stat_gene {ggbio} | R Documentation

## Calculate gene structure

### Description

Calculate gene structure.

### Usage

    ## S4 method for signature 'TxDb'
    stat_gene(data, ...)

### Arguments

`data` | A `GRanges` or `data.frame` object.
`...` | Extra parameters such as aes() passed to `geom_alignment`.

### Value

A 'Layer'.

### Author(s)

Tengfei Yin

### See Also

`geom_alignment`

### Examples

    ## Not run:
    ## loading package
    ## Deprecated
    library(TxDb.Hsapiens.UCSC.hg19.knownGene)
    data(genesymbol, package = "biovizBase")
    txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene

    ## made a track comparing full/reduce stat.
    p1 <- ggplot() + geom_alignment(txdb, which = genesymbol["RBM17"])
    p1 <- ggplot() + stat_gene(txdb, which = genesymbol["RBM17"])
    ## or
    p1 <- ggplot(txdb) + stat_gene(which = genesymbol["RBM17"])

    p1 <- ggplot(txdb) + stat_gene(which = genesymbol["RBM17"])
    p2 <- ggplot(txdb) + stat_gene(which = genesymbol["RBM17"], stat =
    "reduce")
    p2 <- ggplot(txdb) + stat_gene(which = genesymbol["RBM17"], stat = "reduce")
    ## ggplot(txdb) + geom_alignment(which = genesymbol["RBM17"]) + stat_reduce()
    ## ggplot(txdb) + geom_alignment(which = genesymbol["RBM17"])
    tracks(full = p1, reduce = p2, heights = c(3, 1))

    ## change y labels
    ggplot(txdb) + stat_gene(which = genesymbol["RBM17"], names.expr =
    "tx_id:::gene_id")

    ## End(Not run)

[Package ggbio version 1.42.0 Index]