dagLogo: Create sequence logo.

In dagLogo: dagLogo: a Bioconductor package for visualizing conserved amino acid sequence pattern in groups based on probability theory

Description

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

Usage

dagLogo(
  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

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")
dagLogo(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))))
dagLogo(t1, groupingSymbol = getGroupingSymbol(t1@group))
dagLogo(t2, groupingSymbol = getGroupingSymbol(t2@group))
dagLogo(t3, groupingSymbol = getGroupingSymbol(t3@group))
dagLogo(t4, groupingSymbol = getGroupingSymbol(t4@group))

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