Package 'vipor'

Title: Plot Categorical Data Using Quasirandom Noise and Density Estimates
Description: Generate a violin point plot, a combination of a violin/histogram plot and a scatter plot by offsetting points within a category based on their density using quasirandom noise.
Authors: Scott Sherrill-Mix, Erik Clarke
Maintainer: Scott Sherrill-Mix <[email protected]>
License: GPL (>= 2)
Version: 0.4.7
Built: 2024-11-13 06:34:02 UTC
Source: CRAN

Help Index

the ave() function but with arguments passed to FUN

Description

A function is applied to subsets of x where each subset consist of those observations with the same groupings in y

Usage

aveWithArgs(x, y, FUN = mean, ...)

Arguments

x

a vector to apply FUN to
y

a vector or list of vectors of grouping variables all of the same length as x
FUN

function to apply for each factor level combination.
...

additional arguments to FUN

Value

A numeric vector of the same length as x where an each element contains the output from FUN after FUN was applied on the corresponding subgroup for that element (repeated if necessary within a subgroup).

See Also

ave

Examples

aveWithArgs(1:10,rep(1:5,2))
aveWithArgs(c(1:9,NA),rep(1:5,2),max,na.rm=TRUE)

Census ata on US counties

Description

A dataset containing data from the US census burea

Usage

counties

Format

A data frame with 3143 rows and 8 variables:

id

GEO.id from original data

state

state in which the county is located

county

name of the county

population

population of the county

housingUnits

housing units in the county

totalArea

Area in square miles - Total area

waterArea

Area in square miles - Water area

landArea

Area in square miles - Land area

Source

http://factfinder.census.gov/bkmk/table/1.0/en/DEC/10_SF1/GCTPH1.US05PR (link now dead), system.file("data-raw", "makeCounties.R", package = "vipor")

References

https://web.archive.org/web/20150326040847/https://www.census.gov/prod/cen2010/cph-2-1.pdf

Convert a vector of integers representing digits in an arbitrary base to an integer

Description

Takes a vector of integers representing digits in an arbitrary base e.g. binary or octal and converts it into an integer (or the integer divided by base^length(digits) for the number of digits if fractional is TRUE). Note that the first digit in the input is the least significant.

Usage

digits2number(digits, base = 2, fractional = FALSE)

Arguments

digits

a vector of integers representing digits in an arbitrary base
base

the base for the numeral system (e.g. 2 for binary or 8 for octal)
fractional

divide the output by the max for this number of digits and base. Note that this is base^length(digits) not base^length(digits)-1.

Value

an integer

References

https://en.wikipedia.org/wiki/Radix

Examples

digits2number(c(4,4,1),8)
digits2number(number2digits(100))

Generate a permutation string meeting Tukey criteria

Description

Find a random string of concatenated permutations of 1:n fulfilling Tukey's criteria that there are no runs of 3 or more increases or decreases in a row. Tukey just uses the default n=5.

Usage

generatePermuteString(nReps = 20, n = 5)

Arguments

nReps

number of permutations to concatenate
n

permutations from 1 to n

Value

a vector of nReps*n integers giving concatenated permutations

Examples

tukeyPermutes()
tukeyPermutes(6,3)

Data on HIV integration sites from several studies

Description

A dataset containing data from a meta-analysis looking for differences between active and inactive HIV integrations. Each row represents a provirus integrated somewhere in a human chromosome with whether viral expression was detectd, the distance to the nearest gene and the number of reads from H4K12ac ChIP-Seq mapped to within 50,000 bases of the integration.

Usage

integrations

Format

A data frame with 12436 rows and 4 variables:

study

the cell population infected by HIV

latent

whether the provirus was active (expressed) or inactive (latent)

nearestGene

distance to nearest gene (transcription unit) (0 if in a gene)

H4K12ac

number of reads aligned within +- 50,000 bases in a H4K12ac ChIP-Seq

Source

https://retrovirology.biomedcentral.com/articles/10.1186/1742-4690-10-90, system.file("data-raw", "makeIntegrations.R", package = "vipor")

References

https://retrovirology.biomedcentral.com/articles/10.1186/1742-4690-10-90

Convert an integer to an arbitrary base

Description

Takes an integer and converts it into an arbitrary base e.g. binary or octal. Note that the first digit in the output is the least significant.

