Plot baits in a linkSet object
Usage
plotBaits(
linkset,
scoreCol = "score",
countCol = "count",
n = 4,
baits = NULL,
plotBaitNames = TRUE,
plevel1 = 5,
plevel2 = 3,
outfile = NULL,
width = 20,
height = 20,
extend.base = 1e+06,
bgCol = "black",
lev2Col = "blue",
lev1Col = "red",
...
)Arguments
- linkset
A linkSet object
- scoreCol
Column name containing scores for coloring points
- countCol
Column name containing counts for y-axis values
- n
Number of random baits to plot if baits parameter is NULL
- baits
Vector of specific baits to plot. If NULL, n random baits are selected
- plotBaitNames
Logical indicating whether to show bait names in plot titles
- plevel1
Upper threshold for score coloring (red)
- plevel2
Lower threshold for score coloring (blue)
- outfile
Output file path. If NULL, plot is displayed rather than saved
- width
Width of output plot in inches
- height
Height of output plot in inches
- extend.base
Base pairs to extend view range on either side of bait
- bgCol
Color for points below plevel2 threshold
- lev2Col
Color for points between plevel2 and plevel1 thresholds
- lev1Col
Color for points above plevel1 threshold
- ...
Additional plotting parameters