Visualizing Linear Model Coefficients in R
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@nathanguy14-13284
Last seen 4.2 years ago

Hi All,

I'm analyzing an RNA-seq dataset using DESeq2, using a linear model that includes interaction terms.  Some of these interactions are a bit hard for me to visualize (especially the 3-way interactions).  I found this really great tutorial on linear models in R that includes some awesome visuals, for example:

http://genomicsclass.github.io/book/pages/figure/interactions_and_contrasts-spider_interactions2-1.png

But I don't know how to recapitulate such a graph for my data, and the code used to generate the above image was not provided.  Ideally, I would like to tell R to make this type of plot for any gene of interest in my data using the model that DESeq2 generates.  I'm a total newcomer to R, so any pointers in this direction would be greatly appreciated!  

Nathan

R deseq2 graph linear model • 747 views
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@mikelove
Last seen 2 hours ago
United States

Hi Nathan,

I made that tutorial as well :) [by the way the code for every genomics class lecture can be found by clicking on the Rmd link from the main 'book' page. It will take you to the 'labs' repo.]

It would help if you can provide your design and colData, so I can suggest how to plot the fitted model.

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