pedigreeGrid {MinimumDistance} | R Documentation

## Plot the log R ratios and BAFs on a grid given by precomputed viewports

### Description

Plot the log R ratios and BAFs on a grid given by precomputed viewports

### Usage

    pedigreeGrid(g, vps, figs)

### Arguments

`g` | a `MDRanges` object
`vps` | a list of viewports. See `pedigreeViewports`.
`figs` | a list of trellis objects created by the function `plotDenovo`.

### See Also

`plotDenovo` `pedigreeViewports`

### Examples

    library(VanillaICE)
    require(grid)
    ##marker-level summaries
    data(md_exp)
    seqlevels(md_exp, pruning.mode="coarse") <- "chr22"
    ## segmentation results
    data(md_gr)
    posteriorCalls <- MAP2(md_exp, md_gr, MinDistParam())
    g <- denovoHemizygous(posteriorCalls)
    g
    vps <- MinimumDistance:::pedigreeViewports()
    param <- HmmTrellisParam()
    p <- plotDenovo(md_exp, g[1], param)
    p <- pedigreeGrid(g=g[1], vps=vps, figs=p)
    leg <- mdLegend(g[1])
    upViewport(0)
    pushViewport(vps[["legend"]])
    grid.text(leg, x=unit(0.02, "npc"), y=unit(0.95, "npc"), just=c("left", "top"),
              gp=gpar(cex=0.6, fontfamily="mono"))
    ##
    ## combine adjacent denovo hemizygous
    ##
    g2 <- reduce(denovoHemizygous(posteriorCalls), min.gapwidth=500e3)
    post <- MAP2(md_exp, g2)
    g2 <- denovoHemizygous(post)
    p <- plotDenovo(md_exp, g2, param)
    p <- pedigreeGrid(g=g2, vps=vps, figs=p)
    leg <- mdLegend(g2)
    upViewport(0)
    pushViewport(vps[["legend"]])
    grid.text(leg, x=unit(0.02, "npc"), y=unit(0.95, "npc"), just=c("left", "top"),
              gp=gpar(cex=0.6, fontfamily="mono"))

[Package MinimumDistance version 1.38.0 Index]