dagLogo {dagLogo} | R Documentation |
Create sequence logo for visualizing results of testing differential usage of amino acids.
dagLogo( testDAUresults, type = c("diff", "zscore"), pvalueCutoff = 0.05, groupingSymbol = getGroupingSymbol(testDAUresults@group), font = "Helvetica", fontface = "bold", fontsize = 5, title = NULL, legend = FALSE, labelRelativeToAnchor = FALSE, labels = NULL, alpha = 1 )
testDAUresults |
An object of |
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. |
A sequence Logo is plotted without returned values.
Jianhong Ou, Haibo Liu
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) dagLogo(t1, groupingSymbol = getGroupingSymbol(t1@group)) dagLogo(t2, groupingSymbol = getGroupingSymbol(t2@group)) dagLogo(t3, groupingSymbol = getGroupingSymbol(t3@group)) dagLogo(t4, groupingSymbol = getGroupingSymbol(t4@group))