| Maintainer: | Jason Waddell <jason.waddell@openanalytics.eu> |
| License: | GPL-3 + file LICENSE |
| Title: | OpenAnalytics Plots Package |
| Type: | Package |
| LazyLoad: | yes |
| Author: | Jason Waddell, Willem Ligtenberg |
| Description: | Offers a suite of functions for enhancing R plots. |
| Version: | 0.0.25 |
| Date: | 2015-11-29 |
| URL: | http://www.openanalytics.eu |
| Depends: | oaColors |
| Imports: | ggplot2 |
| Suggests: | RColorBrewer |
| NeedsCompilation: | no |
| Packaged: | 2015-11-30 13:36:15 UTC; Jason |
| Repository: | CRAN |
| Date/Publication: | 2015-11-30 14:51:34 |
Function for adding a legend to an existing device
Description
Function for adding a legend to an existing device
Usage
addLegend(x = "center", y = NULL, legend, font = NULL, bty = "n",
xjust = 0.5, yjust = 0.5, ...)
Arguments
x |
legend x location |
y |
legend y location |
legend |
vector of legend labels |
font |
legend text font |
bty |
A character string which determined the type of box which is drawn about plots. If bty is one of "o" (the default), "l", "7", "c", "u", or "]" the resulting box resembles the corresponding upper case letter. A value of "n" suppresses the box. |
xjust |
how the legend is to be justified relative to the legend x location. A value of 0 means left justified, 0.5 means centered and 1 means right justified. |
yjust |
the same as xjust for the legend y location. |
... |
additional optional arguments to be passed to legend() |
Value
none; legend is added to the current device
Author(s)
Jason Waddell
Examples
layout <- c(2,3);
side <- "left"
proportion <- 0.2
prepLegend(layout = layout, side = side, proportion = proportion)
for(i in 1:(layout[1]*layout[2]))
plot(1:7, 1:7, col = 1:7, pch = 19, cex = 2.2, xaxt = "n",
yaxt = "n", ann = FALSE)
addLegend(legend = paste("Group", 1:7), font = 2,
pch = 19, pt.cex = 2, text.col = 1:7, col = 1:7,
y.intersp = 1.5, cex = 1.5)
layout = rbind(c(1, 2, 3), c(0, 4, 3), c(0, 4, 5))
side = "right"
proportion = 0.15
prepLegend(layout = layout, side = side, proportion = proportion)
for(i in 1:max(layout))
plot(1:7, 1:7, col = 1:7, pch = 19, cex = 2.2, xaxt = "n",
yaxt = "n", xlab = "", ylab = "", main = paste("Plot", i))
addLegend(legend = paste("Group", 1:7), font = 2,
pch = 19, pt.cex = 2, text.col = 1:7, col = 1:7,
y.intersp = 1.5, cex = 1.5)
Create a Blank Plot
Description
Create a Blank Plot
Usage
blankPlot(xlim, ylim)
Arguments
xlim |
x limits for the plot |
ylim |
y limits for the plot |
Value
none, plot is created on the current device
Author(s)
Jason Waddell
Function for plotting a colored polygon as part of a density legend
Description
Function for plotting a colored polygon as part of a density legend
Usage
colorPoly(de1, tempDex, col, side)
Arguments
de1 |
a density() object |
tempDex |
a set of indices corresponding to the range of the current segment to be plotted (which indices of the density object to ues) |
col |
the color of the polygon to be plotted |
side |
the side of the plot that the density legend should be plotted on |
Value
none, graphics are added to the current device
Author(s)
Jason Waddell
Custom rounding function to round to the nearest specified interval
Description
Custom rounding function to round to the nearest specified interval
Usage
customRound(x, roundTo)
Arguments
x |
numeric value(s) |
roundTo |
rounding interval |
Value
rounded numeric value(s)
Author(s)
Jason Waddell
Create a colored density legend for visually representing the distribution of a color variable on a plot
Description
Create a colored density legend for visually representing the distribution of a color variable on a plot
Usage
densityLegend(x, colorPalette, colorBreaks, side = "right", main = NULL)
Arguments
x |
a numeric vector used to create the density trace |
colorPalette |
a vector of color values |
colorBreaks |
a vector of cutoff values for the color regions |
side |
the side of the plot to place the desntiy legend |
main |
the main title for the density legend (optional, recommended to use a title that describes x |
Value
none, graphics are added to the current device
Author(s)
Jason Waddell
Examples
library(ggplot2)
library(RColorBrewer)
# subset the data object
dsub <- subset(diamonds, x > 5 & x < 6 & y > 5 & y < 6)
