plotFindArguments: Plot Arguments
In siggenes: Multiple Testing using SAM and Efron's Empirical Bayes Approaches

Description Usage Arguments Value Author(s) See Also

Utility function for generating a plot of the posterior probabilities in an html file when searching for the optimal value of the fudge factor in an EBAM analysis.

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  plotFindArguments(onlyTab = FALSE, logit = TRUE, pos.legend = NULL,
        legend.cex = 0.8, col = NULL, main = NULL, xlab = NULL, ylab = NULL,
        only.a0 = FALSE, lty = 1, lwd = 1, y.intersp = 1.1)

`onlyTab`	if `TRUE`, then this plot is not generated and only the table of the number of differentially expressed genes and the estimated FDR for the different values of the fudge factor is shown.
`logit`	should the posterior probabilities be logit-transformed before they are plotted?
`pos.legend`	an integer between 0 and 4. See `help.finda0(plot)` for how `pos.legend` can be specified, and for its default.
`legend.cex`	the size of the text in the legend relative to the default size
`col`	a vector specifying the colors of the lines for the different values of the fudge factor. For a description of how colors can be specified, see `par`.
`main`	a character string naming the main title of the plot.
`xlab`	a character string naming the label of the x axis.
`ylab`	a character string naming the label of the y axis.
`only.a0`	if `TRUE`, only the values of a0 are shown in the legend. If `FALSE`, both the values of a0 and the corresponding number of differentially expressed genes are shown.
`lty`	a value or vector specifying the line type of the curves. For details, see `par`.
`lwd`	a numeric value specifying the width of the plotted lines. For details, see `par`.
`y.intersp`	a numeric value specifying the space between the rows of the legend.