plot_coverage: Plot coverage gaps in data

In mrc-ide/mipmapper: Filtering and analysis of MIP panel genetic datasets

Description

Plot coverage gaps in data

Usage

plot_coverage(dat, type = "o", pch = 20, ylim = c(0, 100),
  xlab = "Coverage (unique reads)", ylab = "data completeness (%)",
  log = "x", ...)

Arguments

dat	MIP data. The data must have the following variables: Coverage : The total read coverage as numerics
type	1-character string giving the type of plot desired. The following values are possible, for details, see plot: "p" for points, "l" for lines, "b" for both points and lines, "c" for empty points joined by lines, "o" for overplotted points and lines, "s" and "S" for stair steps and "h" for histogram-like vertical lines. Finally, "n" does not produce any points or lines.
pch	Either an integer or a single character specifying a symbol to be used as the default in plotting points. See points for possible values and their interpretation. Note that only integers and single-character strings can be set as a graphics parameter (and not NA nor NULL).
ylim	the y limits of the plot.
xlab	a label for the x axis, defaults to a description of x.
ylab	a label for the y axis, defaults to a description of y.
log	a character string which contains "x" if the x axis is to be logarithmic, "y" if the y axis is to be logarithmic and "xy" or "yx" if both axes are to be logarithmic.
...	other arguments to plot

Details

Plot a line graph showing the percentage of sites that have more than a given number of unique reads (coverage).

Examples

dat <- dummy_data()
dat2 <- filter_misc(dat)
plot_coverage(dat2)

mrc-ide/mipmapper documentation built on May 20, 2019, 3:27 p.m.