Visualize and Finalize the Result

[HocheolJang426]

Hi

I'm wondering how to sort and finalize the result.
in output folder, MotifEnrichment_preview.html made, but this file is too complicated
NES are not arranged, and many of TF_highConf overlapped
I also checked int folder, motifEnrichment_selfMotifs_wGenes.Rds, also this data.frame is complicated

I want to export my result like;
motif logo ; NES ; TF name ; Target gene
or any other good way to visualize the SCENIC result/output

Is there a good way to visualize the result?

[s-aibar]

Dear @HocheolJang426 ,

I think I don't fully understand your question. You can export and explore the motif enrichment with any format you prefer... The "MotifEnrichment_preview.html", is indeed just that, a preview than you can then re-shape to fit your needs.
If you already know which columns you would like to show, just load the motifEnrichment_selfMotifs_wGenes.Rds file in R, filter, re-shape, and export it with DT::datatable()...

[HocheolJang426]

My first question is...Is it possible to export motif logo in higher magnification?
I'am wondering that I can export or show the result like this;

[s-aibar]

The logo is provided as a fixed image, so there is no easy way to change the magnification (besides your own brower settings).

In RcisTarget vignette you have an example on how to use the package DT to show the motifs... I think that is mostly what you need (just select the appropriate columns, and reshape the TFs if needed...)

[HocheolJang426]

Thanks for your kindness, your answer really helped me

when I use function datatable(), logo disappear
But when I use viewMotif function in SCENIC, logo appear
I think I have to use viewMotif function, especially the output of SCENIC

I have one more question... last question
How can I export html image in R "viewer" menu?
viewMotif or datatable() function both show data in viewer menu in R studio
But I want to export this image like jpg or png(or tiff)
Is it possible?

[s-aibar]

I don't think you can save the table as image, but if I remember correctly, there is an option in the viewer to export as html (otherwise, check the DT manual, there is some way to do it programmatically).