1 Introduction
A heat map is a graphic commonly used to visualize the spatial distribution of a response observed on a two-dimensional grid. For example, a climate scientist may want to visualize the spatial distribution of an aerosol across a grid of locations covering the study area. In general, a heat map can be used to display response variation as a function of two covariates varying in a grid-like pattern, such as the tensile strength of a substance as a function of heat and pressure. Each grid point in a heat map is associated with a polygon, and each polygon is colored using a color scheme related to the level of the response at each grid point. The plot of colored polygons is an image or heat map. A color scale relating the colors to their associated levels often accompanies the image. For clarity, we use the term image to refer to the plot of colored polygons alone and the term heat map to refer to the combination of image(s) and color scale.
The autoimage package (French 2017) makes it easy to plot a sequence of heat maps with straightforward, native options for projection of geographical coordinates. The package makes it simple to add lines, points, and other features to the images, even when the coordinates are projected. The package allows for seamless creation of heat maps for data on regular or irregular grids, as well as data that is not on a grid.
As a quick introduction to some of the autoimage package’s
capabilities, we utilize the narccap data included in the autoimage
package. The narccap data set comes from the North American Regional
Climate Change Assessment Program
(Mearns et al. 2007, updated 2014; Mearns et al. 2009, 2012), which
is a program designed to model climate scenarios in North America (the
United States, Canada, and northern Mexico) by coupling regional and
global climate models. Specifically, the narccap data are the maximum
daily surface air temperature (abbreviated tasmax) in degrees Kelvin (K)
for the five consecutive days between May 15, 2041 and May 19, 2041. The
data were simulated using the Canadian Regional Climate Model (Caya and Laprise 1999)
forced by the Community Climate System Model atmosphere-ocean general
circular model (Collins et al. 2006). The data set contains lon, a 140 \(\times\) 115
matrix of longitude coordinates, lat, a 140 \(\times\) 115 matrix of
latitude coordinates, and tasmax, a 140 \(\times\) 115 \(\times\) 5 array,
where each element of the third dimension of the array corresponds to
the tasmax measurements of the respective day. We create the heat map
shown in Figure 1 for the first four days of the
narccap data by executing the command
autoimage(lon, lat, tasmax[,,1:4])
narccap
data.The outline of the United States and Mexico are somewhat noticeable in the images of Figure 1, but this would be easier to see if the relevant national borders of the countries were included. This is accomplished in Figure 2, which is created by specifying a map in the previous command:
autoimage(lon, lat, tasmax[,,1:4], map = "world")
narccap data,
along with the relevant national borders.Images and heat maps can be created in R using functions from several different R packages. We discuss six functions in more detail. They are
the
imagefunction in the graphics package,the
filled.contourfunction in the graphics package,the
image.plotfunction in the fields package (Douglas Nychka et al. 2015),the
levelplotfunction in the lattice package (Sarkar 2008),the
spplotfunction in the sp package (Pebesma and Bivand 2005; Bivand et al. 2015),and the
geom_tilefunction in the ggplot2 package (Wickham 2009).
In the next section, we compare the native capabilities of these tools with those of the autoimage package. We define the native capabilities of a function or package to be the capabilities of the function or package without loading additional packages or requiring additional user code. This will be followed by a section demonstrating the main capabilities of the autoimage package. We will conclude with a brief summary of conclusions in the final section.
2 Tools for creating heat maps in R
We now compare the capabilities of existing tools for creating heat maps in R.
We begin by discussing the image function included in the graphics
package. This function is included in a standard R installation. The
image function produces an image without a color scale. While one can
discern spatial patterns from the plotted image, one cannot determine
the magnitude of the response values without knowing more about the
coloring scheme. Naturally, members of the R community have provided
solutions to add this functionality. For example, the
spatstat package
(Baddeley and Turner 2005) extends the image function using S3 methods to
automatically include a color scale with the image when an im class
object is plotted. The image function requires the responses to be on
a regular grid. Specifically, if \(x\) and \(y\) are each an increasing
sequence of values, then the coordinates of a regular grid are obtained
by considering all combinations of the elements in \(x\) and \(y\). Regular
grids frequently become irregular when rotated or transformed to a
different coordinate system. This is common for longitude/latitude
coordinates that are transformed using a projection. When a matrix of
images is desired, the user can modify the mfrow argument of the par
function in the graphics package and then plot a sequence of images.
