stat_identity {ggbio} | R Documentation |
Transform the data to a suitable data.frame and then one could use multiple geom or even stat to re-plot the data.
## S4 method for signature 'ANY' stat_identity(data, ...) ## S4 method for signature 'GRanges' stat_identity(data, ..., geom = NULL) ## S4 method for signature 'Rle' stat_identity(data, ..., xlab, ylab, main, geom = NULL) ## S4 method for signature 'RleList' stat_identity(data, ..., xlab, ylab, main, geom = NULL, indName = "sample")
data |
Typically a |
... |
Extra parameters such as aes() passed to |
geom |
The geometric object to use display the data. |
xlab |
x label. |
ylab |
y label. |
main |
title of graphic.. |
indName |
sample name. |
A 'Layer'.
Tengfei Yin
## load set.seed(1) N <- 50 require(GenomicRanges) ## simul ## ====================================================================== ## 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)) ## geom_point_start ggplot() + stat_identity(gr, aes(x = start, y = value), geom = "point") ## or more formal ggplot(gr) + stat_identity(aes(x = start, y = value), geom = "point") ## geom_point_midpoint ggplot(gr) + stat_identity(aes(x = midpoint, y = value), geom = "point") ## geom_rect_all ggplot(gr) + stat_identity(aes(xmin = start, xmax = end, ymin = value - 0.5, ymax = value + 0.5), geom = "rect") ## geom_rect_y ggplot(gr) + stat_identity(aes(y = value), geom = "rect") ## geom_line ggplot(gr) + stat_identity(aes(x = start, y = value), geom = "line") ## geom_segment ggplot(gr) + stat_identity(aes(y = value), geom = "segment") ## Rle/RleList library(IRanges) lambda <- c(rep(0.001, 4500), seq(0.001, 10, length = 500), seq(10, 0.001, length = 500)) xVector <- rpois(1e4, lambda) xRle <- Rle(xVector) xRleList <- RleList(xRle, 2L * xRle) ggplot(xRle) + stat_identity(geom = "point") ggplot(xRleList) + stat_identity(geom = "point")