singlePlot: Whole genome plot of a drawable list

In Rgb: The R Genome Browser

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 vector 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 chromosomes 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 further details.
cap.font.col	Single value defining the color of chromosome names in the caps. See the font argument of par for further details.
cap.bg.col	Single value defining the color of chromosome cap background. See the col argument of rect for further 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 further details.
cap.font	Single value defining the font type of chromosome names in the caps. See the font argument of par for further 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

Rgb documentation built on Aug. 18, 2023, 5:05 p.m.