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Question: Visualizing Linear Model Coefficients in R
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gravatar for nathanguy14
8 weeks ago by
nathanguy140 wrote:

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

ADD COMMENTlink modified 8 weeks ago by Michael Love13k • written 8 weeks ago by nathanguy140
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gravatar for Michael Love
8 weeks ago by
Michael Love13k
United States
Michael Love13k wrote:

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.

ADD COMMENTlink written 8 weeks ago by Michael Love13k
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