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# Copyright (C) 2014 Mohammad H. Ferdosi
#
# HSPhase is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
# HSPhase program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http:#www.gnu.org/licenses/>.
hh <- function (oh, inferredPedigree, realPedigree, pedOnly = TRUE)
{
if (is.null(oh))
stop("Invalid input!")
if (!is.matrix(oh))
stop("Opposing Homozygote matrix should be a MATRIX")
if (nrow(oh) != ncol(oh))
stop("Opposing Homozygote matrix must be a square matrix ")
if (!missing(inferredPedigree) && !missing(realPedigree)) {
# if (nrow(inferredPedigree) != nrow(realPedigree))
# stop("Pedigrees must have the same number of rows")
colour <- c("#E41A1C", "#0000FF", "#00FF00", "#FFA500",
"#E7298A", "#000080", "#00FFFF", "#008000", "#999999",
"#800080", "#008080", "#000000", "#FF4500", "#FFFF00",
"#4DAF4A", "#800000", "#A65628", "#F781BF", "#1B9E77",
"#808000", "#377EB8")
maxrows <- max(nrow(inferredPedigree),nrow(realPedigree))
colour <- rep(colour,ceiling(maxrows/length(colour)))
if(pedOnly == TRUE)
oh = oh[rownames(oh)%in%realPedigree[,1],colnames(oh)%in%realPedigree[,1]]
index1 = match(colnames(oh), realPedigree[, 1])
index2 = match(colnames(oh), inferredPedigree[, 1])
sires <- unique(c(names(table(as.character(realPedigree[,2]))),names(table(as.character(inferredPedigree[,2])))))
realPedigree <- as.character(realPedigree[index1,2])
inferredPedigree <- as.character(inferredPedigree[index2,2])
for(i in 1:length(sires))
{
realPedigree[which(realPedigree==sires[i])] <- colour[i]
inferredPedigree[which(inferredPedigree==sires[i])] <- colour[i]
}
heatmap(oh, symm = T, col = gray.colors(16, start = 0,
end = 1), RowSideColors = inferredPedigree , ColSideColors = realPedigree )
}
else heatmap(oh, symm = T, col = gray.colors(16, start = 0,
end = 1))
}
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