HiveR (version 0.4.0)

plot3dHive: Create (Plot) a 2D or 3D Hive Plot

Description

These functions plot a HivePlotData object in either 2D or 3D, depending upon which function is called.

Usage

plot3dHive(
  HPD,
  ch = 1,
  dr.nodes = TRUE,
  method = "abs",
  axLabs = NULL,
  axLab.pos = NULL,
  LA = FALSE,
  ...
)
plotHive(
  HPD,
  ch = 1,
  method = "abs",
  dr.nodes = TRUE,
  bkgnd = "black",
  axLabs = NULL,
  axLab.pos = NULL,
  axLab.gpar = NULL,
  anNodes = NULL,
  anNode.gpar = NULL,
  grInfo = NULL,
  arrow = NULL,
  np = TRUE,
  anCoord = "local",
  ...
)

Value

None. Side effect is a plot.

Arguments

HPD

An object of S3 class HivePlotData.

ch

Numeric; the size of the central hole in the hive plot.

dr.nodes

Logical; if TRUE nodes will be drawn.

method

Character. Passed to manipAxis (see there for allowed values - the default given above plots using the native or absolute coordinates of the data).

axLabs

A vector of character strings for the axis labels.

axLab.pos

Numeric; An offset from the end of the axis for label placement. Either a single value or a vector of values. If a single value, all labels are offset the same amount. If a vector of values, there should be a value for each axis. This allows flexibility with long axis names. The units depend upon the method employed (see Details).

LA

(Applies to plot3dHive only) Logical: should splines be drawn with line_antialias = TRUE? See Details.

...

Additional parameters to be passed downstream.

bkgnd

Any valid color specification. Used for the background color for plotHive.

axLab.gpar

(Applies to plotHive only) A list of name - value pairs acceptable to gpar. These control the label and arrow displays. See the examples.

anNodes

(Applies to plotHive only) The path to a csv file containing information for labeling nodes. If present, a line segment will be drawn from the node to the specified text. The text is positioned near the end of the line segment. The columns in the csv file must be named as follows (description and use in parentheses): node.lab (node label from HPD$nodes$lab), node.text (the text to be drawn on the plot), angle (polar coordinates: angle at which to draw the segment), radius (polar coordinates: radius at which to draw the text), offset (additional distance along the radius vector to offset text), hjust, vjust (horizontal and vertical justification; nominally in [0...1] but fractional and negative values also work). The first two values will be treated as type character, the others as numeric.

anNode.gpar

(Applies to plotHive only) A list of name - value pairs acceptable to gpar. These control both the text used to annotate the nodes and the line segments connecting that text to the node. See the examples.

grInfo

(Applies to plotHive only) The path to a csv file containing information for adding graphic decorations to the plot. If present, a line segment will be drawn from the node to the specified location and the graphic is positioned near the end the line segment. The columns in the csv file must be named as follows (description and use in parentheses): node.lab (node label from HPD$nodes$lab), angle (polar coordinates: angle at which to position the graphic), radius (polar coordinates: radius at which to position the graphic), offset (additional distance along radius vector to offset the graphic), width (the width of the graphic), path (a valid path to the graphics in jpg or png format). The path should include the extension is it is autodetected. Valid extensions are jpg, JPG, jpeg, JPEG, png, or PNG. All image files must be of the same type (all jpg, or all png).

arrow

(Applies to plotHive only) A vector of 5 or 6 values: a character string to label the arrow, and 4 numeric values giving the angle of the arrow, the radius at which to start the arrow, the radius at which to end the arrow, and a value to offset the arrow label from the end of the arrow. A 5th numeric value (the 6th argument overall) can specify an offset in the y direction for the arrow useful when nx = 2. See the examples.

np

(Applies to plotHive only) Logical; should a new device (page) be opened when drawing the hive plot? If you are making multiple plots within some sort of grid scheme then this should be set to FALSE.

anCoord

(Applies to plotHive only) One of c("local", "global"). Controls how the position of node labels and graphic decorations are specified. See Details.

Functions

• plot3dHive(): Create a 3D Hive Plot

• plotHive(): Create a 2D Hive Plot

Author

Bryan A. Hanson, DePauw University.

Details

General. plotHive uses grid graphics to produce a 2D hive plot in a style similar to the original concept. For a 2D plot, axis number 1 is vertical except in the case of 2 axes in which case it is to the right. plot3dHive produces a 3D hive plot using rgl graphics. Functions from either package can be used to make additional modifications after the hive plot is drawn, either via the ... argument or by subsequent function calls. See the examples.

Units and Annotations. If you add node labels, arrows or graphic decorations, the units that you must specify are those intrinsic to the data itself, modified by your setting of ch and method. These generally cannot be known precisely ahead of time, so some experimentation will be necessary to polish the plots. For instance, if you have data with node radii that run from 4-23 then you have an idea of how to position your annotations if using method = "abs". But the same data plotted with method = "norm" or method = "rank" will require that you move your annotation positions accordingly. In the first case no radius is larger than 23, but the maximum radius is 1 when the data is normed and when it is ranked, the maximum value will depend upon which axis has the most nodes on it, and the number of unique radii values.

