olBarplot {systemPipeR} | R Documentation

## Bar plot for intersect sets

### Description

Generates bar plots of the intersect counts of `VENNset` and `INTERSECTset` objects generated by the `overLapper` function. It is an alternative to Venn diagrames (e.g. `vennPlot`) that scales to larger numbers of label sets. By default the bars in the plot are colored and grouped by complexity levels of the intersect sets.

### Usage

    olBarplot(x, mincount = 0, complexity="default", myxlabel = "default", myylabel="Counts", mytitle = "default", ...)

### Arguments

`x` | Object of class `VENNset` or `INTERSECTset`.
`mincount` | Sets minimum number of counts to consider in the bar plot. Default `mincount=0` considers all counts.
`complexity` | Allows user to limit the bar plot to specific complexity levels of intersects by specifying the chosen ones with an integer vector. Default `complexity="default"` considers all complexity levels.
`myxlabel` | Defines label of x-axis.
`myylabel` | Defines label of y-axis.
`mytitle` | Defines main title of plot.
`...` | Allows to pass on additional arguments to `geom_bar` from `ggplot2`. For instance, `fill=seq(along=vennlist(x))` or `fill=seq(along=intersectlist(x))` will assign a different color to each bar, or `fill="blue"` will color all of them blue. The default bar coloring is by complexity levels of the intersect sets.

### Value

Bar plot.

### Note

The functions provided here are an extension of the Venn diagram resources on this site: http://manuals.bioinformatics.ucr.edu/home/R_BioCondManual#TOC-Venn-Diagrams

### Author(s)

Thomas Girke

### See Also

`overLapper`, `vennPlot`

### Examples

    ## Sample data: list of vectors with object labels
    setlist <- list(A=sample(letters, 18), B=sample(letters, 16),
                    C=sample(letters, 20), D=sample(letters, 22),
                    E=sample(letters, 18), F=sample(letters, 22))

    ## 2-way Venn diagram
    vennset <- overLapper(setlist[1:2], type="vennsets")
    vennPlot(vennset)

    ## 3-way Venn diagram
    vennset <- overLapper(setlist[1:3], type="vennsets")
    vennPlot(vennset)

    ## 4-way Venn diagram
    vennset <- overLapper(setlist[1:4], type="vennsets")
    vennPlot(list(vennset, vennset))

    ## Pseudo 4-way Venn diagram with circles
    vennPlot(vennset, type="circle")

    ## 5-way Venn diagram
    vennset <- overLapper(setlist[1:5], type="vennsets")
    vennPlot(vennset)

    ## Alternative Venn count input to vennPlot (not recommended!)
    counts <- sapply(vennlist(vennset), length)
    vennPlot(counts)

    ## 6-way Venn comparison as bar plot
    vennset <- overLapper(setlist[1:6], type="vennsets")
    olBarplot(vennset, mincount=1)

    ## Bar plot of standard intersect counts
    interset <- overLapper(setlist, type="intersects")
    olBarplot(interset, mincount=1)

    ## Accessor methods for VENNset/INTERSECTset objects
    names(vennset)
    names(interset)
    setlist(vennset)
    intersectmatrix(vennset)
    complexitylevels(vennset)
    vennlist(vennset)
    intersectlist(interset)

    ## Coerce VENNset/INTERSECTset object to list
    as.list(vennset)
    as.list(interset)

    ## Pairwise intersect matrix and heatmap
    olMA <- sapply(names(setlist),
    		function(x) sapply(names(setlist),
    		function(y) sum(setlist[[x]] %in% setlist[[y]])))
    olMA
    heatmap(olMA, Rowv=NA, Colv=NA)

    ## Presence-absence matrices for large numbers of sample sets
    interset <- overLapper(setlist=setlist, type="intersects", complexity=2)
    (paMA <- intersectmatrix(interset))
    heatmap(paMA, Rowv=NA, Colv=NA, col=c("white", "gray"))

[Package systemPipeR version 1.20.0 Index]