Usage
plotSinglescan(data.obj, singlescan.obj,
chr = NULL, traits = NULL, show.alpha.values = NULL,
standardized = TRUE, show.marker.labels = FALSE,
mark.covar = FALSE, mark.chr = TRUE, plot.type = "h",
overlay = FALSE, trait.colors = NULL,
show.rejected.markers = FALSE, show.selected.markers = FALSE,
relative.spacing = FALSE, gap.grades = 10,
min.gap = 1, max.gap = 10, min.gap.genome = 1000,
max.gap.genome = 1000000, fixed.scale = FALSE,
ymax = NULL, cex.axis = 0.5, cex.points = 1,
cex.alpha = 0.5, cex.labels = 2, cex.legend = 0.7)
Arguments
singlescan.obj
The object in which the results from singlescan are stored.
chr
An optional vector indicating which chromosomes should be plotted. If NULL, the default, all chromosomes are plotted.
traits
An optional vector indicating which traits should be plotted. If NULL, the default, all traits are plotted.
show.alpha.values
A numeric vector indicating which alpha values specified in singlescan should be plotted. If NULL, all alpha values calculated in singlescan are plotted.
standardized
A logical value. If TRUE, the absolute value of the regression t statistics ($\beta/\sigma$) are plotted. If FALSE, the raw regression coefficients ($\beta$) are plotted.
show.marker.labels
A logical value indicating whether marker names should be printed along the plot axes.
mark.covar
A logical value. If TRUE, the covarates for the pair scan are marked in red. If FALSE, all markers are plotted in black.
mark.chr
A logical value. If TRUE, alternating chromosomes are shaded in gray to aid in visualizing chromosome boundaries.
plot.type
A character indicating whether the marker effects should be plotted as vertical lines ("h"), points ("p"), lines ("l"), or both lines and points ("b").
overlay
A logical value indicating whether plots of scans should be overlayed on top of each other or plotted in separate panels.
trait.colors
If overlay is TRUE, this argument specifies different colors for the ovelayed scans. There are four default colors (black, blue, purple, darkgreen). Alternate or additional colors can be specified manally.
show.rejected.markers
A logical value. If select.markers.for.pairscan has been run, setting this value to TRUE places indicators above markers that have been rejected from being included in the pair scan. show.selected.markers and show.rejected markers cannot be set to TRUE simultaneously.
show.selected.markers
A logical value. If select.markers.for.pairscan has been run, setting this value to TRUE places indicators above markers that have been selected for the pair scan.
relative.spacing
A logical value indicating whether markers should be plotted at even intervals (FALSE) or spaced relative to their actual genomic locations (TRUE).
min.gap
The minimum plotted gap between markers.
max.gap
The maximum plotted gap between markers.
min.gap.genome
The minimum gap between markers in genomic distance.
max.gap.genome
The maximum gap between markers in genomic distance.
gap.grades
An integer indicating how finely to bin between minimum gap distance and maximum gap distance.
fixed.scale
A logical value to indicate whether the y axes of multiple plots should have the same minimum and maximum.
ymax
An optional numeric value indicating a fixed maximum for the y axes.
cex.axis
A numeric value indicating the size of the font for the axes.
cex.points
A numeric value indicating the pointsize or line width for data plotting.
cex.alpha
A numeric value indicating the font size for writing alpha values.
cex.labels
A numeric value indicating the font size for labels.
cex.legend
A numeric value indicating the size of the legend.