pgParams {plotgardener} | R Documentation

## pgParams: plotgardener parameters object

### Description

Creates an object of class "pgParams" that can be used by plotgardener functions. pgParams can be used to set a set of parameters to be shared across multiple functions.

### Usage

    pgParams(assembly = "hg38", gene = NULL, geneBuffer = NULL, ...)

### Arguments

`assembly` | String defining the genome build. Default value is `assembly = "hg38"`.
`gene` | (optional) String naming a gene used to set the chrom, chromstart, and chromend arguments.
`geneBuffer` | (optional) Integer base-pairs to extend the start and end of a gene defined by argument `gene`. Can be one integer or a vector of length 2, where the first integer will extend the start of the gene and the second integer will extend the end of the gene.
`...` | This function will take any plotgardener function parameters and their values: `alpha` `altchrom` `altchromend` `altchromstart` `archHeight` `arrow` `at` `axis` `axisLine` `baseline` `baseline.color` `baseline.lwd` `bg` `binCap` `binSize` `border` `boxHeight` `boxWidth` `breaks` `BSgenome` `cex` `check.overlap` `chrom` `chromend` `chromstart` `clip` `collapse` `colorbyStrand` `colorTrans` `column` `commas` `curvature` `data` `default.units` `digits` `display.column` `draw` `extend` `file` `fill` `flip` `fontcolor` `fontsize` `geneBackground` `geneHighlights` `gene.id.column` `geneOrder` `Genome` `half` `height` `id` `id.lengths` `image` `interpolate` `just` `label` `labels` `leadSNP` `legend` `length` `limitLabel` `linecolor` `lineend` `linejoin` `lty` `lwd` `main` `margin` `matrix` `negData` `norm` `OrgDb` `orientation` `palette` `pch` `plot` `quiet` `r` `range` `resolution` `res_scale` `rot` `scale` `scientific` `scipen` `sequence` `shift` `showBands` `showGuides` `sigCol` `sigLine` `sigVal` `spaceHeight` `spaceWidth` `strand` `strandLabels` `strandSplit` `stroke` `style` `tcl` `ticks` `title` `TxDb` `type` `width` `x` `xgrid` `x0` `x1` `y` `ygrid` `ymax` `y0` `y1` `zrange`

### Details

pgParams generates arguments from exported plotgardener functions at loading time of the package. Arguments defined in a pgParams object can be passed into the `params` argument of plotgardener functions. params arguments can be overridden from within plotgardener functions.

pgParams also provides an alternative region definition mechanism. Given a gene name and genome assembly, pgParams returns the appropriate "chrom", "chromstart", and "chromend" with a default buffer of `(gene length) / 2` added to the ends of the gene coordinates. The buffer amount can be set manually with the `geneBuffer` parameter. Buffer extending beyond the length of the chromosome will be trimmed.

### Value

Returns an object of class `pgParams` containing plotgardener function arguments.

### Examples

    ## Load hg19 genomic annotation packages
    library("TxDb.Hsapiens.UCSC.hg19.knownGene")
    library("org.Hs.eg.db")

    ## Define parameters
    p1 <- pgParams(gene = "IL1B", assembly = "hg19")

    ## Optionally add more parameters
    p2 <- pgParams(fontsize = 10, assembly = "hg19")

    ## Combine parameters and pass them to a plotgardener function
    plotGenes(params = c(p1, p2))

[Package plotgardener version 1.0.17 Index]