intensity_plot: Generates an intensity plot from x, y datasets

In QCGWAS: Quality Control of Genome Wide Association Study Results

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

QCGWAS documentation built on May 30, 2022, 5:05 p.m.