Package 'prettyGraphs'

Title: Publication-Quality Graphics
Description: Simple and crisp publication-quality graphics for the ExPosition family of packages. See An ExPosition of the Singular Value Decomposition in R (Beaton et al 2014) <doi:10.1016/j.csda.2013.11.006>.
Authors: Derek Beaton
Maintainer: Derek Beaton <[email protected]>
License: GPL-2
Version: 2.1.10.9999
Built: 2025-02-17 04:29:13 UTC
Source: https://github.com/derekbeaton/exposition1

Help Index

add.alpha

Description

A function to add alpha levels to RGB colors.

Usage

add.alpha(col, alpha = 0.65)

Arguments

col

color from colors()
alpha

alpha level (between 0 and 1)

Note

This code was created by Markus Gesmann. Derek Beaton included the code in prettyGraphs because it is a versatile function and used in prettyGraphs. See: https://magesblog.com/post/2013-04-30-how-to-change-alpha-value-of-colours-in/

Author(s)

Markus Gesmann

contributionBars

Description

Produces bar charts for multivariate analyses. Plots the contribution to the variance from each data point for upwards of two axes (components).

Usage

contributionBars(
  factor_scores,
  contributions,
  x_axis = 1,
  y_axis = 2,
  col = NULL,
  main = NULL,
  upper = "steelblue4",
  lower = "firebrick2",
  threshold = 0,
  sortContributions = TRUE,
  pretty = FALSE,
  show.bg.bars = FALSE
)

Arguments

factor_scores

The factor scores, or x- and y-axis points of a data set.
contributions

The amount of contribution to the variance (between 0-1) by each data point.
x_axis

Which axis is the x-axis? Default is 1.
y_axis

Which axis is the y-axis? Default is 2.
col

A single-column matrix of colors for each data point.
main

A title to be placed at the top of the graph.
upper

The color used to identify the upper bound items that contribute above average variance.
lower

The color used to identify the lower bound items that contribute above average variance.
threshold

A threshold (between 0-1) to draw upper and lower bounds for important items. Default is 1/number of items.
sortContributions

boolean, if TRUE, items will be sorted by contribution. if FALSE, items will appear in their row order.
pretty

a boolean. If FALSE, use the current version. If TRUE, make the bars with prettyBars.
show.bg.bars

a boolean. Only used if pretty is TRUE. If TRUE, background bars are plotted for a fill effect.

Author(s)

Derek Beaton

correlationPlotter

Description

Computes and plots a correlation circle (used in multivariate analyses). Correlation is computed between measured items and components (factors, dimensions, principal axes, etc...).

Usage

correlationPlotter(
  data_matrix,
  factor_scores,
  x_axis = 1,
  y_axis = 2,
  col = NULL,
  pch = NULL,
  xlab = "",
  ylab = "",
  main = "",
  axis.lwd = 3,
  circle.lwd = 3,
  circle.col = "#00000040",
  asp = 1,
  dev.new = TRUE
)

Arguments

data_matrix

A set of data (i.e., original measures and observations)
factor_scores

One set of factor scores that were computed from the original data matrix.
x_axis

Which axis is the x-axis? Default is 1.
y_axis

Which axis is the y-axis? Default is 2.
col

A single-column matrix of colors for each data point.
pch

A single-column matrix of pch for each data point. Indicates which point style to use for each item. See par.
xlab

A label to be placed along the x-axis.
ylab

A label to be placed along the y-axis.
main

A title to be placed at the top of the graph.
axis.lwd

numeric. Line width for the axes.
circle.lwd

numeric. Line width for the circle.
circle.col

color for the circle
asp

numeric. Aspect ratio (see asp in par).
dev.new

boolean. If TRUE, dev.new is called internally to create new device. If FALSE, a device must already be open.

Author(s)

Derek Beaton

createColorVectorsByDesign

Description

Produces a color vector for items by using a design matrix.

Usage

createColorVectorsByDesign(design_matrix, hsv = TRUE, offset = NULL)

Arguments

design_matrix

A dummy coded design matrix.
hsv

a boolean. If TRUE, use prettyGraphsHSVColorSelection. If FALSE, use prettyGraphsColorSelection.
offset

numeric. An offset value to be passed to prettyGraphsHSVColorSelection or prettyGraphsColorSelection.

Value

Produces a list with the following items

oc

The colors of the observations (based on group)
gc

The colors of the groups

Author(s)

Derek Beaton

minmaxHelper

Description

Computes the x- and y- axis constraints for all prettyGraphs functions.

