plotDiffNoise {RaceID}

Function for plotting differentially variable genes

Description

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

Usage

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

Arguments

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.

Value

None