The ggbio documentation for making karyograms (layout_karyogram) gives an examples of a karyogram with a line plot on top.  (http://www.tengfei.name/ggbio/docs/man/layout_karyogram-method.html)

Here is extract of the code from the documentation page (full, reproducible code available there)

values(dn)$pvalue <- rnorm(length(dn))
p + layout_karyogram(dn, aes(x = start, y = pvalue), ylim = c(10, 30), geom = "line", color = "red")

Question: How can I put a yaxis on these line graphs?

Putting a y-axis on the lin graphs is essential - it is very unlikely for a journal to accept a figure with no scale or axis ticks whatsoever...