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# Part of the SMITIDstruct R package.
# Copyright (C) 2018 Jean-François Rey <jean-francois.rey@inra.fr>
#
# This program 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 2
# of the License, or (at your option) any later version.
#
# This 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, write to the Free Software Foundation, Inc.,i
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
#
#' plotDiversity.pDistance
#' @description plot Mean Pairwise Distance for an host viralpop over time
#' @param host an Host object
#' @param lvpop a ViralPopSet object
#' @export
plotDiversity.pDistance <- function(host, lvpop){
host_pD <- getDiversity.pDistance(host, lvpop)
if(nrow(host_pD) > 0) {
if( is.timestamp(host_pD$time[1]) ) host_pD$time <- getDate(host_pD$time)
ggplot(host_pD, environment=environment(),mapping = aes_string(x='time', y='p_distance', group='1')) +
geom_point(color= "blue") +
geom_line(color="steelblue") +
labs(title=paste("Mean Pairwise Distance for host",host@ID)) +
theme(plot.title = element_text(size="25",face="bold", hjust=0.5))
}
else ggplot(data.frame()) + geom_blank()
}
#' plotDiversity.sfs
#' @description plot Allele frequency spetrum for an host viralpop over time
#' @param host an Host object
#' @param lvpop an ViralPopSet object
#' @export
plotDiversity.sfs <- function(host, lvpop) {
host_sfs <- getDiversity.sfs(host,lvpop)
if(length(host_sfs) > 0) {
toplot <- data.frame(Times=numeric(), Freq=numeric(), time=character(),stringsAsFactors = FALSE)
for( i in 1:length(host_sfs)) {
df <- data.frame(table(host_sfs[[i]]), stringsAsFactors = FALSE)
colnames(df) <- c("Times","Freq")
#toplot <- rbind(toplot,cbind(df,time=rep(names(host_sfs[i]),nrow(df))))
toplot <- rbind(toplot,data.frame(df,time=rep(names(host_sfs[i]),nrow(df)), stringsAsFactors=FALSE))
}
if( is.timestamp(as.numeric(toplot$time[1])) ) toplot$time <- getDate(as.numeric(toplot$time))
ggplot(data=toplot, aes_string(x='Times', y='Freq')) +
geom_bar(stat="identity", fill="steelblue") +
geom_text(aes_string(label="Freq"), vjust=1.6, color="white", size=3.5) +
ggtitle(paste("Allele Frequency Spectrum for host",host@ID)) +
facet_grid(. ~ time, drop=TRUE, scales="free_x") +
theme(plot.title = element_text(size="25",face="bold", hjust=0.5))
#theme_minimal()
}
else ggplot(data.frame()) + geom_blank()
}
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