dsub <- dsub[-which(dsub$z > 4), ]
dsub <- dsub[-which(dsub$z < 3), ]
# define color pallette, color vector and color region breaks
colorPalette <- brewer.pal(9, "Blues")[4:9]
colorObj <- splitColorVar(colorVar = dsub$z, colorPalette)
colorVec <- colorObj$colorVec
breaks <- colorObj$breaks
# plot the data
prepLegend(side = "right", proportion = 0.3)
oaTemplate(xlim = range(dsub$x), ylim = range(dsub$y),
main = "Diamond Length by Width \n Colored by Depth",
xlab = "Length (mm)", ylab = "Width (mm)")
points(x = dsub$x, y = dsub$y, col = colorVec, pch = 19, cex = 0.6)
# add the legend
densityLegend(x = dsub$z, colorPalette = colorPalette, side = "right",
main = "Diamond Depth", colorBreaks = breaks)
Draw a Split Density Plot
Description
Draw a Split Density Plot
Usage
drawSplitDensity(x = NULL, y = NULL, densityObj = NULL, yshift = 0,
colVec, outerCol, lwd = 2, split = NULL, yScale = NULL,
fillBackground = FALSE)
Arguments
x |
x vector from a density object. e.g. data <- rnorm(100); x <- density(data)$x |
y |
y vector from a density object |
densityObj |
an object created by the function density() |
yshift |
vertical shift to be applied to the y object |
colVec |
color vector for the shaded regions that compose the interior of the plot. The length of 'colVec' should be one greater than the length of split |
outerCol |
the color for the outer density line |
lwd |
line width for the outer density line |
split |
vector of x values at which to split the density plot |
yScale |
vertical scale at which to plot the density. For example, a call with 'yScale = 1' will produce a density curve scaled between 0 and 1 |
fillBackground |
binary specification of whether to fill in the background the outerCol color |
Value
none. Graph is plotted to the current device
Author(s)
Jason Waddell
Examples
library(RColorBrewer)
data <- rnorm(1000)
x <- density(data)$x
y <- density(data)$y
colVec <- brewer.pal(9, "Blues")[3:8]
outerCol <- brewer.pal(9, "Blues")[9]
oaTemplate(xlim = range(x), ylim = c(0, 1), ygrid = 0, cex.axis = 1.2)
drawSplitDensity(x, y, colVec = colVec, split = c(-8),
outerCol = outerCol,
yScale = 0.95, yshift = 0)
Returns a Vector of x Locations
Description
Returns a Vector of x Locations
Usage
findLocations(n, space, center)
Arguments
n |
number of observations for a given value |
space |
space between points |
center |
center plotting value |
Value
numeric vector of location values
Author(s)
Jason Waddell
Divide the range of x into intervals, returning the breakpoints of these intervals
Description
Divide the range of x into intervals, returning the breakpoints of these intervals
Usage
getBreaks(x, breaks, dig.lab = 3L)
Arguments
x |
a numeric vector which is to be converted to a factor by cutting |
breaks |
a single number (greater than or equal to 2) giving the number of intervals into which x is to be cut |
dig.lab |
integer which is used when labels are not given. It determines the number of digits used in formatting the break numbers |
Value
a vector of numeric breakpoints
Author(s)
Jason Waddell
Create a OA Plot Template
Description
Create a OA Plot Template
Usage
oaTemplate(xlim, ylim, xgrid = NULL, ygrid = NULL, xlab = NULL,
ylab = NULL, main = NULL, bgCol = gray(0.9), col.axis = gray(0.6),
col.lab = gray(0.4), col.main = gray(0.3), cex.axis = 0.7,
cex.lab = 1, cex.main = 1.5, xaxs = "r", yaxs = "r", add = FALSE,
box = FALSE, box.col = "black", box.lwd = 1, ylabels = NULL,
xlabels = NULL, buffer = 0, gridLabelBuffer = 0.01, ylabBuffer = 0.1,
xlabBuffer = 0.08, mainBuffer = 0.07)
Arguments
xlim |
x limits for the plot |
ylim |
y limits for the plot |
xgrid |
values at which to draw the x axis gridlines |
ygrid |
values at which to draw the y axis gridlines |
xlab |
a title for the x axis |
ylab |
a title for the y axis |
main |
an overall title for the plot |
bgCol |
background color for the plot |
col.axis |
color for the axis labels |
col.lab |
color for the xlab and ylab titles |
col.main |
color for the main title |
cex.axis |
size of the axis labels |
cex.lab |
size of the xlab and ylab titles |
cex.main |
size of the main title |
xaxs |
