Closed deleod closed 4 years ago
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 notifications@github.com 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.
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:
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 notifications@github.com 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 https://github.com/z0on/GO_MWU/issues/5?email_source=notifications&email_token=AIT7WWDWTWR3XGRGXQSAYS3QKJNMXA5CNFSM4IYA4PUKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD7AYGXI#issuecomment-532775773, or mute the thread https://github.com/notifications/unsubscribe-auth/AIT7WWF4CSFD2YOKOGT5EE3QKJNMXANCNFSM4IYA4PUA .
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 notifications@github.com 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 <notifications@github.com mailto:notifications@github.com> 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 <notifications@github.com mailto:notifications@github.com> 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 <https://github.com/z0on/GO_MWU/issues/5?email_source=notifications&email_token=AIT7WWDWTWR3XGRGXQSAYS3QKJNMXA5CNFSM4IYA4PUKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD7AYGXI#issuecomment-532775773 https://github.com/z0on/GO_MWU/issues/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 https://github.com/z0on/GO_MWU/issues/5?email_source=notifications&email_token=ABZUHGC4FJOQXIAP2QW4W4DQKJ2H7A5CNFSM4IYA4PUKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD7BCVKY#issuecomment-532818603, or mute the thread https://github.com/notifications/unsubscribe-auth/ABZUHGANNDGSZD3UUUFXUIDQKJ2H7ANCNFSM4IYA4PUA.
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:
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 notifications@github.com 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 <notifications@github.com mailto:notifications@github.com> 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 <notifications@github.com mailto:notifications@github.com> 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 < https://github.com/z0on/GO_MWU/issues/5?email_source=notifications&email_token=AIT7WWDWTWR3XGRGXQSAYS3QKJNMXA5CNFSM4IYA4PUKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD7AYGXI#issuecomment-532775773 < https://github.com/z0on/GO_MWU/issues/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 < https://github.com/z0on/GO_MWU/issues/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 https://github.com/z0on/GO_MWU/issues/5?email_source=notifications&email_token=AIT7WWCD3W5RGICFF53CTS3QKO6CTA5CNFSM4IYA4PUKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD7ELF6Y#issuecomment-533246715, or mute the thread https://github.com/notifications/unsubscribe-auth/AIT7WWD5F3ACDAQCU3KQIDDQKO6CTANCNFSM4IYA4PUA .
does it happen with any GO division, BP, MF and CC?
On Sep 19, 2019, at 1:18 PM, deleod notifications@github.com 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 <notifications@github.com mailto:notifications@github.com> 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 <notifications@github.com mailto:notifications@github.com> 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 <notifications@github.com mailto:notifications@github.com <mailto:notifications@github.com mailto:notifications@github.com>> 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 <notifications@github.com mailto:notifications@github.com <mailto:notifications@github.com mailto:notifications@github.com>> 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 < https://github.com/z0on/GO_MWU/issues/5?email_source=notifications&email_token=AIT7WWDWTWR3XGRGXQSAYS3QKJNMXA5CNFSM4IYA4PUKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD7AYGXI#issuecomment-532775773 https://github.com/z0on/GO_MWU/issues/5?email_source=notifications&email_token=AIT7WWDWTWR3XGRGXQSAYS3QKJNMXA5CNFSM4IYA4PUKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD7AYGXI#issuecomment-532775773 < https://github.com/z0on/GO_MWU/issues/5?email_source=notifications&email_token=AIT7WWDWTWR3XGRGXQSAYS3QKJNMXA5CNFSM4IYA4PUKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD7AYGXI#issuecomment-532775773 https://github.com/z0on/GO_MWU/issues/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 < https://github.com/z0on/GO_MWU/issues/5?email_source=notifications&email_token=ABZUHGC4FJOQXIAP2QW4W4DQKJ2H7A5CNFSM4IYA4PUKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD7BCVKY#issuecomment-532818603 https://github.com/z0on/GO_MWU/issues/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 <https://github.com/z0on/GO_MWU/issues/5?email_source=notifications&email_token=AIT7WWCD3W5RGICFF53CTS3QKO6CTA5CNFSM4IYA4PUKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD7ELF6Y#issuecomment-533246715 https://github.com/z0on/GO_MWU/issues/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 https://github.com/z0on/GO_MWU/issues/5?email_source=notifications&email_token=ABZUHGDFJ2OHDLHJYZCGYK3QKO66RA5CNFSM4IYA4PUKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD7EL3RA#issuecomment-533249476, or mute the thread https://github.com/notifications/unsubscribe-auth/ABZUHGAK2DZEMGNQXP6AWTDQKO66RANCNFSM4IYA4PUA.
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
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
This worked great, thanks!
On Thu, Sep 26, 2019 at 12:20 PM Mikhail V Matz notifications@github.com wrote:
Closed #5 https://github.com/z0on/GO_MWU/issues/5.
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/z0on/GO_MWU/issues/5?email_source=notifications&email_token=AIT7WWHE7KNMMEFFF5KHIITQLTOL5A5CNFSM4IYA4PUKYY3PNVWWK3TUL52HS4DFWZEXG43VMVCXMZLOORHG65DJMZUWGYLUNFXW5KTDN5WW2ZLOORPWSZGOT3TJCEA#event-2665910544, or mute the thread https://github.com/notifications/unsubscribe-auth/AIT7WWDR3GI7SW2YV4334U3QLTOL5ANCNFSM4IYA4PUA .
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