Usage

minmaxHelper(mat1, mat2 = NULL, axis1 = 1, axis2 = 2, findBounds = TRUE)

Arguments

mat1

Matrix that will be plotted. Must be at least 2 rows by 2 columns.
mat2

if NULL, mat2=mat2. Second matrix that will be plotted. Must be at least 2 rows by 2 columns.
axis1

Which column of the matrix will be the x-axis? Default = 1.
axis2

Which column of the matrix will be the y-axis? Default = 2.
findBounds

a boolean. If TRUE, min and max values are found for positive and negative on axis1 and axis2. If FALSE, one value is used for all constraints.

Value

minMaxList

A list with the following values: minx, miny, maxx, maxy

Author(s)

Derek Beaton

Examples

data(beavers)
	minMaxList <- minmaxHelper(as.matrix(beaver1),as.matrix(beaver1),1,2)

peeledHull

Description

Computes and plots a peeled hull around a set of points onto a current graphics device.

Usage

peeledHull(
  data_matrix,
  x_axis = 1,
  y_axis = 2,
  percentage = 1,
  col = "black",
  lwd = 3,
  lty = 1
)

Arguments

data_matrix

A set of data you would like to plot on 2 dimensions (e.g., a scatter plot). Can be original data or factor scores or anything with at least 2 columns.
x_axis

Which axis is the x-axis? Default is 1.
y_axis

Which axis is the y-axis? Default is 2.
percentage

The percentage of points that should be enveloped by the hull.
col

The color of the hull (see col in plot()).
lwd

The thickness of the hull line (see lwd in plot())
lty

The line type (see lty in plot()).

Note

The code for this function was (barely) adapted from Michael Greenacre's book on correspondence analysis. All credit for this code should go to Michael Greenacre; I only turned it into a function. The original code can be found at http://carme-n.org/?sec=code2

Author(s)

Derek Beaton turned Michael Greenacre's code into a function.

References

Greenacre, M. J. (2007). Correspondence Analysis in Practice. Chapman and Hall.

prettyBars

Description

prettyBars creates simple, crisp, publication-style quality bar graphs.

Usage

prettyBars(
  data,
  axis = 1,
  cex.names = 0.5,
  fg.col = NULL,
  axis.lims = NULL,
  show.bg.bars = FALSE,
  threshold.line = FALSE,
  main = "",
  bg.border = "white",
  bg.col = NULL,
  bg.lims = NULL,
  sort.data = TRUE,
  horiz = TRUE,
  dev.new = TRUE
)

Arguments

data

A set of data you would like to plot with bars for 1 dimension. Can be original data or factor scores or anything with at least 1 column.
axis

which axis (column of data) should be plotted?
cex.names

size of the text
fg.col

a matrix (single column) of colors for bars corresponding to rows of data.
axis.lims

two values in the form of c(min,max) for plot limits. If NULL, the min and max are computed.
show.bg.bars

a set of bars to be plotted under the bars in data. Used for a fill effect.
threshold.line

boolean. If TRUE, a line perpendicular to the bars is plotted. The lines appear at bg.lims.
main

A title to be placed at the top of the graph.
bg.border

color for show.bg.bars borders (see border in barplot)
bg.col

a matrix (single column) of colors for background bars to be plotted under fg.col.
bg.lims

two values in the form of c(min,max) for where to plot background bars or threshold line.
sort.data

a boolean. Will sort the bars by descending values.
horiz

see horiz in barplot.
dev.new

boolean. If TRUE, dev.new is called internally to create new device. If FALSE, a device must already be open.

Value

bp.cols

locations of bars (as would be returned by barplot).

Author(s)

Derek Beaton

See Also

barplot, prettyPlot

Examples

##stolen from ?barplot
	#tN <- table(Ni <- stats::rpois(100, lambda = 5))
	#the.colors <- rainbow(length(tN))
	#dev.new()
	#r <- barplot(tN, col = the.colors)
	#prettyBars(as.matrix(tN),axis=1,fg.col=as.matrix(the.colors),horiz=FALSE,dev.new=TRUE)

prettyGraphs: for publication-quality graphics.

Description

prettyGraphs is a package that produces simple, crisp, publication-quality graphics for multivariate analyses.

Details

Package: prettyGraphs
Type: Package
Version: 2.1.10
Date: 2022-08-30
License: GPL-2
Suggests: ExPosition

Author(s)

Derek Beaton <[email protected]>

References

Three functions were copied/derived for use in prettyGraphs: peeledHull, add.alpha, and repmat.

For peeledHull see:
http://carme-n.org/?sec=code2
Greenacre, M. J. (2007). Correspondence Analysis in Practice. Chapman and Hall.

