Usage
plotSinglescan.heat(data.obj, singlescan.obj,
standardized = TRUE, show.marker.labels = FALSE,
show.chr.boundaries = TRUE, label.chr = TRUE,
threshold.above = NULL, color = "blue",
light.dark = "light", scale.fun = NULL)
Arguments
singlescan.obj
The object in which the results of singlescan are stored.
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.
show.chr.boundaries
A logical value. If TRUE the boundaries of the chromosomes are marked with vertical lines.
label.chr
A logical value. If TRUE, the chromosomes are labeled with their numbers
threshold.above
A numeric value. Effects above this value are colored white. This is useful in preventing large effects from swamping out differences between smaller effects.
color
The color to be used in the raster image.
light.dark
Either "light", or "dark" to indicate the range of colors that should be plotted.
scale.fun
The name of function, such as sqrt or log10, that will scale the values in the matrix to increase contrast in the image.