plot.sparge: Visually compare all points from different univariate...

In caroline: A Collection of Database, Data Structure, Visualization, and Utility Functions for R

Visually compare all points from different univariate distributions

Description

Visually compare continuuous univariate distributions using jittered and [progressive levels of] transparent points. This type of diagram plots positions of raw numerical data of comparable univariate distributions with a boxplot overlay indicating quartiles surrounding the central tendency of the underlying points. The distributions are vertically stacked (between) and jittered (within) as well as translucent in order to reduce overlapping points on larger-|N| datasets.

Usage

## S3 method for class 'sparge'
plot(x, f=NULL, out.range=range(unlist(x)), cat.names=names(x), 
           cpd=0, cpw=.4, jit.f=1, horiz=TRUE, add=FALSE, lgnd='auto', zl=FALSE,  
                                        col=1, box.brdrs='gray',alpha=.3, ...)
 

Arguments

x	a list of numeric vectors OR a dataframe with both numeric and factor columns
f	either a factor [that is same length as a numeric 'x'] OR a model formula
out.range	range of all possible outcome variable values (recursive loop prespecification)
cat.names	level names of the primary categorical variable partitioning the distributions
cpd	position dodge: shifts all categorical plotting positions this factor
cpw	position width: width of the swath of jittered categorical positions
jit.f	factor for random jittering (see 'jitter()'
horiz	should rotate existing plot horizontally? (be sure to double check x & y labels match)
add	should we add to the existing plot?
lgnd	added automatically by default but can be suppressed by setting to NULL or FALSE
zl	should we add a horizontal [zero] line at x=0?
col	(vector of) [base] colors of the points of the distribution(s)
box.brdrs	the color of the borders of the box plots surrounding all distributions
alpha	transparency level for [overlapping] points
...	other parameters passed on to plot

Details

The function can currently take three different forms of input. First, x can be a list of numeric vectors with no need for f. Second, x can be a single vector that is to be split by factor f, of the same length. Third, x can be a dataframe and f specifies a model formula in the form of "outcome ~ control" (simple plot) or "out ~ predictor | control" (two series plot with legend).

Value

a 'sparge' [sprinkler/smear] plot of point distributions

See Also

See also 'boxplot' and 'stripchart' in package 'graphics' as well as 'sina', 'violin', 'bean', 'ridgelines', and 'raincloud' plots.

Examples

x <- lapply(sample(1:5), function(avg) (rnorm(500,avg)))
names(x) <- letters[1:length(x)]
plot.sparge(x, col=rep('blue',length(x)), main='sparge plots:\nfor distributional comparison')

## four random distributrions (from the 'boxplot' examples)
distros <- list(Uni05 = (1:100)/21, Norm = rnorm(100), `5T` = rt(100, df = 5), 
                                               Gam2 = rgamma(100, shape = 2))
plot.sparge(distros, ylab='distribution',xlab='')


# three more random distributions (from the 'sinaplot' examples)
bimodal <- c(rnorm(300, -2, 0.6), rnorm(300, 2, 0.6))
uniform <- runif(500, -4, 4)
normal <- rnorm(800,0,3)
distributions <- list(uniform = uniform, bimodal = bimodal, normal = normal)
plot.sparge(distributions, ylab='distribution',xlab='')


## using 'f' [as a factor] argument as grouping factor on just one treatment

# Orchard spray by treatment (compare with 'strip chart' plot)
OS <- with(OrchardSprays, split(decrease, treatment))
plot.sparge(OS, log = "x", main = "OrchardSprays", xlab='decrease',ylab='treatment')

# Tooth Growth
plot.sparge(x=ToothGrowth$len, f=ToothGrowth$sup, xlab='lenght', ylab='supplement')


# multi-predictor using model-based parsing of 'f' [as a formula] and 'x' as a dataset

# Tooth Growth 
plot.sparge(x=ToothGrowth, f="len ~ dose | supp", xlab='dose',ylab='tooth length', horiz=FALSE)
# or model-based with out the supplement sub-splitting
plot.sparge(x=ToothGrowth, f="len ~ dose",  xlab='dose',ylab='tooth length', horiz=FALSE)

# from the CO2 dataset
plot.sparge(CO2, 'uptake ~ Type | Treatment', horiz=FALSE,
            xlab='Type',ylab='Uptake', main='CO2')

# Joyner-Boore earthquake data (heavily rounded)
attenu$magnitude <- as.factor(round(attenu$mag))
attenu$distance <- as.factor(round(log10(attenu$dist)))
plot.sparge(x=attenu, f="accel ~ distance | magnitude", horiz=FALSE, 
  xlab='log10(distance)',ylab='acceleration', main='earthquake attenuation')

# Motor Trend cars data (rounded)
mtcars$cylinders <- as.factor(mtcars$cyl)
plot.sparge(x=mtcars, f="qsec ~ gear | cylinders", horiz=FALSE, 
         xlab='number of gears', ylab='seconds', main='Motor Trend Cars')

# fertility dataset 
infert$education <- as.factor(infert$education)
infert$ages <- jitter(infert$age, amount=1/2)
plot.sparge(x=infert, f="ages ~ spontaneous | education ", horiz=FALSE, 
       ylab='[jittered] ages, yrs', xlab='spontaneous' , main='fertility')

caroline documentation built on Oct. 21, 2024, 9:06 a.m.