Parameter specification helper for mhtplot(). This function creates a list
of graphical and behavioural settings used when generating Manhattan plots.
Usage
mht.control(
type = "p",
usepos = FALSE,
logscale = TRUE,
base = 10,
cutoffs = NULL,
colors = NULL,
labels = NULL,
gap = NULL,
cex = 0.4,
lab.cex = 1,
axis.cex = 1.2,
axis.lwd = 1.2,
axis.tck = -0.02,
yline = 3,
xline = 3,
verbose = FALSE
)Arguments
- type
Character. Either
"p"(points) or"l"(lines).- usepos
Logical. Use real chromosomal positions instead of ordinal marker order.
- logscale
Logical. If
TRUE, values are transformed using-log(base)(value)before plotting.- base
Numeric. Base of logarithm used when
logscale = TRUE.- cutoffs
Numeric vector of horizontal reference lines to draw.
- colors
Vector of chromosome colours. Recycled as needed.
- labels
Optional chromosome labels for the x-axis.
- gap
Numeric. Gap inserted between chromosomes on the x-axis.
- cex
Numeric. Scaling factor for plotted points.
- lab.cex
Numeric. Scaling factor for chromosome labels on the x-axis.
- axis.cex
Numeric. Scaling factor for axis tick labels. Increase when exporting high-resolution figures.
- axis.lwd
Numeric. Line width for axes and tick marks.
- axis.tck
Numeric. Length and direction of tick marks. Negative values draw ticks outward (recommended for publication plots).
- yline
Numeric. Margin line for the y-axis label.
- xline
Numeric. Margin line for the x-axis label.
- verbose
Logical. Print plotting progress messages.
Value
a named list of control parameters for mhtplot().
Examples
mht.control()
#> $type
#> [1] "p"
#>
#> $usepos
#> [1] FALSE
#>
#> $logscale
#> [1] TRUE
#>
#> $base
#> [1] 10
#>
#> $cutoffs
#> NULL
#>
#> $colors
#> NULL
#>
#> $labels
#> NULL
#>
#> $gap
#> NULL
#>
#> $cex
#> [1] 0.4
#>
#> $lab.cex
#> [1] 1
#>
#> $axis.cex
#> [1] 1.2
#>
#> $axis.lwd
#> [1] 1.2
#>
#> $axis.tck
#> [1] -0.02
#>
#> $yline
#> [1] 3
#>
#> $xline
#> [1] 3
#>
#> $verbose
#> [1] FALSE
#>