use ggbio facilities to display GWAS results for selected traits in genomic coordinates

Description

use ggbio facilities to display GWAS results for selected traits in genomic coordinates

Usage

traitsManh(gwr, selr = GRanges(seqnames = "chr17", IRanges(3e+07, 5e+07)), traits = c("Asthma", "Parkinson's disease", "Height", "Crohn's disease"), truncmlp = 25, ...)

Arguments

Details

uses a ggbio autoplot

Value

autoplot value

Note

An xlab is added, concatenating genome tag with seqnames tag.

Author(s)

VJ Carey <stvjc@channing.harvard.edu>

Examples

# do a p-value truncation if you want to reduce compression
data(ebicat38)
library(GenomeInfoDb)
seqlevelsStyle(ebicat38) = "UCSC"
traitsManh(ebicat38)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(gwascat)
Loading required package: Homo.sapiens
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: OrganismDbi
Loading required package: GenomicFeatures
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: GO.db

Loading required package: org.Hs.eg.db

Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene
gwascat loaded.  Use data(ebicat38) for hg38 coordinates;
 data(ebicat37) for hg19 coordinates.
Warning message:
replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'ggbio' 
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/gwascat/traitsManh.Rd_%03d_medium.png", width=480, height=480)
> ### Name: traitsManh
> ### Title: use ggbio facilities to display GWAS results for selected traits
> ###   in genomic coordinates
> ### Aliases: traitsManh
> ### Keywords: models graphics
> 
> ### ** Examples
> 
> # do a p-value truncation if you want to reduce compression
> data(ebicat38)
> library(GenomeInfoDb)
> seqlevelsStyle(ebicat38) = "UCSC"
> traitsManh(ebicat38)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>