intensity_plot {QCGWAS}

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.

Details

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

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.

See Also

match_alleles