Positioning Node Labels and Graphics. In addition to the nuances just above, there are two ways to specify the location of node labels and graphic decorations. Polar coordinates are used in both cases. If annCoord = "local" then the angle, radius and offset arguments are relative to the node to be annotated. An angle of 0 positions the label horizontally to the right of the node. Thus the label can be placed within a circular area around the node. If annCoord = "global" then the specifications are relative to dead center on the plot. These two methods give one lots of flexibility in lining up labels in different ways. See the examples.

Size of Graphics. The size of graphic decorations is controlled by the column 'width' in grInfo. The ultimate call to display the graphic is done with as.raster. Specifying only the width preserves the aspect ratio of the graphic. See ?as.raster for further discussion.

Colors. For any of the gpar arguments, watch out: In grid graphics the default color for text and arrows is black, so if are using the default bkgnd = "black" in the hive plot be sure to specify col = "white" (or some other non-black color) for the labels and arrows or you won't see them.

Speed and 3D Hive Plots. For most work with plot3dHive, use LA = FALSE for speed of drawing. LA = TRUE is over 20 times slower, and is more appropriate for high quality hive plots. These are probably better made with R CMD BATCH script.R rather than interactive use.

Examples

### 2D Hive Plots
require("grid")
# Generate some random data
test2 <- ranHiveData(nx = 2)
test3 <- ranHiveData(nx = 3)

# First the nx = 2 case.
# Note that gpar contains parameters that apply to both the
# axis labels and arrow. A 6th value in arrow offsets the arrow vertically:
plotHive(test2,
  ch = 5, axLabs = c("axis 1", "axis 2"), rot = c(-90, 90),
  axLab.pos = c(20, 20), axLab.gpar = gpar(col = "pink", fontsize = 14, lwd = 2),
  arrow = c("radius units", 0, 20, 60, 25, 40)
)

# Now nx = 3:
plotHive(test3) # default plot

# Add axis labels & options to nx = 3 example.  Note that rot is not part of gpar
plotHive(test3,
  ch = 5, axLabs = c("axis 1", "axis 2", "axis 3"),
  axLab.pos = c(10, 15, 15), rot = c(0, 30, -30),
  axLab.gpar = gpar(col = "orange", fontsize = 14)
)

# Call up a built-in data set to illustrate some plotting tricks
data(HEC)
require("grid") # for text additions outside of HiveR (grid.text)

plotHive(HEC,
  ch = 0.1, bkgnd = "white",
  axLabs = c("hair\ncolor", "eye\ncolor"),
  axLab.pos = c(1, 1),
  axLab.gpar = gpar(fontsize = 14)
)
grid.text("males", x = 0, y = 2.3, default.units = "native")
grid.text("females", x = 0, y = -2.3, default.units = "native")
grid.text("Pairing of Eye Color with Hair Color",
  x = 0, y = 4,
  default.units = "native", gp = gpar(fontsize = 18)
)

# Add node labels and graphic decorations
# The working directory has to include
# not only the grInfo and anNodes files but also the jpgs.
# So, we are going to move to such a directory and return you home afterwards.

currDir <- getwd()
setwd(system.file("extdata", "Misc", package = "HiveR"))
plotHive(HEC,
  ch = 0.1, bkgnd = "white",
  axLabs = c("hair\ncolor", "eye\ncolor"),
  axLab.pos = c(1, 1),
  axLab.gpar = gpar(fontsize = 14),
  anNodes = "HECnodes.txt",
  anNode.gpar = gpar(col = "black"),
  grInfo = "HECgraphics.txt",
  arrow = c("more\ncommon", 0.0, 2, 4, 1, -2)
)

grid.text("males", x = 0, y = 2.3, default.units = "native")
grid.text("females", x = 0, y = -2.3, default.units = "native")
grid.text("Pairing of Eye Color with Hair Color",
  x = 0, y = 3.75,
  default.units = "native", gp = gpar(fontsize = 18)
)
grid.text("A test of plotHive annotation options",
  x = 0, y = 3.25,
  default.units = "native", gp = gpar(fontsize = 12)
)
grid.text("Images from Wikipedia Commons",
  x = 0, y = -3.5,
  default.units = "native", gp = gpar(fontsize = 9)
)
setwd(currDir)

# Use the node label concept to create tick marks

currDir <- getwd()
setwd(system.file("extdata", "Misc", package = "HiveR"))
plotHive(HEC,
  ch = 0.1, bkgnd = "white",
  axLabs = c("hair\ncolor", "eye\ncolor"),
  axLab.pos = c(1, 1),
  axLab.gpar = gpar(fontsize = 14),
  anNodes = "HECticks.txt",
  anNode.gpar = gpar(col = "black"),
  arrow = c("more\ncommon", 0.0, 2, 4, 1, -2),
  dr.nodes = FALSE
)

grid.text("males", x = 0, y = 2.3, default.units = "native")
grid.text("females", x = 0, y = -2.3, default.units = "native")
grid.text("Pairing of Eye Color with Hair Color",
  x = 0, y = 3.75,
  default.units = "native", gp = gpar(fontsize = 18)
)
grid.text("Adding tick marks to the nodes",
  x = 0, y = 3.25,
  default.units = "native", gp = gpar(fontsize = 12)
)
setwd(currDir)


### 3D Hive Plots. The following must be run interactively.
if (FALSE) {
require("rgl")
test4 <- ranHiveData(nx = 4, type = "3D")
plot3dHive(test4)
}