The style of axis interval calculation to be used for the x-axis. Possible values are "r", "i". Style "r" (regular) first extends the data range by 4 percent at each end and then finds an axis with pretty labels that fits within the extended range. Style "i" (internal) just finds an axis with pretty labels that fits within the original data range. |
yaxs |
The style of axis interval calculation to be used for the y-axis. See xaxs above. |
add |
A logical value specifying whether to add the template to an existing plot. If FALSE, a new plot will be created |
box |
binary specifying whether to draw a bounding box around the plot |
box.col |
color of the bounding box |
box.lwd |
width of the bounding box lines |
ylabels |
labels to print at the y tickmarks |
xlabels |
labels to print at the x tickmarks |
buffer |
optional buffer around all edges of the plot (as a percentage of the plot) |
gridLabelBuffer |
buffer between plot and grid labels (as a proportion of plotting range) |
ylabBuffer |
distance between plot and y-axis title, as proportion of total plot width |
xlabBuffer |
distance between plot and x-axis title, as proportion of total plot height |
mainBuffer |
distance between plot and main title, as proportion of total plot height |
Value
none, objects are plotted to the current device
Author(s)
Jason Waddell
Examples
par(plt = c(0, 1, 0, 1))
oaTemplate(xlim = c(0, 10), ylim = c(20, 50), add = FALSE, xlab = "X Label", ylab = "Y Label",
main = "Main Title")
Apply OA ggplot2 theme
Description
Apply OA ggplot2 theme
Usage
oaTheme(p, useOAColors = TRUE, expand = "both", bgColor = gray(0.9))
Arguments
p |
ggplot2 plot object |
useOAColors |
boolean which indicates wether or not to use the oaColors package to provide a color scheme. Default: TRUE |
expand |
specify wether or not to expand the axis valid options are: (both, x, y, none) Default: both |
bgColor |
specify a different background color (useful for plotting colors with alpha values) Default: gray(0.9) |
Value
ggplot2 plot object
Author(s)
Willem Ligtenberg
A function for creating the segmented color bars in a density legend
Description
A function for creating the segmented color bars in a density legend
Usage
plotBars(de1, side, colorPalette, colorBreaks)
Arguments
de1 |
a density() object |
side |
the side of the plot that the density legend should be plotted on |
colorPalette |
A vector of color values |
colorBreaks |
A vector of cutoff values for the color regions |
Value
none, graphics are added to the current device
Author(s)
Jason Waddell
Function for plotting the density trace outline in a density legend
Description
Function for plotting the density trace outline in a density legend
Usage
plotDensityTrace(de1, side)
Arguments
de1 |
a density() object |
side |
the side of the plot that the density legend should be plotted on |
Value
none, graphics are added to the current device
Author(s)
Jason Waddell
Adds Points on a Pre-existing Plot using Shifted Locations
Description
Adds Points on a Pre-existing Plot using Shifted Locations
Usage
plotDots(vec = NULL, xLeft = 0.8, xRight = 1.2, ...)
Arguments
vec |
numeric vector |
xLeft |
left x boundary of the point plotting region |
xRight |
right x boundary of the point plotting region |
... |
further arguments to be handed to the points function |
Value
points are added to the current graphics device
Author(s)
Jason Waddell
Examples
x <- sample(1:5, size = 25, replace = TRUE)
plot(x = -1, y = -1, xlim = c(0.5,1.5), ylim = range(x),
ylab = "", xlab = "", xaxt = "n")
colVec <- c(rep("olivedrab", 15), rep("goldenrod", 5), rep("red", 5))
plotDots(vec = x, xLeft = 0.8, xRight = 1.2, pch = 19,
col = colVec, cex = 2)
Function to plot all colored density regions of a density legend
Description
Function to plot all colored density regions of a density legend
Usage
plotPolygonRegions(de1, side, colorPalette, colorBreaks)
Arguments
de1 |
a density() object |
side |
the side of the plot that the density legend should be plotted on |
colorPalette |
a vector of color values |
colorBreaks |
a vector of cutoff values for the color regions |
Value
none, graphics are added to the current device
Author(s)
Jason Waddell
Generic pointsOnBoxplot function. Calls pointsOnBoxplot.default or pointsOnBoxplot.formula
Description
Generic pointsOnBoxplot function. Calls pointsOnBoxplot.default or pointsOnBoxplot.formula
Usage
pointsOnBoxplot(x, ...)
