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
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.