However, the matrix of images will not include individual color scales
or a common color scale. The image function has no capabilities
related to coordinate projection. Existing images can be added to using
standard graphics functions such as lines and points. It is worth
noting that the standard R installation also includes a heatmap
function in the stats package, but this displays a different result
than the image function. The heatmap function documentation
indicates that the heatmap function produces, “... a false color
image ... with a dendrogram added to the left side and to the top.
Typically, reordering of the rows and columns according to some set of
values (row or column means) within the restrictions imposed by the
dendrogram is carried out.” Consequently, a heat map is sometimes called
an image plot by researchers whose data analysis is primarily done in
R. We will continue to use the more general terminology “heat map” to
describe this type of graphic in what follows.
The filled.contour function in the graphics package produces an
image with a vertical color scale on the right side of the image. The
algorithm used to color the polygons in the filled.contour function
differs slightly from the image function, but produces similar
results. The filled.contour function requires the responses to be on a
regular grid. The filled.contour function cannot natively produce a
sequence of heat maps with a common color scale or individual color
scales because the function internally calls the layout function.
Coordinate projection is not natively supported by the filled.contour
function. An existing image can be added to using graphics functions
such as lines, points, or text.
Another popular tool for creating heat maps in R is the image.plot
function in the fields package. The image.plot function retains the
strengths of the image function while providing additional
functionality. The image.plot function automatically includes a color
scale with the plotted image. More uniquely, the image.plot function
can natively produce heat maps for data observed on an “irregular grid”.
Let x be an \(r\times c\) matrix of \(x\) coordinates and y be an
\(r\times c\) matrix of \(y\) coordinates. Then x and y define an
irregular grid if x[i,j]\(\leq\)x[i+1,j], y[i,j]\(\leq\)y[i+1,j],
x[i,j]\(\leq\) x[i,j+1], and y[i,j]\(\leq\) y[i,j+1] for all valid
choices of i and j. The image.plot function can be used to
construct a matrix of heat maps with individual color scales by
specifying the mfrow argument of the par function and calling
image.plot the desired number of times. The image.plot function
cannot natively create a matrix of images with a common color scale.
Though the image.plot function includes functionality to create images
for geographically-referenced irregular grids, it does not include any
native functionality for projecting coordinates. Features can be added
to existing images using the lines, points, and related functions.
The lattice package provided the first well-known alternative to the
base graphics system in R. The lattice package produces heat maps
using the levelplot function. Images produced by the levelplot
function automatically include a color scale. The levelplot function
can only produce heat maps for responses observed on a regular grid. The
levelplot function can natively create a matrix of heat maps sharing a
common color scale. To obtain a matrix of heat maps with individual
color scales, one must combine a sequence of levelplot function calls
with the grid.arrange function in the
gridExtra package
(Auguie 2016). The levelplot function includes no functionality
related to coordinate projection. Adding lines, points, or other
features is usually accomplished by defining an appropriate panel
function.
The sp package provides powerful classes for representing
geographically-referenced data. The sp package can produce heat maps
automatically for SpatialGriddedDataFrame class objects using the
spplot function. The spplot function produces heat maps by extending
the levelplot function in the lattice package, and the two functions
have similar feature sets. One major difference between the two
functions is that the sp package includes coordinate projection
information within the SpatialGriddedDataFrame, so the spTransform
function in the sp package can be used to easily project coordinates
to a different system. However, if the projected set of coordinates is
not regular, the spplot function will no longer produce a heat map for
the transformed data, but will instead produce a scatterplot of colored
points with a related color scale.
The grammar of graphics plotting system implemented in the ggplot2
package continues to grow in popularity. A heat map can be constructed
using ggplot2 by combining the geom_tile geometry (or the
geom_rect or geom_raster geometries) with a ggplot object. The
heat map automatically includes a color scale with the image. Similar to
the image, levelplot, and spplot functions, the ggplot2 package
requires locations to be on a regular grid. A matrix of images sharing a
common color scale can be created directly in ggplot2 using
facet_wrap or facet_grid. A matrix of heat maps with individual
color scales can be created by supplementing ggplot2 with
additionality functionality provided by the gridExtra or
cowplot (Wilke 2016)
packages. The coord_map function can be used to natively project
geographic coordinates on a regular grid to an irregular grid.
Additional features can be added to the images by specifying the
appropriate geometry calls when creating the heat maps. These additional
features are automatically projected if the coord_map function is
utilized.
