plot sequence logo for test results

Description

plot sequence logo for test results

Usage

dagLogo(testDAUresults, type=c("diff", "zscore"), pvalueCutoff=0.05, namehash=NULL,
                    font="Helvetica-Bold", textgp=gpar(), legend=FALSE, 
                    labelRelativeToAnchor=FALSE,
                    labels=NULL)

Arguments

Value

none

Author(s)

Jianhong Ou

See Also

nameHash

Examples

    data("seq.example")
    data("proteome.example")
    bg <- buildBackgroundModel(seq.example, proteome=proteome.example, permutationSize=10)
    t <- testDAU(seq.example, bg)
    dagLogo(t)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(dagLogo)
Loading required package: biomaRt
Loading required package: grImport
Loading required package: grid
Loading required package: XML
Loading required package: motifStack
Loading required package: MotIV
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


Attaching package: 'MotIV'

The following object is masked from 'package:stats':

    filter

Loading required package: ade4

Attaching package: 'ade4'

The following object is masked from 'package:BiocGenerics':

    score

Loading required package: Biostrings
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: XVector
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/dagLogo/dagLogo.Rd_%03d_medium.png", width=480, height=480)
> ### Name: dagLogo
> ### Title: plot sequence logo for test results
> ### Aliases: dagLogo
> ### Keywords: figure
> 
> ### ** Examples
> 
>     data("seq.example")
>     data("proteome.example")
>     bg <- buildBackgroundModel(seq.example, proteome=proteome.example, permutationSize=10)
>     t <- testDAU(seq.example, bg)
>     dagLogo(t)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>