Modified code of ggseqlogo to display non-canonical (e.g. phosphorylated) amino acids in different color
Plotting the sequence logo of peptides with modifications in purple. Modified residues have to be in lowercase letters of the respective amino acid.
Default values are for sequences inlcuding phosphorylated residues (i.e. sequences over an alphabet of 23 amino acids, 20 canonical amino acids plus s, t, and y).
ggseqlogoMOD is a further developed version of the ggseqlogo function of the package ggseqlogo (Wagih, Omar. ggseqlogo: a versatile R package for drawing sequence logos. Bioinformatics 33, no. 22 (2017): 3645-3647. https://doi.org/10.1093/bioinformatics/btx469 PMID: 29036507), with minor changes for modified amino acids.
R package ggplot2.
devtools::install_github("GfellerLab/ggseqlogo")
ggseqlogoMOD(data,
smallSampleCorr = FALSE,
col_scheme = "phosphorylated",
additionalAA = "sty",
seq_type = "aa",
font = "helvetica_phosphorylated",
legendText = FALSE,
ylim = c(0, 4.32),
title = NULL,
titleSize = 24,
titlePos = 0.5,
axisTextSizeX = 18,
axisTextSizeY = 18,
axisTitleSize = 18,
...)
data A list of sequences or a position weight matrix.
smallSampleCorr Include small-sample correction in information content or not.
col_scheme Color scheme of plot.
additionalAA Amino acids that include a modification.
seq_type Sequence type of input.
font Font for plot.
legendText Plot legend or not.
ylim Range of y-axis.
title Title of plot.
titleSize Size of title.
titlePos Horizontal position of title.
axisTextSizeX Size of x tick labels.
axisTextSizeY Size of y tick labels.
axisTitleSize Size of axis title.
Load package:
library(ggseqlogo)
Load example data:
data(data_B0702, package="ggseqlogo")
Plot phosphorylated binding motif of HLA-B0702:
ggseqlogoMOD(b7p)
Marthe Solleder (marthe.solleder@unil.ch) and David Gfeller (david.gfeller@unil.ch).