#' Plot pc1 and pc2
#'
#' @export
plotPc <- function( genotype, scale = FALSE, xpcindex = 1, ypcindex = 2, ... ) {
pc = prcomp(genotype, scale = scale) # Remark when setting T : there are some outliers but if we set F they disappear !!
ggplot2::qplot( x = pc$x[,xpcindex], y = pc$x[,ypcindex], ...) +
ggplot2::theme(legend.position="none")
}
#' Plot folded allele frequency spectrum
#'
#' @param genotype A matrix of genotype of size nbIndiv x nbLocus
#'
#' @export
plotSNPfoldedspectrum <- function( genotype ) {
spectrum = apply( genotype, MARGIN = 2, FUN = function(x) min(sum(x==1),sum(x==0)))
plot(table(spectrum))
}
#' The allele frequency spectrum
#'
#' @param genotype A matrix of genotype of size nbIndiv x nbLocus
#' @param allel 0 or 1 for allele which you want the spectrum
#'
#' @export
plotSNPspectrum <- function( genotype, allele = 1 ) {
spectrum = apply( genotype, MARGIN = 2, FUN = function(x) sum(x==allele))
plot(table(spectrum))
}
#' Manhattan plot
#'
#' @export
manhattanPlot <- function( p.values ) {
ggplot( data = data.frame(p.values = -log(p.values), index = 1:length(p.values) ), aes( x = index, y = p.values ) ) +
geom_point(colour = rainbow(1))
}
#' Multiple graphs on one page
#'
#' @export
multiplot <- function(..., plotlist=NULL, file, cols=1, layout=NULL) {
# Make a list from the ... arguments and plotlist
plots <- c(list(...), plotlist)
numPlots = length(plots)
# If layout is NULL, then use 'cols' to determine layout
if (is.null(layout)) {
# Make the panel
# ncol: Number of columns of plots
# nrow: Number of rows needed, calculated from # of cols
layout <- matrix(seq(1, cols * ceiling(numPlots/cols)),
ncol = cols, nrow = ceiling(numPlots/cols))
}
if (numPlots==1) {
print(plots[[1]])
} else {
# Set up the page
grid::grid.newpage()
grid::pushViewport(grid::viewport(layout = grid::grid.layout(nrow(layout), ncol(layout))))
# Make each plot, in the correct location
for (i in 1:numPlots) {
# Get the i,j matrix positions of the regions that contain this subplot
matchidx <- as.data.frame(which(layout == i, arr.ind = TRUE))
print(plots[[i]], vp = grid::viewport(layout.pos.row = matchidx$row,
layout.pos.col = matchidx$col))
}
}
}
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