| stat_aggregate {ggbio} | R Documentation |
Generates summaries on the specified windows
## S4 method for signature 'GRanges'
stat_aggregate(data, ..., xlab, ylab, main, by, FUN, start = NULL,
end = NULL, width = NULL, y = NULL, frequency = NULL,
delta = NULL, simplify = TRUE, window = NULL, facets =
NULL, type = c("mean", "median", "max", "min", "sum",
"count", "identity"), geom = NULL)
data |
A |
xlab |
Label for x |
ylab |
Label for y |
main |
Title for plot. |
by |
An object with 'start', 'end', and 'width' methods. Passed to |
FUN |
The function, found via 'match.fun', to be applied to each window of
'x'. Passed to |
start |
Start of the window. If 'by' is missing, then must supply two of the 'start', 'end', 'width'. If 'window' is provided then you don't have to specify it. |
end |
End of the window. If 'by' is missing, then must supply two of the 'start', 'end', 'width'. If 'window' is provided then you don't have to specify it. |
width |
Width of the window. If 'by' is missing, then must supply two of the 'start', 'end', 'width'. If 'window' is provided then you don't have to specify it. |
y |
A character indicate the varialbe column for which aggregation is
taken on. Notice for geom like 'boxplot', we don't compute or
aggregate the variable, we simply want to use the idenitcal y as y
axis, in that case please put y in the |
frequency |
Optional arguments that specify the sampling frequency within the window. |
delta |
Optional arguments that specify the sampling increment within the window. |
... |
Arguments passed to plot function. such as aes() and color. |
simplify |
A logical value specifying whether or not the result should be simplified to a vector or matrix if possible. |
window |
Integer value indicate window size. |
facets |
Faceting formula to use. |
type |
|
geom |
The geometric object to use display the data. |
A 'Layer'.
Tengfei Yin
library(GenomicRanges)
set.seed(1)
N <- 1000
## ======================================================================
## 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))
## 36,37 doesn't work
## ggplot(gr) + stat_aggregate(y = "value",fill = "gray40")
## ggplot(gr) + stat_aggregate(window = 30, y = "value",fill = "gray40", geom = "histogram")
## ggplot(gr) + stat_aggregate(window = 100, fill = "gray40",y = "value",
## type = "max", geom = "histogram")