXIAP2QW4W4DQKJ2H7A5CNFSM4IYA4PUKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD7BCVKY#issuecomment-532818603>>, > or mute the thread < > https://github.com/notifications/unsubscribe-auth/ABZUHGANNDGSZD3UUUFXUIDQKJ2H7ANCNFSM4IYA4PUA <https://github.com/notifications/unsubscribe-auth/ABZUHGANNDGSZD3UUUFXUIDQKJ2H7ANCNFSM4IYA4PUA> > >. > > > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub > <#5?email_source=notifications&email_token=AIT7WWCD3W5RGICFF53CTS3QKO6CTA5CNFSM4IYA4PUKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD7ELF6Y#issuecomment-533246715 <#5?email_source=notifications&email_token=AIT7WWCD3W5RGICFF53CTS3QKO6CTA5CNFSM4IYA4PUKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD7ELF6Y#issuecomment-533246715>>, > or mute the thread > <https://github.com/notifications/unsubscribe-auth/AIT7WWD5F3ACDAQCU3KQIDDQKO6CTANCNFSM4IYA4PUA <https://github.com/notifications/unsubscribe-auth/AIT7WWD5F3ACDAQCU3KQIDDQKO6CTANCNFSM4IYA4PUA>> > . > — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#5?email_source=notifications&email_token=ABZUHGDFJ2OHDLHJYZCGYK3QKO66RA5CNFSM4IYA4PUKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD7EL3RA#issuecomment-533249476>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABZUHGAK2DZEMGNQXP6AWTDQKO66RANCNFSM4IYA4PUA>.

[deleod]

It happens with all divisions. I also ran it on another dataset and I'm having a similar issue, though some of the tree appears to be there (attached).
MF_GOMWU_Rplot.pdf

[z0on]

Got it! it is because your GO annotations table have duplicated entries for the same gene.
GO_MWU actually includes a script (nrify_GOtable.pl) to fix that:

perl nrify_GOtable.pl myseqs2go.tab >myseqs2go_NR.tab

and then use myseqs2go_NR.tab in GO_MWU

[deleod]

This worked great, thanks!

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On Thu, Sep 26, 2019 at 12:20 PM Mikhail V Matz ***@***.***> wrote: Closed #5 <#5>. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#5?email_source=notifications&email_token=AIT7WWHE7KNMMEFFF5KHIITQLTOL5A5CNFSM4IYA4PUKYY3PNVWWK3TUL52HS4DFWZEXG43VMVCXMZLOORHG65DJMZUWGYLUNFXW5KTDN5WW2ZLOORPWSZGOT3TJCEA#event-2665910544>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AIT7WWDR3GI7SW2YV4334U3QLTOL5ANCNFSM4IYA4PUA> .