Function for plotting differentially variable genes
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 )
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.None
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