The autoimage package was created to easily produce a sequence of heat
maps while natively working with projected coordinates, even when the
data are not on a regular grid. The autoimage package utilizes the
base R graphics system (like the image, filled.contour, and
image.plot functions) to quickly and straightforwardly create heat
maps. The autoimage function is the most important function in the
autoimage package. The autoimage function automatically supplies a
color scale with the constructed image(s). The autoimage function can
automatically create heat maps for responses on an irregular grid,
similar to the image.plot function. In fact, the autoimage function
relies on the poly.image function from the fields package to create
heat maps for this type of data, which is the function used by the
image.plot function for the same purpose. Additionally, the
autoimage package can natively create heat maps for non-gridded data
by automatically interpolating the surface onto a regular grid before
plotting using the akima
package1 (Akima and Gebhardt 2016). The autoimage function can create a matrix of
heat maps with either individual or shared color scales automatically,
without the use of additional user code or R packages. Additionally,
functionality for coordinate projection is available automatically in
the autoimage function using the mapproject function in the
mapproj package
(McIlroy 2015). Additional features can be added to the plotted
images (even for projected coordinates) using the plines, ppoints,
ptext, and related functions available in the autoimage package.
We now summarize the similarities and differences between the native
functionality of the autoimage package and the previous tools
discussed. Most of the tools automatically include a color scale with
the plotted image, similar to the autoimage function. The lattice,
sp, and ggplot2 packages can create a sequence of heat maps with a
common color scale. The image.plot function can be used in combination
with the par function to create a matrix of heat maps with individual
color scales. The lattice, sp, and ggplot2 packages can be used in
combination with the gridExtra package to produce a matrix of heat
maps with individual color scales. The autoimage function has native
functionality for creating a matrix of heat maps with either a common or
individual color scales. In contrast, only the autoimage and
image.plot functions can natively create heat maps for data on an
irregular grid. Additionally, only the autoimage package can
natively create heat maps for non-gridded data (by automatically
interpolating the responses onto a regular grid before plotting). The
sp, ggplot2, and autoimage packages support coordinate projection
of longitude/latitude coordinates, though only the ggplot2 and
autoimage packages can produce heat maps if the projected coordinates
result in an irregular grid. Table 1 summarizes the
features of the heat map-generating tools mentioned above. If a feature
is not natively available, but becomes available by using a relevant
package or function, then the appropriate tool is listed.
| Package or function name | Color scale | Irregular grid | Non-gridded data | Shared color scale | Individual color scales | Coordinate projection |
|---|---|---|---|---|---|---|
image |
||||||
filled.contour |
x | |||||
| fields | x | x | par |
|||
| lattice | x | x | gridExtra | |||
| sp | x | x | gridExtra | x | ||
| ggplot2 | x | x | gridExtra | x | ||
| autoimage | x | x | x | x | x | x |
The feature set for creating heat maps using the ggplot2 package largely overlaps with the autoimage package, especially if additional packages are used to extend the functionality of ggplot2. A user may wonder whether the the autoimge package has any other advantages that would support its use over the more well-known and broadly capable ggplot2 package. As previously mentioned, ggplot2 requires that the original (unprojected) data be observed on a regular grid, while the autoimage package supports heat map creation for data on regular and irregular grids, as well as non-gridded data. Another advantage of the autoimage package is that it renders a sequence of heat maps for projected coordinates faster than the ggplot2 package. In order to compare the speed of heat map generation using the autoimage and ggplot2 packages when natively projecting the coordinates before plotting, we constructed a matrix of 36 heat maps (with a common color scale) using coordinates observed on a regular 116\(\times\)50 grid and projected the coordinates using the Lambert projection. Creating the heat maps on a mid-2012 MacBook Pro with a 2.6 GhZ Intel Core i7 processor and 16 GB of RAM took roughly 4 seconds using the autoimage package, but over 12 minutes using the ggplot2 package. This is by no means an exhaustive timing comparison, but the result suggests that when coordinate projections are utilized in creating a matrix of heat maps, the autoimage package can render the plot more quickly than the ggplot2 package.
