geom_arch {ggbio} | R Documentation |
Show interval data as arches.
## S4 method for signature 'data.frame' geom_arch(data, ..., n = 25, max.height = 10) ## S4 method for signature 'GRanges' geom_arch(data, ..., xlab, ylab, main, facets = NULL, rect.height = 0, n = 25, max.height = 10)
data |
A |
... |
Extra parameters passed to autoplot function,
|
xlab |
Label for x |
ylab |
Label for y |
main |
Title for plot. |
n |
Integer values at which interpolation takes place to create 'n' equally spaced points spanning the interval ['min(x)', 'max(x)']. |
facets |
Faceting formula to use. |
rect.height |
When data is |
max.height |
Max height of all arches. |
To draw a interval data as arches, we need to provide a special geom for
this purpose. Arches is popular in gene viewer or genomoe browser,
when they try to show isoforms or gene model.geom_arch
,
just like any other geom_*
function in ggplot2, you can pass
aes() to it to map variable to height of arches.
A 'Layer'.
Tengfei Yin
set.seed(1) N <- 100 library(GenomicRanges) ## ======================================= ## simmulated GRanges ## ======================================= gr <- GRanges(seqnames = sample(c("chr1", "chr2", "chr3"), size = N, replace = TRUE), IRanges( start = sample(1:300, size = N, replace = TRUE), width = sample(70:75, size = N,replace = TRUE)), strand = sample(c("+", "-", "*"), size = N, replace = TRUE), value = rnorm(N, 10, 3), score = rnorm(N, 100, 30), sample = sample(c("Normal", "Tumor"), size = N, replace = TRUE), pair = sample(letters, size = N, replace = TRUE)) ## ======================================= ## default ## ======================================= ggplot(gr) + geom_arch() # or ggplot() + geom_arch(gr) ## ======================================= ## facetting and aesthetics ## ======================================= ggplot(gr) + geom_arch(aes(color = value, height = value, size = value), alpha = 0.2, facets = sample ~ seqnames)