I extended the subview function to support embed image file in a ggplot object.
set.seed(123)
d = data.frame(x=rnorm(10), y=rnorm(10))
imgfile <- tempfile(, fileext=".png")
download.file("https://avatars1.githubusercontent.com/u/626539?v=3&u=e731426406dd3f45a73d96dd604bc45ae2e7c36f&s=140",
destfile=imgfile, mode='wb')
p = ggplot(d, aes(x, y))
subview(p, imgfile, x=d$x[1], y=d$y[1]) + geom_point(size=5)
emojifont is available in CRAN, you can use the following command to install it.
install.packages("emojifont")
An example of using emoji font in R plot is showed below:
To answer the issue, I extend the covplot function to support viewing coverage of a list of GRanges objects or bed files.
library(ChIPseeker)
files <- getSampleFiles()
peak=GenomicRanges::GRangesList(CBX6=readPeakFile(files[[4]]),
CBX7=readPeakFile(files[[5]]))
p <- covplot(peak)
print(p)
Phylip is also a widely used tree format, which contains taxa sequences with Newick tree text.
In ggtree, we can use read.phylip() function to parse the file and use ggtree() to visualize the tree.
This is a question from ggtree user. In ape and phytools, it’s easy to label edge using the edgelabels function.
set.seed(1)
tr = rtree(30)
library(ape)
plot(tr, main="ape")
edgelabels()
ggtree implemented a function, subview, that can add subplots on a
ggplot2 object. It had successful applied to plot pie graphs on map.
set.seed(2016-01-04)
tr <- rtree(30)
tr <- groupClade(tr, node=45)
p <- ggtree(tr, aes(color=group)) + geom_tippoint()
cpos <- get_clade_position(p, node=45)
p1 <- p + geom_hilight(node=45)
p2 <- with(cpos, p+xlim(xmin, xmax*1.01)+ylim(ymin, ymax))
with(cpos, subview(p2+geom_tiplab(), p1+theme_transparent(), x=xmin+(xmax-xmin)*.15, y=ymin+(ymax-ymin)*.85))
