R: Draw text in a cell, specifically for genomic graphics

circos.genomicText {circlize} | R Documentation

## Draw text in a cell, specifically for genomic graphics

### Description

Draw text in a cell, specifically for genomic graphics

### Usage

    circos.genomicText(region, value = NULL, y = NULL, labels = NULL, labels.column = NULL,
        numeric.column = NULL, sector.index = get.cell.meta.data("sector.index"),
        track.index = get.cell.meta.data("track.index"), posTransform = NULL,
        direction = NULL, facing = "inside", niceFacing = FALSE,
        adj = par("adj"), cex = 1, col = "black", font = par("font"), padding = 0,
        extend = 0, ...)

### Arguments

`region` | A data frame contains 2 column which correspond to start position and end position
`value` | A data frame contains values and other information
`y` | A vector or a single value indicating position of text.
`labels` | Labels of text corresponding to each genomic positions
`labels.column` | If labels are in `value`, index of column in `value`
`numeric.column` | Which column in `value` data frame should be taken as y-value. If it is not defined, only the first numeric columns in `value` will be taken.
`sector.index` | Pass to `circos.rect`
`track.index` | Pass to `circos.rect`
`posTransform` | Self-defined function to transform genomic positions, see `posTransform.default` for explanation
`facing` | Passing to `circos.text`. Settings are similar as `col`
`niceFacing` | Should the facing of text be adjusted to fit human eyes?
`direction` | Deprecated, use `facing` instead.
`adj` | Pass to `circos.text`. Settings are similar as `col`
`cex` | Pass to `circos.text`. Settings are similar as `col`
`col` | Pass to `circos.text`. The length of `col` can be either one or number of rows of `region`.
`font` | Pass to `circos.text`. Settings are similar as `col`
`padding` | pass to `posTransform` if it is set as `posTransform.text`
`extend` | pass to `posTransform` if it is set as `posTransform.text`
`...` | Mysterious parameters

### Details

The function is a low-level graphical function and usually is put in `panel.fun` when using `circos.genomicTrackPlotRegion`.

### References

Gu, Z. (2014) circlize implements and enhances circular visualization in R. Bioinformatics.

### Examples

    ## Not run:
    circos.par("track.height" = 0.1, cell.padding = c(0, 0, 0, 0))
    circos.initializeWithIdeogram(plotType = NULL)

    bed = generateRandomBed(nr = 20)

    circos.genomicTrackPlotRegion(bed, ylim = c(0, 1), panel.fun = function(region, value, ...) {
        circos.genomicText(region, value, y = 0.5, labels = "text", ...)
    })

    bed = cbind(bed, sample(letters, nrow(bed), replace = TRUE))
    circos.genomicTrackPlotRegion(bed, panel.fun = function(region, value, ...) {
        circos.genomicText(region, value, labels.column = 2, ...)
    })

    circos.clear()

    ## End(Not run)

[Package circlize version 0.4.5 Index]