‘graphicsutils’, an overview

Kevin Cazelles

Source: vignettes/overview.Rmd

Abstract

The package graphicsutils is a set of miscellaneous functions to be used with the graphics library.

The “graphicsutils” package includes a set of functions built on the top of the graphics package. This vignette is basically a guided tour of the package, a cook book that exemplifies the functions implemented.

An important aspect of graphicsutils is that functions have been written in a layer-oriented perspective meaning that the default behavior of the functions provides functions that are rather minimalist and the user should call other functions (such as axis, box2, etc.) or change the default parameters values in order to customize his plot. Even though that this takes more command lines, we think that this approach makes it easier to get very personalized figures and we hope the functions we provide will help users making beautiful figures.

Empty your plot with plot0()

In the layer-oriented approach we are using, it is very convenient to start with an empty plot of a given dimension, just like a canevas. To help creating such canevas, we wrote plot0(). Note that by default x and y ranges are c(-1, 1). Moreover the argument fill color the plot region (it is equivalent to calling the plotAreaColor()).

par(mar = c(1, 1, 1, 1), mfrow = c(2, 2))
#
plot0()
text(0, 0, "plot0")
#
plot0(fill = "#8eb5e3")
#
plot0()
plotAreaColor(col = "#8eb5e3")
#
plot0()
plotAreaColor(col = "#8eb5e3", border = "grey20", lty = 2, lwd = 4)
plot0() and plotAreaColor()

plot0() and plotAreaColor()

The fill and grid.col make the customization of the background fairly easy:

plot0(c(-10, 10), fill = "grey90", grid.col = 'white')

Another parameter text that adds a text in the middle of the plot area which makes plot0() a helpful function to add piece of legend :

plot0(c(-10, 10), asp = 1, fill = 8, text = 'cool', srt = 45, cex = 4, col = 2)

Add plot components

box2()

The box2() function allows the user to add any axes around the plot. A limitation of the box() function is does not allowed all the combination of axes. box2() proposes a simple way to select the sides to be added on the plot: 1 = bottom; 2 = left; 3 = top; 4 = right.

par(mar = rep(2, 4))
plot0()
box2(which = "figure", lwd = 2, fill = "grey30")
box2(side = 12, lwd = 2, fill = "grey80")
axis(1)
axis(2)

Add text with a box around

First example

plot(1, type = "n", ann = FALSE, las = 1)
coords <- textBox(x = 1, y = 1, labels = "AqA")
str(coords)
#>  List of 4
#>   $ box   : num [1:4] 0.97 0.983 1.03 1.017
#>   $ labels: chr "AqA"
#>   $ x     : num 1
#>   $ y     : num 1
rect(coords$box[1], coords$box[2], coords$box[3], coords$box[4], border = 3)
text(x = coords$x, y = coords$y, labels = coords$labels, col = "red")

Padding

plot(1, type = "n", ann = FALSE, las = 1)
# all borders
textBox(x = 1, y = 1.2, labels = "Hello World (1)", padding = 0.05)
# bottom/top and left/right
textBox(x = 1, y = 1.0, labels = "Hello World (2)", padding = c(0.05, 0.20))
# bottom, left, top, right
textBox(x = 1, y = 0.8, labels = "Hello World (3)",
  padding = c(0.05, 0.05, 0.05, 0.35))

Colors & box type

plot(1, type = "n", ann = FALSE, las = 1)
textBox(x = 1, y = 1.2, labels = "Hello World (1)", padding = 0.05,
  col = "yellow", border = "green", fill = "red")
textBox(x = 1, y = 1.0, labels = "Hello World (2)", padding = 0.05, lwd = 3,
  lty = 3)
textBox(x = 1, y = 0.8, labels = "Hello World (3)", padding = 0.05,
  density = 30, angle = 45, fill = "gray")

Text fonts

plot(1, type = "n", ann = FALSE, las = 1)
textBox(x = 1, y = 1.2, labels = "Hello World (1)", padding = 0.05,
  family = "mono")
textBox(x = 1, y = 1.0, labels = "Hello World (2)", padding = 0.05,
  family = "serif")
textBox(x = 1, y = 0.8, labels = "Hello World (3)", padding = 0.05,
  family = "serif", font = 3, cex = 3)