3 autoimage examples
We now examine the capabilities of the autoimage package in more
detail. The most important functions in autoimage are the pimage and
autoimage functions. We illustrate the basic usage of these functions
using two data sets: the first is the irregularly-gridded narccap data
previously discussed, while the second is a set of non-gridded
geochemical measurements for 960 locations in the state of Colorado. The
Colorado geochemical measurements were obtained by the United States
Geological Survey (USGS) as a baseline for the natural variation in soil
geochemistry in Colorado (Smith and Ellefsen 2010) . The data are stored as a data frame
with 960 rows and 31 columns. easting, northing, latitude, and
longitude variables are provided in the data frame, as well as
Aluminum (Al), Calcium (Ca), Iron (Fe), and many more chemical
measurements. The Colorado data are available in the co data set in
the gear package (French 2015).
The autoimage function is a generalization of the pimage function,
so we discuss the pimage function first.
Basic usage of the pimage function
The most important arguments of the pimage function are x, y, and
z. x and y are the coordinate locations and z is the responses
associated with the coordinates. x, y, and z can have differing
formats depending on the type of data to be plotted. If the data are
observed on a regular grid, then z will be a matrix with dimensions
matching the dimensions of the grid and x and y will be vectors of
increasing values that define the grid lines. If the data are observed
on an irregular grid, then z will be a matrix with dimensions matching
the dimensions of the grid, and x and y will be matrices whose
coordinates specify the \(x\) and \(y\) coordinates of each value in z. If
the data are not on a grid, then x and y will be vectors specifying
the coordinate locations, and z will be the vector of responses at
each coordinate. If the data are not on a grid, then the data are
automatically interpolated onto a grid before plotting. The command
pimage(x = lon, y = lat, z = tasmax[,,1])is used to create a heat map of the tasmax measurements for the first
day of the narccap data. This heat map is shown in
Figure 3. Recall that the narccap data are observed
on an irregular grid.
narccap data.A heat map of the Aluminum measurements for the non-gridded co data
set is created by executing the commands
data(co, package = 'gear')
pimage(co$longitude, co$latitude, co$Al)with the resulting heat map shown in Figure 4.
co data
set.We now discuss other basic arguments used by the pimage function.
The first two arguments we discuss are the col and legend arguments.
The color scheme used for coloring a heat map is of great importance.
The default color scheme used in the autoimage package is the
viridis color scheme from the
viridisLite package.
This color scheme is, “…designed in such a way that [it] will
analytically be perfectly perceptually-uniform, both in regular form and
also when converted to black-and-white. [It is] also designed to be
perceived by readers with the most common form of color blindness.”
(Garnier 2016) The color scale can be modified by passing a vector of
colors to the col argument through the ellipses argument (...), as
in the image function in the graphics package. The orientation of
the color scale can be changed using the legend argument. The default
value is legend = ’horizontal’, which produces a color scale
horizontally underneath the image. The color scale can be removed by
specifying legend = ’none’ or can be placed vertically along the right
side of the image by specifying legend = ’vertical’. A heat map of the
first day of narccap tasmax measurements with a vertical color scale
using 6 colors from the magma color palette in the viridisLite package
is created by executing the command
pimage(lon, lat, tasmax[,,1], col = viridisLite::magma(6), legend = 'vertical')The resulting heat map is shown in Figure 5.
narccap data using a custom color scheme and vertical color
scale.We now discuss arguments related to coordinate projection and adding
geographic maps to an image. Longitude and latitude coordinates can be
projected before plotting by specifying the proj, parameters, and
orientation arguments. When specified, the coordinates are projected
using the mapproject function in the mapproj package. proj
specifies the name of the projection to utilize (the default is
’none’, i.e. no projection). The parameters argument specifies the
parameter values of the chosen projection, and orientation can be used
to change the orientation of the projection. See the mapproject
function in the mapproj function for more details regarding these
arguments. Several geographic maps can be automatically added to the
image by specifying the map argument. The available geographic maps
come from the maps package
(Brownrigg et al. 2016), and include the world, usa, state, county,
france, nz (New Zealand), italy, lakes, and world2 maps.
Interested users can find more details about these maps in the maps
package. We now create a heat map with projected coordinates for the
first day of narccap tasmax measurements. We utilize the Bonne
projection using 45 degrees as the standard parallel. We also add a
geographic map of the continental United States (U.S.). Note that a grid
is automatically added to the image because latitude and longitude
parallels are not straight for most projections. The command
pimage(lon, lat, tasmax[,,1], proj = 'bonne', parameters = 45, map = 'usa')produces the heat map in Figure 6.
narccap data using projected coordinates with an added geographic
map of the continental U.S.The last major argument to the pimage function is the lratio
argument. This argument controls the relative height or width of the
color scale in comparison with the main plotting area. Increasing
lratio increases the thickness of the color scale, while decreasing
lratio decreases the thickness of the color scale.