For repmat see:
http://cran.r-project.org/doc/contrib/R-and-octave.txt

For add.alpha see:
https://magesblog.com/post/2013-04-30-how-to-change-alpha-value-of-colours-in/

See Also

prettyPlot contributionBars correlationPlotter peeledHull minmaxHelper repmat

prettyGraphsColors

Description

A function to return only a subset of R colors used by the prettyGraphs package.

Usage

prettyGraphsColors()

Value

possibleColors

A list of colors used by prettyGraphs

Author(s)

Derek Beaton

Algorithmically select colors from prettyGraphs

Description

This function uses prime numbers to select colors from prettyGraphsColors.

Usage

prettyGraphsColorSelection(n.colors = 1, offset = NULL, starting.color = 163)

Arguments

n.colors

number of colors needed
offset

numeric. Should be a prime number, if it is not, the closest prime is selected. This number decides the distance between indices for color selection.
starting.color

numeric. This is the starting location (e.g., color) in a matrix of prettyGraphsColors.

Value

a matrix

a matrix of colors are returned.

Author(s)

Derek Beaton

prime number selection from here:
http://stackoverflow.com/questions/3789968/generate-a-list-of-primes-in-r-up-to-a-certain-number

See Also

prettyGraphsColors, prettyGraphsHSVColorSelection

Algorithmically select HSV colors.

Description

This function uses an HSV color selection algorithm to create HSV color palletes.

Usage

prettyGraphsHSVColorSelection(
  n.colors = 1,
  offset = NULL,
  h = 13,
  s = 0.75,
  v = 0.75
)

Arguments

n.colors

number of colors needed
offset

numeric (decimal/percentage). This number decides the distance between indices for color selection. If NULL, the golden ratio is selected.
h

numeric. The initial hue (see hsv).
s

numeric. The initial saturation (see hsv).
v

numeric. The initial value (see hsv).

Value

a matrix

a matrix of colors are returned.

Author(s)

Derek Beaton

HSV selection from here:
http://martin.ankerl.com/2009/12/09/how-to-create-random-colors-programmatically/

See Also

prettyGraphsColors, prettyGraphsColorSelection

prettyPlot

Description

prettyPlot creates simple, crisp, publication-style quality graphics for multivariate analyses.

Usage

prettyPlot(
  data_matrix,
  x_axis = 1,
  y_axis = 2,
  col = NULL,
  pch = NULL,
  cex = NULL,
  text.cex = NULL,
  pos = 3,
  xlab = "",
  ylab = "",
  main = "",
  display_names = TRUE,
  display_points = TRUE,
  constraints = NULL,
  contributionCircles = FALSE,
  contributions = NULL,
  axes = TRUE,
  fg.line.width = 3,
  fg.type = "l",
  fg.col = "black",
  bg.line.width = 1.5,
  bg.lty = 3,
  bg.col = "black",
  flip = FALSE,
  asp = 1,
  findBounds = TRUE,
  dev.new = TRUE,
  new.plot = TRUE
)

Arguments

data_matrix

A set of data you would like to plot on 2 dimensions (e.g., a scatter plot). Can be original data or factor scores or anything with at least 2 columns.
x_axis

Which axis is the x-axis? Default is 1.
y_axis

Which axis is the y-axis? Default is 2.
col

any acceptable color format. A single-column matrix of colors for each data point. A single value can be used.
pch

A single-column matrix of pch for each data point. A single value can be used. Indicates which point style to use for each item. See par.
cex

a single column of continuous values. A single value can be used. Indicates the size of the points. See par. Used multiplicatively for points with contributions.
text.cex

A replacement for the cex parameter in text() (to avoid collisions with cex). Used additively for points with contributions. See par and text.
pos

integer between 1-4. Determines position of text for points. See par.
xlab

A label to be placed along the x-axis.
ylab

A label to be placed along the y-axis.
main

A title to be placed at the top of the graph.
display_names

boolean. If TRUE, the names of the points will be displayed on the plot.
display_points

boolean. If TRUE, the points will be displayed on the plot.
constraints

A list that contains the plot constraints. Default is NULL (constraints are computed each time).
contributionCircles

boolean. If TRUE, items plotted will vary in size, dependent on amount of contribution to the variance.
contributions

