plotDoublePerturbation: Double Perturbation Plot
In RNAinteract: Estimate Pairwise Interactions from multidimensional features

Description Usage Arguments Details Value Author(s) See Also Examples

These function draws a double perturbation plot for interaction screens. All interactions of one gene are displayed in one panel. The double perturbation readout level is plotted against the single perturbation level.

plotDoublePerturbation( sgi, screen, channel, target,
                       withoutgroups = c("neg", "pos"), design,
                       main, xlab, ylab, range,
                       show.labels = "none", label.par, label,
		       avoid.overlap, col, fill,
                       D , MT, MQ, PV, QV, PI, ...)

`sgi`	An object of class `RNAinteract`.
`target`	A character name of the target gene.
`screen`	The character name of the screen to display. If not specified, the first screen is used. Does not have to be specified, if `sgi` contains only one screen.
`channel`	The character name of the channel to display. If not specified, the first channel is used. Does not have to be specified, if `sgi` contains only one channel.
`withoutgroups`	Interactions to genes from these groups (as specified in the reagent or target annotation) are excluded from the plot, e.g. positive and negative controls.
`design`	The Either `"template"` (default) or `"query"`. The single perturbation effects are either the template main effects or the query main effects.
`main`	An overall title of the plot.
`xlab`	A title of the x-axis.
`ylab`	A title of the y-axis.
`range`	A numeric vector of length two. range equals the `xlim`, `ylim` argument in plot.
`show.labels`	Automatically select text labels for the points. `'all'` shows a text label for all genes, `"q.value"` and `"p.value"` show a text label for all genes with a q.value (p.value) larger than `label.par`, `"none"` does not show any text label. This argument has no effect, if `label` is specified.
`label.par`	Cut-off value for q.value or p.value for displaying text labels (See `show.labels`).
`label`	Either a character vector with gene names, or a named vector of text labels. The names of the vector represent the gene names.
`avoid.overlap`	If `TRUE` (default), text is moved such that text labels are not overlapping.
`col`	A named vector with colors. The names of `col` define which points are colored (See also `fill`).
`fill`	A list up to four values. `colors` defines a set of colors from which a colorramp is created. If `colramp` is specified, colors has no effect. `colramp` directly specifies the colorramp. `values` define the values that are color coded. If `values` is not specified, the pairwise interaction term is used instead. `at` is a numeric vector defining the breakpoints along the values. If not specified, breakpoints are selected to range three times the standard deviation of the values around zero. `fill` has no effect, if `col` is specified.
`D,MT,MQ,PV,QV,PI`	Internal usage.
`...`	Further argument passed to `grid.doublePerturbation` or `doublePerturbationGrob`.