stat_gene-method: Calculate gene structure

In lawremi/ggbio: Visualization tools for genomic data

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)

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