inmoose.edgepy.plotQLDisp

inmoose.edgepy.plotQLDisp(glmfit, xlab='Average Log2 CPM', ylab='Quarter-Root Mean Deviance', col_shrunk='red', col_trend='blue', col_raw='black')

Plot the genewise quasi-likelihood dispersion against the gene abundance (in log2 counts per million)

This function displays the quarter-root of the quasi-likelihood dispersions for all genes, before and after shrinkage towards a trend. If glmfit was constructed without an abundance trend, the function instead plots a horizontal line (of color col_trend) at the common value towards which dispersions are shrunk. The quarter-root transformation is applied to improve visibility for dispersions around unity.

Parameters:

  • glmfit (DGEGLM) – a DGEGLM object produced by glmQLFit()

  • xlab (str) – label for the x-axis

  • ylab (str) – label for the y-axis

  • col_shrunk (str) – color of the points representing the squeezed quasi-likelihood dispersions

  • col_trend (str) – color of the line showing dispersion trend

  • col_raw (str) – color of the line showing the unshrunk dispersions