IdMappingAnalysis (version 1.16.0)

plot.IdMapDiffCounts: Produce a fountain plot representing the quantitative relationship of the compound events

Description

Produce a fountain plot representing the quantitative relationship of the compound events <'excess both',="" 'excess="" left',="" right',="" 'same="" list',="" 'in="" left="" only',="" right="" neither'="">

Usage

"plot"(x, valRange=c(-20, 20, 10), reverse=FALSE, pairLabels=NULL, guideline.col="darkgrey", guideline.lty=2, guideline.lwd=par.zoom, cols=c("red", "blue", "green"), sides=2, cex=1, cex.side=0.75 * cex, srt=0, adj=0.5, par.zoom=1, ...)

Arguments

valRange

numeric 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)

pairLabels

optional decorated names for ID Map pair in consideration. If NULL (default), the original ID Map names are used.

guideline.col

guideline(horisontal group divider) lines color. Default is 'darkgrey'.

guideline.lty

guideline lines type. Default is 2 (dashed).

guideline.lwd

guideline lines color. Default is par.zoom.

cols

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

sides

How compound events labels and counts are placed on plot. Possible values are 1 or 2. 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 side 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.

par.zoom

graphics parameters zoom factor. Scales the graphical parameters like cex, lwd, mai etc.

...

Additional graphical parameters

See Also

For more information see IdMapDiffCounts.

Examples

 #create IdMapDiffCounts object
 IDs<-IdMapBase$primaryIDs(examples$msmsExperimentSet);
 jointIdMap<-JointIdMap(examples$identDfList,primaryIDs=IDs);
 diffs<-jointIdMap$getDiff("NetAffx_F","DAVID_Q",verbose=TRUE);
 diffCounts<-IdMapDiffCounts(diffs);

 # fountain plot of DB pair differences
 # two-sided labels
 diffCounts$plot(sides=2);
 # one-sided labels
 diffCounts$plot(sides=1);