dagLogo {dagLogo} | R Documentation

## Create sequence logo.

### 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))

[Package dagLogo version 1.30.0 Index]