Add points to the graph

[a-pankov]

Can you add points to Figure 1?

Also can you add which method you used for the regression.

[dhimmel]

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.

[dhimmel]

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.

[a-pankov]

Quick GAM/smoothing spline explanation: ISLR - Chapter 7

[dhimmel]

@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

[dhimmel]

@a-pankov, so we used a 'smooth cubic spline'? Can you confirm or deny? Is it natural?