Comments (5)
Can you add points to Figure 1?
No because it would be a disaster. There are 17,685 genes for each metaedge. Additionally, for a specific metaedge, the degree of each gene varies substantially.
Perhaps you would like to see prediction rather than confidence intervals? However, these would be quite wide than therefore visually problematic.
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Also can you add which method you used for the regression.
Here is the line of code that draws the regression:
ggplot2::geom_smooth(method='gam', formula=formula("y ~ s(x, bs='cs')"), linetype=0, n=1000, sp=50)
Figuring this out was painful because of poor documentation. I am not sure what it does. Maybe you can help explain. Here are links to the mgcv::gam
and ggplot2::stat_smooth
documentation. The linetype argument in the above command suppresses line drawing and is not related to model fitting.
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Quick GAM/smoothing spline explanation: ISLR - Chapter 7
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@a-pankov, you can add page numbers to pdf urls by appending #page=X
. For example, here is a link to the GAM section: http://www-bcf.usc.edu/~gareth/ISL/ISLR%20First%20Printing.pdf#page=297
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@a-pankov, so we used a 'smooth cubic spline'? Can you confirm or deny? Is it natural?
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