Additional customizations to heat maps produced by the pimage function
can be made via the ellipses (...) argument. This includes adding
custom geographic maps and points to the image, customizing the grid
lines created when the coordinates are projected, further customizing
the appearance of the color scale, and customizing the axis labels.
These customizations are discussed in detail in the vignette included in
the autoimage package, which can be accessed by executing the command
vignette(’autoimage’).
Basic usage of the autoimage function
We next discuss the autoimage function, which generalizes the pimage
function to create a heat map with a sequence of images. The arguments
for the autoimage and pimage functions are mostly the same, and we
replicate their discussion only when necessary.
The structure of the z argument for the autoimage function may vary
slightly from the pimage function. Specifically, if multiple gridded
images are to be constructed, then z will be a three-dimensional array
instead of a matrix. Each element of the third dimension of z
corresponds to the matrix of gridded values for each image. If images
for multiple non-gridded variables are to be constructed, then z will
be a matrix where each column corresponds to a different variable. The
autoimage function automatically constructs a sequence of images with
a common color scale. If individual color scales are desired for each
image, then the common.legend argument can be set to FALSE. The
size argument can be used to specify the layout of the sequence of
images, similar to the mfrow argument of the par function in the
graphics package. If this is not specified, the autosize function in
the autoimage package is used to automatically choose the layout, with
a tendency to produce a layout closer to square dimensions. We produce a
1\(\times\)3 matrix of images with a common color scale
for the narccap data using the command
autoimage(lon, lat, tasmax[,,1:3], size = c(1, 3))as shown in Figure 7.
narccap data set tasmax measurements in
a 1\(\times\)3 layout.Similarly, we create a 2\(\times\)2 layout of images for
the Colorado geochemical measurements by passing 4 columns of the co
data frame to the autoimage function. The values of each variable have
substantially different ranges, so we use individual color scales for
each image. Titles are added to each image using the main argument by
providing a character vector whose length matches the number of plotted
images. Executing the command
autoimage(co$lon, co$lati, co[,c('Al', 'Ca', 'Fe', 'K')], common.legend = FALSE,
main = c('(a) Aluminum %', '(b) Calcium %', '(c) Iron %', '(d) Potassium %'))produces Figure 8.
It is natural to add a common title to a heat map with multiple images.
This can be accomplished by passing the desired title to the
outer.title argument. The title will be added in the outer margin of
the resulting heat map. The size of the outer margins should be
specified using the oma argument of the par function of the
graphics package before adding the common title. However, a sensible
choice for the size of the outer margins is automatically made by the
autoimage package if this is not specified by the user. We create the
heat map of narccap tasmax measurements shown in
Figure 9 by executing the command
autoimage(lon, lat, tasmax, outer.title = 'tasmax for 5 days')
Additional customizations to heat maps produced by the autoimage
function can be made via the ellipses (...) argument. In addition to
the customizations mentioned in the context of the pimage function,
this includes the ability to change the appearance of the common title.
These customizations are discussed in detail in the vignette included in
the autoimage package, which can be accessed by executing the command
vignette(’autoimage’).
Richer plots using the autolayout and autolegend functions
Suppose we want to add custom features to a sequences of images, with
each image receiving different features. One can create a richer
sequence of images using the autolayout and autolegend functions.
The autolayout function partitions the graphic device into the
sections needed to create a sequence of images. The most important
function arguments include size, legend, common.legend, and
lratio, which correspond to the same arguments in the pimage and
autoimage functions. The outer argument specifies whether a common
title will be utilized in the plot. The default is outer = FALSE,
indicating that no common title will be added to the plot. When
autolayout is called, numbers identify the plotting order of the
sections, though these can be hidden by setting show = FALSE. As an
initial example, we create a 2\(\times\)3 matrix of
images with a common vertical color scale. The command
autolayout(c(2, 3), legend = 'v')produces the plot in Figure 10.
autolayout
function.After creating the layout of a complicated heat map using the
autolayout function, the images should be created using the pimage
function while specifying legend = ’none’. After the desired image or
set of images is created, one can automatically add the appropriate
legend by calling autolegend. The autolegend function recovers
relevant color scale parameters from the most recent pimage call.
Consequently, if a common legend is desired, it is important to specify
a common zlim argument among all relevant pimage calls.
Various features can be added to the images using the ppoints,
plines, ptext, psegments, parrows, and ppolygon functions.
