stat_aggregate {ggbio} | R Documentation

## 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`. When`select != "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)

[Package ggbio version 1.35.2 Index]