Description Usage Arguments Author(s) Examples
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).
1 2 3 4 5 |
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. |
Robert Sehlke [aut]
Sven E. Templer [ctb]
Authors of plotrix package for the plot functionality of arcs [ctb]
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | ## 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)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.