plot.IdMapDiffCounts {IdMappingAnalysis} | R Documentation

## 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', 'excess right', 'same list', 'in left only', 'in right only', 'in neither' >

### Usage

    ## S3 method for class 'IdMapDiffCounts'
    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 <A-A*B, A*B, B-A*B> 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

### Author(s)

Alex Lisovich, Roger Day

### 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);

[Package IdMappingAnalysis version 1.28.0 Index]