Usage

number2digits(n, base = 2)

Arguments

n

the integer to be converted
base

the base for the numeral system (e.g. 2 for binary or 8 for octal)

Value

a vector of length ceiling(log(n+1,base)) respresenting each digit for that numeral system

References

https://en.wikipedia.org/wiki/Radix

Examples

number2digits(100)
number2digits(100,8)

Offset data using quasirandom noise to avoid overplotting

Description

Arranges data points using quasirandom noise (van der Corput sequence), pseudorandom noise or alternatively positioning extreme values within a band to the left and right to form beeswarm/one-dimensional scatter/strip chart style plots. That is a plot resembling a cross between a violin plot (showing the density distribution) and a scatter plot (showing the individual points). This function returns a vector of the offsets to be used in plotting.

Usage

offsetX(y, x = rep(1, length(y)), width = 0.4, varwidth = FALSE, ...)

offsetSingleGroup(
  y,
  maxLength = NULL,
  method = c("quasirandom", "pseudorandom", "smiley", "maxout", "frowney", "minout",
    "tukey", "tukeyDense"),
  nbins = NULL,
  adjust = 1
)

Arguments

y

vector of data points
x

a grouping factor for y (optional)
width

the maximum spacing away from center for each group of points. Since points are spaced to left and right, the maximum width of the cluster will be approximately width*2 (0 = no offset, default = 0.4)
varwidth

adjust the width of each group based on the number of points in the group
...

additional arguments to offsetSingleGroup
maxLength

multiply the offset by sqrt(length(y)/maxLength) if not NULL. The sqrt is to match boxplot (allows comparison of order of magnitude different ns, scale with standard error)
method

method used to distribute the points:

quasirandom:

points are distributed within a kernel density estimate of the distribution with offset determined by quasirandom Van der Corput noise

pseudorandom:

points are distributed within a kernel density estimate of the distribution with offset determined by pseudorandom noise a la jitter

maxout:

points are distributed within a kernel density with points in a band distributed with highest value points on the outside and lowest in the middle

minout:

points are distributed within a kernel density with points in a band distributed with highest value points in the middle and lowest on the outside

tukey:

points are distributed as described in Tukey and Tukey "Strips displaying empirical distributions: I. textured dot strips"

tukeyDense:

points are distributed as described in Tukey and Tukey but are constrained with the kernel density estimate
nbins

the number of points used to calculate density (defaults to 1000 for quasirandom and pseudorandom and 100 for others)
adjust

adjust the bandwidth used to calculate the kernel density (smaller values mean tighter fit, larger values looser fit, default is 1)

Value

a vector with of x-offsets of the same length as y

Examples

## Generate fake data
dat <- list(rnorm(50), rnorm(500), c(rnorm(100), rnorm(100,5)), rcauchy(100))
names(dat) <- c("Normal", "Dense Normal", "Bimodal", "Extremes")

## Plot each distribution with a variety of parameters
par(mfrow=c(4,1), mar=c(2,4, 0.5, 0.5))
sapply(names(dat),function(label) {
  y<-dat[[label]]
  
  offsets <- list(
    'Default'=offsetX(y),
    'Smoother'=offsetX(y, adjust=2),
    'Tighter'=offsetX(y, adjust=0.1),
    'Thinner'=offsetX(y, width=0.1)
  )
  ids <- rep(1:length(offsets), sapply(offsets,length))
  
  plot(unlist(offsets) + ids, rep(y, length(offsets)), 
       ylab=label, xlab='', xaxt='n', pch=21, las=1)
  axis(1, 1:4, c("Default", "Adjust=2", "Adjust=0.1", "Width=10%"))
})

Return all permutations of a vector

Description

Recursively generates all permutations of a vector. The result will be factorial(length(vals)) long so be careful with any longer vectors (e.g. longer than 10).

Usage

permute(vals)

Arguments

vals

a vector of elements to be permuted

Value

A list of vectors containing all permutation of the values

See Also

sample

Examples

permute(letters[1:3])
permute(1:5)

Produce offsets such that points are sorted with most extreme values to right and left

Description

Produce offsets to generate smile-like or frown-like distributions of points. That is sorting the points so that the most extreme values alternate between the left and right e.g. (max,3rd max,...,4th max, 2nd max). The function returns either a proportion between 0 and 1 (useful for plotting) or an order

Usage

topBottomDistribute(x, frowney = FALSE, prop = TRUE)

Arguments

x

the elements to be sorted
frowney

if TRUE then sort minimums to the outside, otherwise sort maximums to the outside
prop

if FALSE then return an ordering of the data with extremes on the outside. If TRUE then return a sequence between 0 and 1 sorted by the ordering

Value

a vector of the same length as x with values ranging between 0 and 1 if prop is TRUE or an ordering of 1 to length(x)

Examples

topBottomDistribute(1:10)
topBottomDistribute(1:10,TRUE)

Find permutations meeting Tukey criteria

Description

Find all permutations of 1:n fulfilling Tukey's criteria that there are no runs of 3 or more increases or decreases in a row. Tukey just uses the default n=5 and limit=2.

