plot.haplovalidate: Make manhattanplot highlighting reconstructed haplotype...

In kathrinannaotte/haplovalidate: Detecting selected haplotype blocks in Evolve and Resequence experiments

Make manhattanplot highlighting reconstructed haplotype blocks

Description

under construction

Usage

plot.haplovalidate(blocks, cmh, label = TRUE)

Arguments

blocks
cmh
label

Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (blocks, cmh, label = TRUE)
{
    neuefarbe.raw <- unique(c(brewer.pal(8, "Set1"), brewer.pal(7,
        "Dark2"), brewer.pal(7, "Set2"), brewer.pal(12, "Set3"),
        brewer.pal(12, "Paired"), brewer.pal(7, "Accent"), brewer.pal(7,
            "Spectral")))
    neuefarbe <- colorRampPalette(neuefarbe.raw)(max(as.numeric(factor(blocks$tag)),
        na.rm = TRUE))
    col.sub <- neuefarbe[as.numeric(factor(blocks$tag))]
    blocks[, `:=`(groupcol, col.sub)]
    for (j in unique(blocks$chr)) {
        cluster.sub <- blocks[chr == j, ]
        png(paste(j, "_haplovalidate.png", sep = ""), 2400, 1200)
        maxy <- round(max(as.numeric(cmh[chr == j, score]), na.rm = TRUE),
            -1) + round(max(as.numeric(cmh[chr == j, score]),
            na.rm = TRUE), -1) * 0.05
        cmh[chr == j, plot(pos/1e+06, as.numeric(score), pch = 19,
            col = "#414547", ylim = c(0, maxy), xlab = "position Mb",
            ylab = "cmh score", lwd = 3, cex.axis = 1.5, cex.lab = 2,
            main = paste("sim ", no, " merge chr", j, sep = ""),
            xaxp = c(0, 50, 50))]
        cluster.sub[, points(as.numeric(pos)/1e+06, as.numeric(score),
            cex = 2, lwd = 3, pch = 19, col = groupcol)]
        count <- 0
        cluster.sub.ord <- cluster.sub[order(score, decreasing = TRUE),
            ]
        for (k in na.exclude(unique(cluster.sub.ord$groupcol))) {
            group.sub <- cluster.sub.ord[groupcol == k, ]
            distance <- group.sub$pos/1e+06
            levi <- maxy - count
            points(distance, rep(levi, length(distance)), col = k,
                pch = 19, cex = 3)
            if (label)
                text(distance[1], levi, unique(group.sub[, tag]),
                  cex = 2)
            count <- count + round(max(as.numeric(cmh[chr ==
                j, score]), na.rm = TRUE), -1) * 0.01
        }
        dev.off()
    }
  }

kathrinannaotte/haplovalidate documentation built on May 21, 2022, midnight