Ideogram {ggbio} | R Documentation |
Plot single chromosome with cytobands.
plotIdeogram(obj, subchr = NULL, zoom.region = NULL, which = NULL, xlab, ylab, main, xlabel = FALSE, color = "red", fill = "red", alpha = 0.7, zoom.offset = 0.2, size = 1, cytobands = TRUE, aspect.ratio = 1/20, genome) ## constructor Ideogram(obj, subchr = NULL, which = NULL, xlabel = FALSE, cytobands = TRUE, color = "red", fill = "red", alpha = 0.7, zoom.region = NULL, zoom.offset = 0.2, size = 1, aspect.ratio = 1/20, ..., genome)
obj |
A |
subchr |
A single character of chromosome names to show. |
which |
|
zoom.region |
A numeric vector of length 2 indicating zoomed region. |
xlab |
Label for x |
ylab |
Label for y |
main |
Title for plot. |
xlabel |
A logical value. Show the x label or not. |
color |
color for highlight region. |
fill |
fill color for highlight region. |
alpha |
alpha for highlight regio. |
zoom.offset |
zoomed highlights region offset around chromosome plotting region. |
size |
size for zoomed region rectangle boundary. |
cytobands |
If FALSE, plot just blank chromosome without cytobands. default is TRUE. es |
aspect.ratio |
aspect ratio for the chromosome ideogram plot, default is NULL. |
genome |
genome character passed to |
... |
passed to ggbio constructor. |
User could provide the whole ideogram and use subchr to point to particular chromosome.
A ggplot
object.
Tengfei Yin
## Not run: library(biovizBase) p.ideo <- Ideogram(genome = "hg19") p.ideo library(GenomicRanges) p.ideo + xlim(GRanges("chr2", IRanges(1e8, 1e8+10000))) Ideogram(genome = "hg19", xlabel = TRUE) ## End(Not run)