Usage

tukeyPermutes(n = 5, limit = 2)

Arguments

n

permutations from 1 to n
limit

the maximum number of increases or decreases in a row

Value

a list of vectors containing valid permutations

Examples

tukeyPermutes()
tukeyPermutes(6,3)

Combine multiple permutation strings into one

Description

Combine base+1 permutation strings to generate offsets

Usage

tukeyT(nReps = 10, base = 5)

Arguments

nReps

number of permutations to paste together
base

generate permutations of integers 1:base

Value

A nReps*base length vector giving offset positions based on Tukey's algorithm

Examples

tukeyT()
tukeyT()
tukeyT(5,4)

Generate random positions based on Tukey texture algorithm

Description

Generate partly random, partly constrained lateral displacements based on Tukey texture algorithm from Tukey and Tukey 1990

Usage

tukeyTexture(
  x,
  jitter = TRUE,
  thin = FALSE,
  hollow = FALSE,
  delta = diff(stats::quantile(x, c(0.25, 0.75))) * 0.03
)

Arguments

x

the points to be jittered. really only used to calculate length
jitter

if TRUE add random jitter to each point
thin

if TRUE then push points to the center in thin regions
hollow

if TRUE then expand points outward to avoid “hollowness”
delta

a “reasonably small value” used in edge straightening and thinning

Value

a vector of length length(x) giving displacements for each corresponding point in x

Examples

x<-rnorm(200)
plot(tukeyTexture(x),x)
x<-1:100
plot(tukeyTexture(x),x)
plot(tukeyTexture(log10(counties$landArea),TRUE,TRUE),log10(counties$landArea),cex=.25)

Generate van der Corput sequences

Description

Generates the first (or an arbitrary offset) n elements of the van der Corput low-discrepancy sequence for a given base

Usage

vanDerCorput(n, base = 2, start = 1)

Arguments

n

the first n elements of the van der Corput sequence
base

the base to use for calculating the van der Corput sequence
start

start at this position in the sequence

Value

a vector of length n with values ranging between 0 and 1

References

https://en.wikipedia.org/wiki/Van_der_Corput_sequence

Examples

vanDerCorput(100)

Functions to generate violin scatter plots

Description

Arranges data points using quasirandom noise (van der Corput sequence) to create a plot resembling a cross between a violin plot (showing the density distribution) and a scatter plot (showing the individual points). The development version of this package is on https://github.com/sherrillmix/vipor

Details

The main functions are:

offsetX:

calculate offsets in X position for plotting (groups of) one dimensional data

vpPlot:

a simple wrapper around plot and offsetX to generate plots of grouped data

Author(s)

Scott Sherrill-Mix, [email protected]

See Also

https://github.com/sherrillmix/vipor

Examples

dat<-list(rnorm(100),rnorm(50,1,2))
ids<-rep(1:length(dat),sapply(dat,length))
offset<-offsetX(unlist(dat),ids)
plot(unlist(dat),ids+offset)

Plot data using offsets by quasirandom noise to generate a violin point plot

Description

Arranges data points using quasirandom noise (van der Corput sequence), pseudorandom noise or alternatively positioning extreme values within a band to the left and right to form beeswarm/one-dimensional scatter/strip chart style plots. That is a plot resembling a cross between a violin plot (showing the density distribution) and a scatter plot (showing the individual points) and so here we'll call it a violin point plot.

Usage

vpPlot(x = rep("Data", length(y)), y, xaxt = "y", offsetXArgs = NULL, ...)

Arguments

x

a grouping factor for y (optional)
y

vector of data points
xaxt

if 'n' then no x axis is plotted
offsetXArgs

a list with arguments for offsetX
...

additional arguments to plot

Value

invisibly return the adjusted x positions of the points

See Also

offsetX

Examples

dat<-list(
  'Mean=0'=rnorm(200),
  'Mean=1'=rnorm(50,1),
  'Bimodal'=c(rnorm(40,-2),rnorm(60,2)),
  'Gamma'=rgamma(50,1)
)
labs<-factor(rep(names(dat),sapply(dat,length)),levels=names(dat))
vpPlot(labs,unlist(dat))