IdMappingAnalysis (version 1.16.0)

diffCounts.plot.JointIdMap: Interactive wrapper for IdMapDiffCounts$plot

Description

Interactive wrapper of the IdMapDiffCounts.plot allowing to select the ID Map pairs encapsulated within the given JointIdMap object for a fountaine plot through the dialog.

Usage

"diffCounts.plot"(this, idMapNames="loop", valRange=c(-20, 20, 10), reverse=FALSE, pairLabels=NULL, new.plot=FALSE, file.copy=FALSE, copy.zoom=1, cols=c("red", "blue", "green"), sides=2, cex=1, cex.side=0.75 * cex, srt=0, adj=0.5, verbose=TRUE, ...)

Arguments

idMapNames

either ID Maps pair names, 'menu' or 'loop'. If ID Map pairs, the functionality is similar to IdMapDiffCounts.plot If 'menu' or 'loop', user can select the pair of ID Maps interactively from the graphical selection dialog simultaneously controlling the plot destination (same or new graphic device) and wherther or not the plot should be saved in a file. If 'loop', the interactive drawing cycle repeats untill the user cancells the process.

valRange

numericl vector of length 3 where the first and second elements are minimum and maximum count values to be displayed on horizontal axis and the third element is a distance between horizontal axis tick marks. Default is c(-20,20,10).

reverse

logical indicating the plot orientation (top to bottom or bottom to top). Default is FALSE.

pairLabels

optional decorated names for ID Map pair in consideration. If NULL, the original ID Map names are used. Default is@ NULL.

cols

colors corresponding to the events from which the plot is composed.

sides

(1 or 2): how compound events labels and counts are placed on plot. If sides=1 both event labels and counts are placed on one (left) side. If sides=2 then labels are placed on left side and counts on the right.

cex

plot title font size.

cex.side

compound events labels font size.

srt

compound events labels orientation.

adj

compound events labels position adjustment (0 - 1), where 0/1 corresponds to the minimum/maximum labels position shift inwards the plot.

new.plot

logical indicating if the new graphic device should be created for plot. In interactive mode can be selected graphically. Default is FALSE.

file.copy

logical or a character string indicating if the plot should be saved to a file. If character string, it's content used as a file name and if TRUE, the default file named is used If logical, in interactive mode can be toggled graphically. Default is FALSE.

copy.zoom

Zoom factor used when saving plot in a file. Default is 1.

verbose

if TRUE enables diagnostic messages. Default is FALSE.

...

Not used

See Also

For more information see JointIdMap.

Examples

 jointIdMap<-JointIdMap(examples$identDfList);

 #non-interactive fountain plot of differences
 #between two DBs encapsulated within the JointIdMap object
 jointIdMap$diffCounts.plot(idMapNames=c("NetAffx_F","DAVID_Q"));
 ## Not run: 
#  #interactive plot allowing to choose the DB pair to be plotted
#  jointIdMap$diffCounts.plot();
#  ## End(Not run)