A matrix of contribution values for data_matrix (should also be the same size & dimensionality as data_matrix)
axes

boolean. If TRUE, a new set of axes are plotted.
fg.line.width

integer. Determines thickness of foreground (default: solid) axis lines, see points and lwd under par.
fg.type

character or string Determines type of points for foreground (default: solid) axis lines, see points and type under par.
fg.col

any acceptable color format. Determines color for foreground (default: solid) axis lines, see points and col under par.
bg.line.width

integer. Determines thickness of background (default: dashed) axis lines, see abline and lwd under par.
bg.lty

integer. Determines type of background (default: dashed) axis lines, see abline and lty under par.
bg.col

any acceptable color format. Determines color of background (default: dashed) axis lines, see abline and col under par.
flip

boolean. If TRUE, exchanges bg and col for all applicable pch values.
asp

numeric. Aspect ratio, see par.
findBounds

boolean. If TRUE, finds the min and max of each plotted axes. If FALSE, the largest value is used for all constraints.
dev.new

boolean. If TRUE, dev.new is called internally to create new device. If FALSE, a device must already be open.
new.plot

boolean. If TRUE, plot is called for a new plot on the current device. If FALSE, items will be overlayed much like points.

Details

All items after contributions (i.e., axes onward) are parameters for very fine-grained detail. They are quite powerful but in most cases not required.

Value

Returns a three item list:

col

A matrix of colors where each element is the color for each item plotted.
pch

A matrix of pch values where each element is the pch number for each item plotted.
constraints

A list (from minmaxHelper) of the plot constraints (i.e., min and max for axes)

Author(s)

Derek Beaton

prettyScree

Description

prettyScree creates simple, crisp, publication-style scree plots and “tests” for SVD-based analyses.

Usage

prettyScree(
  eigs,
  retain.col = "mediumorchid4",
  dismiss.col = "gray",
  perc.exp = 1,
  n.comps = NULL,
  broken.stick = TRUE,
  kaiser = TRUE,
  main = ""
)

Arguments

eigs

a vector of positive eigenvalues.
retain.col

a color for components that are kept.
dismiss.col

a color for components that are dismissed.
perc.exp

a value between 0 and 1. Used to retain components that explain perc.comp * 100 variance. Note: perc.exp retains cumsum(explained variance) < (perc.exp * 100) + 1 component.
n.comps

a value between 1 and length(eigs). Used to retain n.comps number of components.
broken.stick

a boolean. If TRUE (default), the broken-stick test is performed (see details).
kaiser

a boolean. If TRUE (default), all components with eigenvalues greater than the mean(eigs) are retained.
main

A title to be placed at the top of the graph.

Details

prettyScree visualizes the distribution of eigenvalues/explained variance from SVD-based analyses. Further, prettyScree performs several rudimentary “tests”. Two rudimentary criteria are implemented: 1) user selected explained variance, and 2) user selected number of components. Additionally, two rudimentary “tests” are implemented: 1) the “broken-stick” distribution of variance model, and 2) the “Kaiser criterion” where all components that explain more variance than the mean are kept.

prettyScree colors components that “pass” all selected tests with retain.col. Any components that do not pass tests are colored by a more transparent version of retain.col. Components that do not meet any criteria for retention are colored by dismiss.col.

prettyScree should be considered “under development” as of 12.09.2013. The function works, but we will be adding more features in the near future.

Value

comps.tests

a matrix with boolean values. Rows indicate which criteria are used, and columns correspond to components. If TRUE, a component is considered “retained” by that test/criteria. If FALSE, the component is “dismissed” according to that test/criteria.

Note

A private function (add.alpha) was copied from http://lamages.blogspot.com/2013/04/how-to-change-alpha-value-of-colours-in.html

Author(s)

Derek Beaton

References

Cangelosi, R., & Goriely, A. (2007). Component retention in principal component analysis with application to cDNA microarray data. Biology direct, 2(2), 1–21.

Peres-Neto, P. R., Jackson, D. A., & Somers, K. M. (2005). How many principal components? Stopping rules for determining the number of non-trivial axes revisited. Computational Statistics & Data Analysis, 49(4), 974–997.

See Also

Also see (some of) the other packages that perform a wide array of SVD-based analyses: ExPosition, FactoMineR, ca, ade4

Examples

prcomp.res <- prcomp(USArrests, scale = TRUE)
	prettyScree(prcomp.res$sdev^2)
	##or
	princomp.res <- princomp(USArrests, cor = TRUE)	
	prettyScree(princomp.res$sdev^2)

repmat

Description

A function to match repmat in Matlab (Mathworks, Natick, MA)

Usage

repmat(a, n, m)

Arguments

a

Matrix or vector to repeat.
n

Number of row repititions.
m

Number of column repititions.

Note

This code was created by Robin Hankin. Derek Beaton included the code in prettyGraphs because it is a versatile function and used in prettyGraphs.

Author(s)

Robin Hankin.

References

For repmat see:
http://cran.r-project.org/doc/contrib/R-and-octave.txt