Text alignment

text <- "Hello World!\nHow beautiful you are!"
plot(1, type = "n", ann = FALSE, las = 1)
textBox(x = 1, y = 1.2, labels = text, padding = 0.05, align = "l")
textBox(x = 1, y = 1.0, labels = text, padding = 0.05, align = "c")
textBox(x = 1, y = 0.8, labels = text, padding = 0.05, align = "r")

plot(1, type = "n", ann = FALSE, las = 1)
textBox(x = 1, y = 1.2, labels = text, padding = 0.05, align = "l", lheight = 0)
textBox(x = 1, y = 1.0, labels = text, padding = 0.05, align = "l", lheight = 1)
textBox(x = 1, y = 0.8, labels = text, padding = 0.05, align = "l", lheight = 2)

plot(1, type = "n", ann = FALSE, las = 1)
textBox(x = 1, y = 1.2, labels = text, align = "l",
  padding = c(0.05, 0.05, 0.05, 0.35))
textBox(x = 1, y = 1.0, labels = text, align = "c",
  padding = c(0.05, 0.05, 0.05, 0.35))
textBox(x = 1, y = 0.8, labels = text, align = "r",
  padding = c(0.05, 0.05, 0.05, 0.35))

Removing box and/or text

plot(1, type = "n", ann = FALSE, las = 1)
textBox(x = 1, y = 1.2, labels = text, col = "transparent")
textBox(x = 1, y = 1.0, labels = text, lwd = 0)
textBox(x = 1, y = 0.8, labels = text, lwd = 0, col = "transparent")

shadowText()

plot(1, type = "n", ann = FALSE, las = 1)
shadowText(x = 0.7, y = 1.3, labels = "This is a\nshadow text")
shadowText(x = 1.0, y = 1.3, labels = "This is a\nshadow text",
           family = "serif")
shadowText(x = 1.3, y = 1.3, labels = "This is a\nshadow text",
           family = "mono")
shadowText(x = 1.0, y = 1.0, labels = "This is a shadow text",
           family = "serif", cex = 3, col = "yellow", bg = "red")
shadowText(x = 0.7, y = 0.7, labels = "This is a\nshadow text",
           family = "serif", srt = 45)
shadowText(x = 1.0, y = 0.7, labels = "This is a\nshadow text",
           family = "serif", srt = 180)
shadowText(x = 1.3, y = 0.7, labels = "This is a\nshadow text",
           family = "serif", srt = -45)

Add circles

A function that creates circles.

par(mar = c(1, 1, 1, 1), mfrow = c(2, 2))
plot0()
circles(0, 0, 1)
plot0()
circles(0, 0, seq(0, 1, 0.2))
plot0()
circles(0, 0, seq(0, 1, 0.2), lty = 2, lwd = 1.4)
plot0()
circles(0, 0 ,seq(0, 1, 0.2), from = pi, col = "#BBBBFF88", lty = 2, lwd = 1.4)

Add ellipses

plot0(c(-2, 2), c(-2, 2), asp = 1)
ellipse(c(-1, 1), c(1, 1, -1, -1), from = pi*seq(0.25, 1, by = 0.25),
  to = 1.25*pi, col = 2, border = 4, lwd = 3)

Add images on plot

The pchImage() function eases the uses of rasterImage() to add images (including .png and .jpeg files) on a graphic. It allows to change the color of the whole image.

pathLogo <- system.file("img", "Rlogo.png", package = "png")
par(mar = c(4, 1, 4, 1), mfrow = c(1, 2))
plot0()
pchImage(0, 0, file = pathLogo, cex.x =4.5, cex.y = 4)
plot0()
pchImage(0, 0, file = pathLogo, cex.x =4.5, cex.y = 4, col = "grey25", angle = 25)

Add a frame to your plot

frameIt()

Default frame.

