lut_file <- system.file("extdata", "color-lut.csv", package="pixelgram")
pixmap_colors <-read.csv(lut_file, header=T, stringsAsFactors=F, strip.white=T)
devtools::use_data(pixmap_colors, internal=T, overwrite=T)
### These options are from weblogo-3.4:
# Copyright (c) 2003-2005 The Regents of the University of California.
# Copyright (c) 2005 Gavin E. Crooks
# This software is distributed under the MIT Open Source License.
# <http://www.opensource.org/licenses/mit-license.html>
#
# Permission is hereby granted, free of charge, to any person obtaining a
# copy of this software and associated documentation files (the "Software"),
# to deal in the Software without restriction, including without limitation
# the rights to use, copy, modify, merge, publish, distribute, sublicense,
# and/or sell copies of the Software, and to permit persons to whom the
# Software is furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included
# in all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
### Popular color codings for nucleic and amino acids.
# bp
# "TAU", "darkorange", "Weak (2 Watson-Crick hydrogen bonds)"
# "GC", "blue", "Strong (3 Watson-Crick hydrogen bonds)"
# hydrophobicity
# "RKDENQ", "blue", "hydrophilic"
# "SGHTAP", "green", "neutral"
# "O", "magenta", "PNGsite"
# "-*#", "grey", "unknown"
# ".", "white", "transmitted"
# "YVMCLFIW", "black", "hydrophobic"
# chemistry
# "GSTYC", "green", "polar"
# "NQ", "purple", "neutral"
# "KRH", "blue", "basic"
# "O", "cyan", "PNGsite"
# "-*#", "grey", "unknown"
# ".", "white", "transmitted"
# "DE", "red", "acidic"
#"PAWFLIMV", "black", "hydrophobic"
# taylor "W.R. Taylor, Protein Engineering, Vol 10, 743-746 (1997)" - check out this paper!
# "a", "#CCFF00"
# "c", "#FFFF00"
# "d", "#FF0000"
# "e", "#FF0066"
# "f", "#00FF66"
# "g", "#FF9900"
# "h", "#0066FF"
# "i", "#66FF00"
# "k", "#6600FF"
# "l", "#33FF00"
# "m", "#00FF00"
# "n", "#CC00FF"
# "o", "#00FFFF"
# "p", "#FFCC00"
# "q", "#FF00CC"
# "r", "#0000FF"
# "s", "#FF3300"
# "t", "#FF6600"
# "v", "#99FF00"
# "w", "#00CCFF"
# "x", "#FF00FF"
# "y", "#00FFCC"
# "z", "#FF00FF"
# "-", "grey"
# "*", "grey"
# "#", "grey"
# ".", "white"
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