#' An adapted function of the heatmapSexRatio
#' @export heatmapSexRatioAdapted
heatmapSexRatioAdapted <- function( input, highColor = "blue", lowColor = "red", verbose = FALSE, warnings = TRUE, interactive = FALSE ){
input$SR <- as.numeric(input$SR)
for(cont in 1:nrow(input)){
pairDis <- sort(c(input$disA[cont], input$disB[cont]))
input$pairs[cont] <- paste(pairDis[1], pairDis[2], sep="*")
}
objDuplicated1 <- input[ , c('disA' ,'disB', 'SR' ,'pairs')]
objDuplicated2 <- input[ , c('disB' ,'disA', 'SR' ,'pairs')]
colnames( objDuplicated2) <- c('disA' ,'disB', 'SR' ,'pairs')
obj <- rbind( objDuplicated1, objDuplicated2)
m <- max(as.numeric(obj$SR))
n <- min(as.numeric(obj$SR))
sortedCodesA <- unique(obj[with(obj, order(disA)), "disA"])
sortedCodesB <- unique(obj[with(obj, order(disB)), "disB"])
obj$disA <- factor(obj$disA , levels= as.factor(sortedCodesA))
obj$disB <- factor(obj$disB , levels= as.factor(sortedCodesB))
diseases <- unique(c( as.character(obj$disA), as.character(obj$disB)))
mydata <- as.data.frame( matrix( ncol=length(diseases), nrow=length(diseases)))
colnames(mydata) <- diseases[ order(diseases)]
rownames(mydata) <- diseases[ order(diseases)]
for( i in 1:ncol(mydata)){
dis1 <- colnames(mydata)[i]
for( j in 1:nrow(mydata)){
dis2 <- rownames(mydata)[j]
selection <- obj[ obj$disA == dis1 & obj$disB == dis2, ]
if(nrow(selection) == 0){
selection <- obj[ obj$disB == dis1 & obj$disA == dis2, ]
}
mydata[i,j] <- selection[1,"SR"]
}
}
mydata[lower.tri(mydata)] <- NA
mydata <- as.data.frame(mydata)
mydata$dis <- rownames( mydata)
mydata <-(melt(mydata, 'dis', variable_name='variable'))
mydata$variable <- factor(mydata$variable, levels=rev(levels(mydata$variable)))
p <- ggplot2::ggplot(mydata , ggplot2::aes ( variable, dis ) ) +
ggplot2::geom_tile(ggplot2::aes(fill = value), colour = "white") +
ggplot2::scale_fill_gradient(limits = c(n,m), low = lowColor, high = highColor, na.value = "white") +
ggplot2::theme_grey(base_size = 11) +
ggplot2::scale_x_discrete(expand = c(0, 0)) +
ggplot2::geom_text(ggplot2::aes(label = value ) ) +
ggplot2::theme( plot.margin = grid::unit ( x = c ( 5, 15, 5, 15 ), units = "mm" ),
axis.text.x = ggplot2::element_text ( angle = 45, size = 11, hjust = 1 ) )
p
}
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