dagLogo: Create sequence logo.

Description Usage Arguments Value Author(s) Examples

View source: R/dagLogo.R

Description

Create sequence logo for visualizing results of testing differential usage of amino acids.

Usage

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(
  testDAUresults,
  type = c("diff", "zscore"),
  pvalueCutoff = 0.05,
  groupingSymbol = getGroupingSymbol(testDAUresults@group),
  font = "Helvetica",
  fontface = "bold",
  fontsize = 8,
  title = NULL,
  legend = FALSE,
  labelRelativeToAnchor = FALSE,
  labels = NULL,
  alpha = 1,
  markers = list()
)

Arguments

testDAUresults

An object of testDAUresults-class, which cintains results of testing differential amino acid usage).

type

A character vector of length 1. Type of statistics to be displayed on y-axis. Available choices are "diff" or "zscore".

pvalueCutoff

A numeric vector of length 1. A cutoff of p-values.

groupingSymbol

A named character vector.

font

A character vector of length 1. Font type for displaying sequence Logo.

fontface

An integer, fontface of text for axis annotation and legends.

fontsize

An integer, fontsize of text for axis annotation and legends.

title

A character vector of length 1, main title for a plot.

legend

A logical vector of length 1, indicating whether to show the legend.

labelRelativeToAnchor

A logical vector of length 1, indicating whether x-axis label should be adjusted relative to the anchoring position.

labels

A character vector, x-axis labels.

alpha

Alpha channel for transparency of low affinity letters.

markers

A list of marker-class.

Value

A sequence Logo is plotted without returned values.

Author(s)

Jianhong Ou, Haibo Liu

Examples

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data('seq.example') 
data('proteome.example')
bg <- buildBackgroundModel(seq.example, proteome=proteome.example, 
                           numSubsamples=10, testType = "ztest")
t0 <- testDAU(seq.example, bg)
t1 <- testDAU(dagPeptides = seq.example, dagBackground = bg, 
              groupingScheme = "hydrophobicity_KD")
t2 <- testDAU(dagPeptides = seq.example, dagBackground = bg, 
             groupingScheme = "charge_group")
t3 <- testDAU(dagPeptides = seq.example, dagBackground = bg, 
             groupingScheme = "chemistry_property_Mahler")
t4 <- testDAU(dagPeptides = seq.example, dagBackground = bg, 
              groupingScheme = "hydrophobicity_KD_group")
(t0, markers = list(new("marker", type="rect", start=c(5, 8), 
                                gp=gpar(lty=3, fill=NA)),
                            new("marker", type="text", start=9, label="*", 
                                gp=gpar(col=3))))
(t1, groupingSymbol = getGroupingSymbol(t1@group))
(t2, groupingSymbol = getGroupingSymbol(t2@group))
(t3, groupingSymbol = getGroupingSymbol(t3@group))
(t4, groupingSymbol = getGroupingSymbol(t4@group))

dagLogo documentation built on Dec. 5, 2020, 2 a.m.