Arguments
x |
a vector of numeric values to be passed on |
... |
further arguments for the methods, such as a vector of categories 'y' for the default method |
Author(s)
Jason Waddell
See Also
pointsOnBoxplot.default pointsOnBoxplot.formula
Examples
# Examples run in the formula and default methods
x2 <- runif(50, 0, 10);
table(customRound(x2, roundTo = 0.5))
boxplot(x2)
pointsOnBoxplot(x2, pch = 19, roundTo = 0.5)
# Set up input data
x <- c(sample(1:5, size = 25, replace = TRUE), rpois(25, lambda = 4))
colVec <- c(rep("olivedrab", 10), rep("red", 5), rep("goldenrod", 15),
rep("red", 15), rep("olivedrab", 5))
y <- rep(c("Awesome Rats", "Stupid Rats"), each = 25)
y2 <- rep(c("Open", "Analytics"), 25)
x2 <- c(1, 2, 2, 3, 3, 1, 1, 1, 4, 5)
y3 <- c(rep("A", 5), rep("B", 5))
levels(y3) <- c("A", "B", "C")
boxplot(x ~ y, horizontal = TRUE)
pointsOnBoxplot(x ~ y, horizontal = TRUE)
boxplot(x ~ y)
pointsOnBoxplot(x = x, y = y, col = colVec, pch = 19, cex = 2)
boxplot(x ~ y + y2)
pointsOnBoxplot(x ~ y + y2, col = colVec, pch = 19, cex = 2)
Draw Points on Top of a Boxplot using Appropriate Shifting
Description
Draw Points on Top of a Boxplot using Appropriate Shifting
Usage
## Default S3 method:
pointsOnBoxplot(x = NULL, y = NULL, totalSpread = 0.3,
roundTo = NULL, horizontal = FALSE, ...)
Arguments
x |
vector of numeric values that were used to create boxplots |
y |
vector of values representing a categorical variable |
totalSpread |
total spread of point plotting range within a boxplot. Defaults to 0.3 so that points plot between 0.85 and 1.15 |
roundTo |
optional rounding interval. For example, if given roundTo = 0.25, all numeric x values will be rounded to the nearest quarter |
horizontal |
logical indicating if the boxplots should be horizontal; default FALSE means vertical boxes. |
... |
further parameters to be passed to the points function |
Value
points are drawn to the current device
Author(s)
Jason Waddell
Examples
# Examples run in the formula and default methods
x2 <- runif(50, 0, 10);
table(customRound(x2, roundTo = 0.5))
boxplot(x2)
pointsOnBoxplot(x2, pch = 19, roundTo = 0.5)
# Set up input data
x <- c(sample(1:5, size = 25, replace = TRUE), rpois(25, lambda = 4))
colVec <- c(rep("olivedrab", 10), rep("red", 5), rep("goldenrod", 15),
rep("red", 15), rep("olivedrab", 5))
y <- rep(c("Awesome Rats", "Stupid Rats"), each = 25)
y2 <- rep(c("Open", "Analytics"), 25)
x2 <- c(1, 2, 2, 3, 3, 1, 1, 1, 4, 5)
y3 <- c(rep("A", 5), rep("B", 5))
levels(y3) <- c("A", "B", "C")
boxplot(x ~ y, horizontal = TRUE)
pointsOnBoxplot(x ~ y, horizontal = TRUE)
boxplot(x ~ y)
pointsOnBoxplot(x = x, y = y, col = colVec, pch = 19, cex = 2)
boxplot(x ~ y + y2)
pointsOnBoxplot(x ~ y + y2, col = colVec, pch = 19, cex = 2)
Draw Points on Top of a Boxplot using Appropriate Shifting
Description
Draw Points on Top of a Boxplot using Appropriate Shifting
Usage
## S3 method for class 'formula'
pointsOnBoxplot(formula, data = NULL, ...,
na.action = NULL)
Arguments
formula |
a formula of the form a ~ b (+ c, etc.), where a is a numeric vector and all other variables are categorical |
data |
an optional input parameter of a data.frame containing the variables used in the formula |
... |
further arguments to be passed to pointsOnBoxplot.default |
na.action |
parameter specifying how to handle missingness |
Author(s)
Jason Waddell
Function for arranging plotting layout to accomodate a legend panel
Description
Function for arranging plotting layout to accomodate a legend panel
Usage
prepLegend(layout = c(1, 1), type = if (is.matrix(layout)) "layout" else
"mfrow", side = "right", proportion = 0.15, heights = NULL,
widths = NULL)
Arguments
layout |
layout vector or matrix |
type |
type of layout; either "mfrow" or "layout" |
side |
side of the plot to place legend on; one of "top", "bottom", "left" or "right" |
proportion |
proportion of plotting window to allocate to legend |
heights |
height vector for original layout (before the legend panel is appended) |
widths |
width vector for original layout (before the legend panel is appended) |
Value
none; layout is passed to current device
Author(s)
Jason Waddell
Examples
layout <- c(2,3);
side <- "left"
proportion <- 0.2
