arc.plot: Arc Plot

In dieterich-lab/CellPlot: Segmented Bar Chart Plot Methods

Description

Plots a combined barchart for a differential expression experiment GO analysis. Shows enrichment score (or similar), proportions of up- and downregulated set members, as well as set overlap. Bar heights correspond to the number of genes of interest in the term. Overlap between terms is visualized by an arc connecting them. The line width of the arc corresponds to the number of overlapping genes, on the same scale as bar height. Arc colour scale maps to the Jaccard Index ( |Overlap| / |Union| ), bounded between 0 and 1, where black represents maximum overlap, i.e. Jaccard Index of close or equal to 1. A threshold on the Jaccard index may be set to suppress arcs below the specified value. Vertical ordering of terms is the result of hierarchical clustering, using hclust on the pairwise Jaccard Distance matrix (1 - Jaccard Index).

Usage

arc.plot(x, up.list, down.list, y.mar = c(0, 0), x.mar = c(0.5, 0),
  x.bound = NULL, x.ticks = 3, x.scale = 1, x.gap = 0.05,
  x.arc.gap = 0.3, space = 0.1, fixed.scale = NULL, t = 0.2,
  tc = "black", main = "GO Term Analysis", barcol = c("deepskyblue2",
  "coral"), cex.main = 1.3)

Arguments

x	Strictly positive numeric vector.
up.list	List with named vectors, according to x, but only with positive (i.e. fold changes of gene expression) values.
down.list	As up.list, but with negatives.
y.mar	Plot area horizontal margins.
x.mar	Plot area vertical margins.
x.bound	tba
x.ticks	tba
x.scale	tba
x.gap	gap between bar sections
x.arc.gap	gap between rectangles and arcs
space	tba
fixed.scale	tba
t	Threshold for Jaccard distance to display.
tc	NA
main	Plot title.
barcol	Color of ratio bars.
cex.main	Character expansion of the plot title.

Author(s)

Robert Sehlke [aut]
Sven E. Templer [ctb]
Authors of plotrix package for the plot functionality of arcs [ctb]

Examples

## Not run: 

### golub.deg data example
x = subset(golubstat, p<=.05 & significant>4 & !duplicated(genes))
x = head(x, 10)

lfcvec = x$deg.log2fc
genevec = x$genes

uplist = list()
downlist = list()
for (i in 1:length(lfcvec)) {
  names(lfcvec[[i]]) = genevec[[i]] 
  uplist[[i]] = lfcvec[[i]][lfcvec[[i]] > 0]
  downlist[[i]] = lfcvec[[i]][lfcvec[[i]] < 0]
}

arc.plot( x = setNames(x$loge, x$term), up.list = uplist, down.list = downlist)

## End(Not run)

dieterich-lab/CellPlot documentation built on May 15, 2019, 8:29 a.m.