plotDoublePerturbation {RNAinteract} | R Documentation |
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 |
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 |
channel |
The character name of the channel to display. If not specified, the first channel is used. Does not have to be specified, if |
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 |
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 |
show.labels |
Automatically select text labels for the points. |
label.par |
Cut-off value for q.value or p.value for displaying text labels (See |
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 |
col |
A named vector with colors. The names of |
fill |
A list up to four values.
|
D,MT,MQ,PV,QV,PI |
Internal usage. |
... |
Further argument passed to |
Plots a double perturbation plot. It shows the interaction profile for one (query) gene.
A grob is returned.
Bernd Fischer
RNAinteract-package
, grid.doublePerturbation
, reportDoublePerturbation
data("sgi") plotDoublePerturbation( sgi, screen="1", channel="nrCells", target="rl", show.labels="p.value")