stat_aggregate-method: Generates summaries on the specified windows

In lawremi/ggbio: Visualization tools for genomic data

Generates summaries on the specified windows

Description

Generates summaries on the specified windows

Usage

## S4 method for signature 'GRanges'
stat_aggregate(data, ..., xlab, ylab, main, by, FUN,
                          maxgap=-1L, minoverlap=0L,
                          type=c("any", "start", "end", "within", "equal"),
                          select=c("all", "first", "last", "arbitrary"),
                          y = NULL, window = NULL, facets = NULL, 
                          method = c("mean", "median","max",
                                   "min", "sum", "count", "identity"),
                          geom = NULL)

Arguments

data	A GRanges or data.frame object.
...	Arguments passed to plot function. such as aes() and color.
xlab	Label for x
ylab	Label for y
main	Title for plot.
by	An object with 'start', 'end', and 'width' methods. Passed to aggreagate.
FUN	The function, found via 'match.fun', to be applied to each window of 'x'. Passed to aggreagate.
maxgap, minoverlap, type	Used in the internal call to findOverlaps() to detect overlaps. See ?findOverlaps in the IRanges package for a description of these arguments.
select	It passed to findOverlaps. When select is "all" (the default), the results are returned as a Hits object. When select is "first", "last", or "arbitrary" the results are returned as an integer vector of length query containing the first, last, or arbitrary overlapping interval in subject, with NA indicating intervals that did not overlap any intervals in subject. If select is "all", a Hits object is returned. For all other select the return value depends on the drop argument. When select != "all" && !drop, an IntegerList is returned, where each element of the result corresponds to a space in query. Whenselect != "all" && drop, an integer vector is returned containing indices that are offset to align with the unlisted query.
y	A character indicate the varialbe column for which aggregation is taken on, same as aes(y = ).
window	Integer value indicate window size.
facets	Faceting formula to use.
method	customized method for aggregating, if FUN is not provided.
geom	The geometric object to use display the data.

Value

A 'Layer'.

Author(s)

Tengfei Yin

Examples

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))


ggplot(gr) + stat_aggregate(aes(y = value))
## or
## ggplot(gr) + stat_aggregate(y = "value")
ggplot(gr) + stat_aggregate(aes(y = value), window = 36)
ggplot(gr) + stat_aggregate(aes(y = value), select = "first")
## Not run: 
## no hits 
ggplot(gr) + stat_aggregate(aes(y = value), select = "first", type = "within")

## End(Not run)
ggplot(gr) + stat_aggregate(window = 30,  aes(y = value),fill = "gray40", geom = "bar")
ggplot(gr) + stat_aggregate(window = 100, fill = "gray40", aes(y = value),
                           method = "max", geom = "bar")

ggplot(gr) + stat_aggregate(aes(y = value), geom = "boxplot")
ggplot(gr) + stat_aggregate(aes(y = value), geom = "boxplot", window = 60)
## now facets need to take place inside stat_* geom_* for an accurate computation
ggplot(gr) + stat_aggregate(aes(y = value), geom = "boxplot", window = 30,
              facets = sample ~ seqnames)
## FIXME:
## autoplot(gr, stat = "aggregate", aes(y = value), window = 36)
## autoplot(gr, stat = "aggregate", geom = "boxplot", aes(y = value), window = 36)

lawremi/ggbio documentation built on Nov. 1, 2023, 2:40 p.m.