A custom one.

plot0()
frameIt(cex.x = 1.5, col = c(2, 3), border = 1)

addFrame()

addFrame(grid = TRUE)

addFrame(grid = TRUE, lwd = 0.25, lty = 3)

addFrame(at_x = seq(-1, 1, by = 0.1))

## Frame width
addFrame(width = 0.25)

addFrame(at_x = seq(-1, 1, by = 0.01), width = 1.00)

## Colors
addFrame(col = 1:6)

addFrame(col = "lightgray", border = "darkgray")

## Adding to a plot
maps::map()
addFrame(grid = TRUE, add = TRUE, width = 5)
maps::map.axes()

## Other graphical parameters
addFrame(bg = "darkgray", xaxs = "i", yaxs = "i")

Add an envelop

plot0(c(0, 10), c(0, 10))
sz <- 100
seqx <- seq(0, 10, length.out = sz)
seqy1 <- 0.2 * seqx * runif(sz, 0, 1)
seqy2 <- 4 + 0.25 * seqx * runif(sz, 0, 1)
seqy3 <- 8 + 0.25 * seqx * runif(sz, 0, 1)
envelop(seqx, seqy1, seqy2, col = 'grey85', border = NA)
envelop(seqx, seqy2, seqy3, col = 'grey25', border = NA)

Encircle points

coords <- cbind(runif(10), runif(10))
plot0(coords)
points(coords, bg = "grey25", pch = 21)
encircle(coords, border = "#7b11a1", lwd = 2)

Charts

boxplot2()

par(mar = rep(2, 4))
dfa <- data.frame(name = rep(LETTERS[1:4], 25), val = runif(100))
plot0(c(0, 5), c(0, 1))
boxplot2(val ~ name, data = dfa, add = TRUE, vc_cex = c(4, 40, 2))

plotMeans()

dataset <- data.frame(dat = c(rnorm(50, 10, 2), rnorm(50, 20, 2)) , grp = rep(c('A', 'D'), each = 50))
graphics::par(mfrow = c(1, 3))
plotMeans(dat ~ grp, data = dataset, pch = 19)
##
plotMeans(dat ~ grp, data = dataset, FUN_err= function(x) sd(x)*2, pch = 15,
 ylim = c(-5, 30), yaxs = 'i', connect = TRUE, args_con = list(lwd = 2, lty = 2, col = 'grey35'))
##
ser <- function(x) sd(x)/sqrt(length(x))
plot0(c(0, 4), c(0, 30))
plotMeans(dat~grp, data = dataset, FUN_err = ser, pch = 15,
draw_axis = FALSE, add = TRUE, seqx = c(.5, 3.5), mar = c(6, 6, 1, 1), cex = 1.4)
graphics::axis(2)

polarPlot()

polarPlot(1:40, stats::runif(40), to = 1.9 * pi, col = 'grey30', border = 'grey80')

plotImage

img <- png::readPNG(system.file('img', 'Rlogo.png', package = 'png'), native = TRUE)
op <- graphics::par(no.readonly = TRUE)
graphics::par(mfrow = c(2, 2), mar = rep(1, 4))
for (i in 1:4) plotImage(img)

graphics::par(op)

Another example:

img<-png::readPNG(system.file('img', 'Rlogo.png', package = 'png'), native = TRUE)
n<-15
plot0(c(0, 1),c(0, 1))
pchImage(0.1 + 0.8*stats::runif(n), 0.1 + 0.8 * stats::runif(n), 
  cex.x = 0.2 + 1.6 * stats::runif(n),
obj = img, angle = 360*runif(n), col = 2)

Image 2

This function is designed for small matrices so the matrix is translated into a colored image without any rotation of the axes.

image2(matrix(1:9, 3))

image2(matrix(1:27, 3), from = 2, border = 2, lwd = 2)

Colors manipulations

Creating shades of colors

The darken() and lighten() functions ease the creation of shades of a given color. For any color palette, use the showPalette() to display them!

someblue <- darken("blue", 10*1:9)
showPalette(someblue)

somered <- lighten("red", 10*1:9)
showPalette(somered)

showPalette(ramp("blue", "red", 10*3:7))
showPalette(blendColors(c("blue", "purple")))

darken() and lighten() functions are convenient way to produce consistent set of shaded colors with minimal effort; also use showPalette() to display your palette.

someblue <- darken("blue", 10*1:9)
showPalette(someblue)

somered <- lighten("red", 10*1:9)
showPalette(somered, add_codecolor = TRUE)

