plotDiffNoise: Function for plotting differentially variable genes

Description

This is a plotting function for visualizing the output of the diffNoisyGenesTB function as MA plot.

plotDiffNoise(
  x,
  pthr = 0.05,
  mu = TRUE,
  lthr = 0,
  ps = 0.01,
  mthr = -Inf,
  set.name = NULL,
  bgr.name = NULL,
  show_names = TRUE
)

None

x: output of the function diffNoisyGenesTB.
pthr: real number between 0 and 1. This number represents the p-value cutoff applied for displaying differentially variable genes. Default value is 0.05.
mu: logical value. If TRUE then the log2 fold change in variability is plotted as a function of log2 average expresion. Otherwise, it is plotted as a function of mean variability.
lthr: real number between 0 and Inf. Differentially variable genes are displayed only for log2 fold-changes greater than lthr. Default value is 0.
ps: positive real number. Pseudo-count added to component mu.all and epsilon.all of argument x to avoid taking logarithm of zero. Default is 0.01.
mthr: real number between -Inf and Inf. Differentially variable genes are displayed only for log2 mean expression (or mean noise, if mu equals FALSE) greater than mthr. Default value is -Inf.
set.name: name of set, which was used as input to diffNoisyGenesTB. If provided, this name is used in the axis labels. Default value is NULL.
bgr.name: name of bgr, which was used as input to diffNoisyGenesTB. If provided, this name is used in the axis labels. Default value is NULL.
show_names: logical value. If TRUE then gene names displayed for differentially variable genes. Default value is FALSE.