qtplot: Plot a continuous variable by discrete categories

In tobyjohnson/gtx: Genetics ToolboX

Description

Plots a continuous variable (such as a quantitative trait) by discrete categories (such as genotype).

Usage

## S3 method for class 'character'
qtplot(object, x, data, ylab, xlab, ylim, col, points.method = "beeswarm", boxplot.layer = "over", ...)
## S3 method for class 'numeric'
qtplot(object, x, data, ylab, xlab, ylim, col, points.method = "beeswarm", boxplot.layer = "over", ...)

Arguments

object	The name or values of the continuous variable
x	The name or values of the discrete category variable
data	A data frame containing values
ylab	A label for the y axis
xlab	A label for the x axis
ylim	y axis range
points.method	Name of method for plotting individual datapoints, either “stripchart” or “beeswarm”
boxplot.layer	Layer to draw the boxplot relative to individual datapoints, either “over”, “under”, or “none”
col	A vector of colours
...	Other arguments, ignored

Details

Generates a plot displaying numerical data (usually continuous) by levels of a factor.

When displaying such data, it is preferable to avoid the loss of information inherent in a classical boxplot, and to display all the individual datapoints if at all possible. However, the boxplot summary remains a desirable adjunct.

The argument points.method specifies how individual datapoints are drawn. The default, “beeswarm”, is deterministic and avoids overlap of individual datapoints unless absolutely necessary, but may be slow for large numbers of datapoints. The alternative, “stripchart”, is fast but is not deterministic and tends to overlap datapoints.

When datapoints are overlapping, it may be possible to visualise this using transparency in col.

Value

Returns an invisible null. The plot is generated as a side effect.

Author(s)

Toby Johnson [e-mail]

Examples

data(aoex1)
qtplot("bmi", "rs123456", data = aoex1)
with(aoex1, qtplot(bmi, rs123456))
x <- sample(1:2, 1000, replace = TRUE)
y <- rnorm(1000, x, .02)
qtplot(y, x, points.method = "stripchart")
## Not run: 
qtplot(y, x) # takes a long time

## End(Not run)

tobyjohnson/gtx documentation built on Aug. 30, 2019, 8:07 p.m.