prepLegend(layout = layout, side = side, proportion = proportion)
for(i in 1:(layout[1]*layout[2]))
plot(1:7, 1:7, col = 1:7, pch = 19, cex = 2.2, xaxt = "n",
yaxt = "n", ann = FALSE)
addLegend(legend = paste("Group", 1:7), font = 2,
pch = 19, pt.cex = 2, text.col = 1:7, col = 1:7,
y.intersp = 1.5, cex = 1.5)
layout = rbind(c(1, 2, 3), c(0, 4, 3), c(0, 4, 5))
side = "right"
proportion = 0.15
prepLegend(layout = layout, side = side, proportion = proportion)
for(i in 1:max(layout))
plot(1:7, 1:7, col = 1:7, pch = 19, cex = 2.2, xaxt = "n",
yaxt = "n", xlab = "", ylab = "", main = paste("Plot", i))
addLegend(legend = paste("Group", 1:7), font = 2,
pch = 19, pt.cex = 2, text.col = 1:7, col = 1:7,
y.intersp = 1.5, cex = 1.5)
Plot a base-graphics scatterplot with accompanying density legend
Description
Plot a base-graphics scatterplot with accompanying density legend
Usage
scatterplotDL(x, y, colorVar, colorPalette, side = "right",
proportion = 0.3, legendTitle = NULL, ...)
Arguments
x |
the x coordinates to be handed to plot() |
y |
the y coordinates of points in the plot() |
colorVar |
the numeric vector of values used to color the points |
colorPalette |
a color palette. If 'colorPalette' contains, for example, 6 colors, then the values of colorVar will be split and assigned to these 6 colors |
side |
the side of the plot to put the density legend on ("left", "right", "top", or "bottom") |
proportion |
the proportion of the plot (from 0 to 1) to allocate to the density legend (defaults to 0.3) |
legendTitle |
string for labelling the density legend |
... |
additional parameters to be passed to plot() |
Value
none, plot is added to device
Author(s)
Jason Waddell
Examples
library(ggplot2)
library(RColorBrewer)
colorPalette <- brewer.pal(9, "YlOrRd")[4:9]
scatterplotDL(x = mtcars$mpg, y = mtcars$wt, colorVar = mtcars$hp,
legendTitle = "Horse Power", colorPalette = colorPalette, pch = 19,
xlab = "MPG (miles per gallon)", ylab = "Weight (tonnes)",
main = "MPG by Weight in Cars \n Colored by Horse Power")
Function for drawing a split circle (two differently colored semicircles)
Description
Function for drawing a split circle (two differently colored semicircles)
Usage
splitCircle(x, y, radius, splitAngle = pi/4, nv = 100, border = NA,
col1 = NA, col2 = NA, lty = 1, lwd = 1)
Arguments
x |
x location of the circle center |
y |
y location of the circle center |
radius |
radius of the circle |
splitAngle |
angle (in radians) that splits the color in two halves |
nv |
number of vertices used to draw the circle |
border |
binary whether to include a border on the circle |
col1 |
color of the first semicircle |
col2 |
color of the second semicircle |
lty |
line type used for drawing the circle polygon |
lwd |
line width used for darwing the circle polygon |
Value
none, split circle is drawn to the current device
Author(s)
Jason Waddell
Examples
plot(-1, -1, xlim = c(0, 1), ylim = c(0,1), type = "n")
splitCircle(x = 0.5, y = 0.5, radius = 0.48,
splitAngle = pi/4, nv = 1000, border = NA,
col1 = "blue", col2 = "red")
Function to take a numeric vector 'colorVar' and palette 'colorPalette', and return a list containing a vector of color assignments for each element of 'colorVar' (to be used in plot calls), and a vector of breaks defining the color regions (to be used in densityLegend)
Description
Function to take a numeric vector 'colorVar' and palette 'colorPalette', and return a list containing a vector of color assignments for each element of 'colorVar' (to be used in plot calls), and a vector of breaks defining the color regions (to be used in densityLegend)
Usage
splitColorVar(colorVar, colorPalette, breaks = NULL)
Arguments
colorVar |
the numeric vector of values used to color the points |
colorPalette |
a color palette. If 'colorPalette' contains, for example, 6 colors, then the values of colorVar will be split and assigned to these 6 colors |
breaks |
(optional) a numeric vector of two or more unique cut points |
Value
a list containing a vector of color assignments ('colorVec') for each element of 'colorVar' (to be used in plot calls), and a vector of breaks ('breaks') defining the color regions (to be used in densityLegend)
Author(s)
Jason Waddell