QCGWAS (version 1.0-9)

intensity_plot: Generates an intensity plot from x, y datasets

Description

This function is used by match_alleles to generate an intensity plot. This function is currently only partially implemented, so we recommend that users do not bother with it.

Usage

intensity_plot(x, y, strata, nbin = 20,
               xmax = max(x), xmin = min(x),
               ymax = max(y), ymin = min(y),
               strata_colours = c("black", "red", "turquoise3"),
               verbose = TRUE, xlab = "x", ylab = "y", ...)

Arguments

x, y

numerical vectors; the x and y coordiantes of the datapoints.

strata

logical vector; indicates whether the datapoint belongs to strata 1 or 2. If missing, all datapoints are assumed to belong to strata 1.

nbin

integer: the number of bins (categories) on the x and y axis.

xmax, xmin, ymax, ymin

numeric; the range of x and y values shown in the plot.

strata_colours

character vector of length 3, indicating the colours to be used for entries of strata 1, 2 or mixed, respectively.

verbose

logical; determines whether a warning is printed in the console when datapoints are removed.

xlab, ylab, …

arguments passed to plot.

Value

An invisible object of type list with the following two components:

NA_removed

The number of entries removed due to missing values

outliers_removed

The number of entries removed because they exceeded the thresholds specified by the min/max arguments.

Details

This function is intended as an alternative to the standard scatter plot for the allele-frequency correlation graph.

See Also

match_alleles