Since version 1.1-2 a set of color palettes has been added, see gpuPalette(). By default, gpuPalette() displays the color palettes available:

#>  Color palettes currently available are: 
#>    atom, cisl, github, google, google2, insileco, slack

In order to use one of the palette, use its names:

showPalette(gpuPalette("insileco"), add_codecolor = TRUE)
showPalette(gpuPalette("insileco", 25), add_codecolor = TRUE)

Color scale

par(mar = c(0, 0, 0, 0))
plot0(c(0, 10), c(0, 10))
colorScale(1, 8, gpuPalette("cisl", 10))
colorScale(1, 1, gpuPalette("cisl", 10), horiz = FALSE, labels.cex = 0.7)
colorScale(7, 8, gpuPalette("cisl", 10), at = 1:5*2, labels = LETTERS[1:5])
lab <- LETTERS[1:10]
lab[c(1, 3, 5, 7, 9)] <- ""
colorScale(7, 1, gpuPalette("cisl", 10), horiz = FALSE, labels = lab, title = "color scale", labels.cex = 1.1, title.cex = 1.6)

par(mar = c(0, 0, 0, 0))
plot0(c(0, 10), c(0, 10))
colorScale(2, 7, gpuPalette("cisl", 100), percx = 0.6, at = c(5, 25, 50, 75, 95), title = "adj = 0")
colorScale(2, 3, gpuPalette("cisl", 100), percx = 0.6, at = c(5, 25, 50, 75, 95), adj = 1, title = "adj = 1")

Stacked areas chart

A simple stacked areas

plot0(c(0, 10), c(0, 10))
sz <- 100
seqx <- seq(0, 10, length.out = sz)
seqy1 <- 0.2 * seqx * runif(sz, 0, 1)
seqy2 <- 4 + 0.25 * seqx * runif(sz, 0, 1)
seqy3 <- 8 + 0.25 * seqx * runif(sz, 0, 1)
envelop(seqx, seqy1, seqy2, col = "grey85", border = NA)

A complete stacked areas

x <- data.frame(matrix(runif(200, 2, 10), 8, 25))
stackedAreas(x)

Interactive functions

Some functions are interactive and fairly understandable, give them a try.

Chose a color

# NB: not run
pickColors()

Build a layout matrix interactively

# NB: not run
layout2()

Miscellaneous

Gantt chart

dfGantt
#>       milestone                task      start        due  done
#>  1   Manuscript Research & readings 2017-09-01 2017-11-28 FALSE
#>  2   Manuscript    Data preparation 2017-09-14 2017-09-28  TRUE
#>  3   Manuscript            Analyses 2017-09-28 2017-10-28 FALSE
#>  4   Manuscript                Plan 2017-09-21 2017-09-28  TRUE
#>  5   Manuscript        Introduction 2017-09-28 2017-10-28 FALSE
#>  6   Manuscript             Methods 2017-09-14 2017-10-28 FALSE
#>  7   Manuscript             Results 2017-10-28 2017-11-14 FALSE
#>  8   Manuscript          Discussion 2017-11-14 2017-11-28 FALSE
#>  9   Manuscript          Conclusion 2017-11-28 2017-12-04 FALSE
#>  11 Manuscript2 Research & readings 2017-09-04 2017-11-28 FALSE
#>  51 Manuscript2        Introduction 2017-09-28 2017-10-28 FALSE
#>  61 Manuscript2             Methods 2017-09-14 2017-10-28 FALSE
#>  71 Manuscript2             Results 2017-10-28 2017-11-14 FALSE
#>  81 Manuscript2          Discussion 2017-11-14 2017-11-28 FALSE
#>  91 Manuscript2          Conclusion 2017-11-28 2017-12-04 FALSE
par(lwd = 2)
palette(gpuPalette(6)[c(2, 4)])
ganttChart(dfGantt, mstone_lwd = 4, mstone_spacing = 0.6, lighten_done = 80)
#>       milestone                task      start        due done  start_tmp
#>  1   Manuscript Research & readings 2017-09-01 2017-11-28    I 2017-09-01
#>  2   Manuscript    Data preparation 2017-09-14 2017-09-28    C 2017-09-01
#>  3   Manuscript            Analyses 2017-09-28 2017-10-28    I 2017-09-01
#>  4   Manuscript                Plan 2017-09-21 2017-09-28    C 2017-09-01
#>  5   Manuscript        Introduction 2017-09-28 2017-10-28    I 2017-09-01
#>  6   Manuscript             Methods 2017-09-14 2017-10-28    I 2017-09-01
#>  7   Manuscript             Results 2017-10-28 2017-11-14    I 2017-09-01
#>  8   Manuscript          Discussion 2017-11-14 2017-11-28    I 2017-09-01
#>  9   Manuscript          Conclusion 2017-11-28 2017-12-04    I 2017-09-01
#>  10  Manuscript          Manuscript 2017-09-01 2017-12-04    M 2017-09-01
#>  11 Manuscript2 Research & readings 2017-09-04 2017-11-28    I 2017-09-04
#>  12 Manuscript2        Introduction 2017-09-28 2017-10-28    I 2017-09-04
#>  13 Manuscript2             Results 2017-10-28 2017-11-14    I 2017-09-04
#>  14 Manuscript2          Discussion 2017-11-14 2017-11-28    I 2017-09-04
#>  15 Manuscript2          Conclusion 2017-11-28 2017-12-04    I 2017-09-04
#>  16 Manuscript2             Methods 2017-09-14 2017-10-28    I 2017-09-04
#>  17 Manuscript2         Manuscript2 2017-09-04 2017-12-04    M 2017-09-04

