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z0on / GO_MWU

Rank-based Gene Ontology analysis of gene expression data
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gomwuPlot visualization issue #5

Closed deleod closed 4 years ago

deleod commented 4 years ago

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 commented 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

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deleod commented 4 years ago

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

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z0on commented 4 years ago

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

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deleod commented 4 years ago

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

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z0on commented 4 years ago

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.

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deleod commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

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.

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