singlePlot {Rgb} | R Documentation

## Whole genome plot of a drawable list

### Description

This function plots a drawable list on all the chromosomes side by side, with a constant X axis scale. It mainly defines a custom layout for a series of `browsePlot` calls.

### Usage

      singlePlot(drawables, columns = 4, exclude = c("X", "Y"), add = c(5e6, 15e6),
        vertical = FALSE, capWidth = "1 cm", spacer = "1 cm", finalize = TRUE,
        cap.border = "black", cap.font.col = "black", cap.bg.col = NA, cap.adj = c(0.5, 0.5),
        cap.cex = 2, cap.font = 2, mar = c(0,0,0,0), bty = "n", xaxt = "n", xgrid = FALSE,
        yaxt = "n", ylab = "", ysub = "", ...)

### Arguments

`drawables` | A `drawable.list` object containing the tracks to plot, as returned by `drawable.list` or `tk.tracks`.
`columns` | Single integer value, column count in the chromosome layout.
`exclude` | Character vector, the names of the chromosomes to not plot.
`add` | Numeric vctor of length 2, the margins to add before and after each chromosome, in base pairs.
`vertical` | Single logical value, whether to produce a plot showing chromsomes horizontally or vertically. Actually the figure will need to be manually rotated in the resulting file.
`capWidth` | Single value defining the width of the chromosome name caps, in a suitable format for `layout` `widths` argument.
`spacer` | Single value defining the height of the inter-chromosome gaps, in a suitable format for `layout` `heights` argument.
`finalize` | Single logical value, whether to fill unused space with a blank plot and return to default layout or allow further manual addition. If `FALSE`, the next plot will fill the whole blank space left.
`cap.border` | Single value defining the color of chromosome cap borders. See the `border` argument of `rect` for futher details.
`cap.font.col` | Single value defining the color of chromosome names in the caps. See the `font` argument of `par` for futher details.
`cap.bg.col` | Single value defining the color of chromosome cap background. See the `col` argument of `rect` for futher details.
`cap.adj` | Numeric vector of length 2 defining the X and Y adjustment of the chromosome names in the caps, ranging between 0 (left / bottom) to 1 (right / top).
`cap.cex` | Single value defining the character expansion factor for chromosome names in the caps. See the `cex` argument of `par` for futher details.
`cap.font` | Single value defining the font type of chromosome names in the caps. See the `font` argument of `par` for futher details.
`mar` | Refer to ... described here-after. To disable the overriding and let each track define its own value as usual, set this parameter to `NULL`.
`bty` | Refer to ... described here-after. To disable the overriding and let each track define its own value as usual, set this parameter to `NULL`.
`xaxt` | Refer to ... described here-after. To disable the overriding and let each track define its own value as usual, set this parameter to `NULL`.
`xgrid` | Refer to ... described here-after. To disable the overriding and let each track define its own value as usual, set this parameter to `NULL`.
`yaxt` | Refer to ... described here-after. To disable the overriding and let each track define its own value as usual, set this parameter to `NULL`.
`ylab` | Refer to ... described here-after. To disable the overriding and let each track define its own value as usual, set this parameter to `NULL`.
`ysub` | Refer to ... described here-after. To disable the overriding and let each track define its own value as usual, set this parameter to `NULL`.
`...` | Further arguments will be passed to `browsePlot` for each chromosome, which itself will pass it to the `draw` method of each track, overriding the class default and object setting.

### Author(s)

Sylvain Mareschal

### See Also

`browsePlot`, `drawable.list`, `drawable`

[Package Rgb version 1.6.1 Index]