palette(gpuPalette(6)[c(3, 6)])
ganttChart(dfGantt, task_order = FALSE, mstone_add = TRUE, lighten_done = -40)
#>  Warning in ganttChart(dfGantt, task_order = FALSE, mstone_add = TRUE,
#>  lighten_done = -40): spacing set to 0

# restore default palette
palette("default")

Are these points within this polygon?

mat <- matrix(10 * runif(100), 50)
res <- pointsInPolygon(mat, cbind(c(4, 8, 8, 4), c(4, 4, 8, 8)))
# Visual assessment
plot0(c(0, 10), c(0, 10))
graphics::polygon(c(4, 8, 8, 4),c(4, 4, 8, 8))
graphics::points(mat[,1], mat[,2], col = res+1)

compassRose

par(mfrow = c(2, 2), mar = rep(1, 4))
##
plot0(c(-1, 1), asp = 1)
compassRose(0, 0)
##
plot0(c(-1, 1), asp = 1)
compassRose(0.5, 0.5)
##
plot0(c(-1, 1), asp = 1)
compassRose(0, 0, cex.cr = 2)
##
plot0(c(-1, 1), asp = 1)
compassRose(0, 0, rot = 0.75*pi, cex.cr = 2, cex.let = 1.5, offset = -1.25)

also,

compassRose(0, rot = 25, cex.cr = 2, col.let =2, add = FALSE)

Vector fields

systLin <- function(X, beta){
    Y <- matrix(0,ncol = 2)
    Y[1L] <- beta[1, 1] * X[1L] + beta[1, 2] * X[2L]
    Y[2L] <- beta[2, 1] * X[1L] + beta[2, 2] * X[2L]
    return(Y)
}
seqx <- seq(-2, 2, 0.31)
seqy <- seq(-2, 2, 0.31)
beta1 <- matrix(c(0, -1, 1, 0), 2)
# Plot 1:
vecfield2d(coords = expand.grid(seqx, seqy), FUN = systLin, args = list(beta = beta1))

# # Plot 2:
graphics::par(mar = c(2, 2, 2, 2))
vecfield2d(coords = expand.grid(seqx, seqy), FUN = systLin,
   args = list(beta = beta1), cex.x = 0.35, cex.arr = 0.25,
   border = NA,cex.hh = 1, cex.shr = 0.6, col = 8)
graphics::abline(v = 0, h = 0)

Manipulation of figure dimensions

Get pretty ranges

vec <- stats::runif(20)
range(vec)
#>  [1] 0.07859498 0.99634729
#>  [1] 0.05 1.00
prettyRange(c(3.849, 3.88245))
#>  [1] 3.845 3.885

How many row and columns?

This helper function returns suggested numbers of row and column for a given number of panels passed as an argument.

#>  [1] 4 3
#>  [1] 4 4