These are analogues of the points, lines, text, segments,
arrows, and polygon functions in the graphics package, to be used
with images containing projected coordinates.
We provide an (unrealistic, but informative) example of the kinds of
plots these functions can be used to create. Suppose we wish to create a
heat map for both the narccap and Colorado geochemical data sets. We
desire to add a geographic map for each state in the U.S. for the
narccap data while using the Mercator projection to transform the
coordinates before plotting. We desire to plot the Aluminum measurements
for the Colorado data. We want a custom color scale similar to the jet
color scheme in Matlab. We desire to project the coordinates before
plotting using the Bonne projection with a reference latitude of 39
degrees. We also desire to add geographic maps of the relevant U.S.
counties to the map, along with labels for select Colorado cities.
Lastly, we will add a large, purple title to the two heat maps.
We begin by obtaining some of the relevant information for these plots.
The borders for the continental U.S. states is available in the state
map in the maps package. However, we must extract the borders of
Alaska and Hawaii from the world map in the maps package. Executing
the commands
data(worldMapEnv, package = 'maps')
hiak <- maps::map('world', c('USA:Hawaii', 'USA:Alaska'), plot = FALSE)loads and extracts the borders for Hawaii and Alaska. The results are
stored in a list named hiak with named vectors x and y containing
the coordinates of the borders. Each state border is separated by an
NA value. The commands
data(us.cities, package = 'maps')
codf <- us.cities[us.cities$country.etc == 'CO', ]
codf <- codf[c(3, 5, 7:10, 18), ]loads the us.cities data set from the maps package, extracts the
Colorado cities from this data set, then stores a small sample of these
Colorado cities in the codf data frame. Information related to the
name, longitude, and latitude of each city is included in the data
frame.
Having obtained the relevant information, we setup a 1\(\times\)2 matrix of images with individual horizontal color scales and an area for a common title using the command:
autolayout(c(1, 2), legend = "h", common.legend = FALSE, outer = TRUE)We now create a heat map for the first day of NARCCAP tasmax measurements using the command
pimage(lon, lat, tasmax[,,1], legend = 'none', proj = 'mercator',
map = 'state', lines.args = list(col = 'grey'))Note that legend = ’none’ since this will be added afterward using the
autolegend function. The Mercator projection was chosen via the proj
argument, and the state geographic map was added. The color of the
geographic map was changed by passing the lines.args argument to
pimage. The lines.args argument is a named list with components
matching the arguments of the lines function in the graphics
package, and changes the appearance of any geographic maps plotted using
the pimage function. We next add the state borders for Hawaii and
Alaska using the plines function, title the heat map, and add the
color scale to the image by executing the following commands:
plines(hiak, proj = 'mercator', col = 'grey')
title('tasmax for North America')
autolegend()Note the specification of the projection and line color in the plines
function call.
Next, we construct the image for the Colorado Aluminum measurements using the commands
pimage(co$lon, co$lat, co$Al, map = 'county', legend = 'none',
proj = 'bonne', parameters = 39, paxes.args = list(grid = FALSE),
col = fields::tim.colors(64), lines.args = list(col = 'grey'))Note the custom color scheme specified by the col argument. Also, the
paxes.args argument is passed to the pimage function to suppress the
grid lines that would normally be plotted when a projection is used. The
locations and names of the Colorado cities are added to the image using
the commands
ppoints(codf$lon, codf$lat, pch = 16, proj = 'bonne')
ptext(codf$lon, codf$lat, labels = codf$name, proj = 'bonne', pos = 4)A title and color scale are added to the image using the commands
title('Colorado Aluminum levels (%)')
autolegend()Lastly, we specify a large common title for the heat maps using the
mtext function in the graphics package. Specifically, we execute the
command:
mtext('Two complicated maps', col = 'purple', outer = TRUE, cex = 2)The plot resulting from the commands listed in this section is shown in Figure 11.
autolayout and autolegend functions.4 Summary
We have introduced the autoimage package for constructing heat maps. The autoimage package natively supports: 1. automatic inclusion of a color scale with the plotted image, 2. construction of heat maps for responses observed on regular or irregular grids, as well as non-gridded data, 3. construction of a matrix of heat maps with a common color scale, 4. construction of a matrix of heat maps with individual color scales, 5. projecting coordinates before plotting, 6. easily adding geographic borders, points, and other features to the heat maps. We believe that the breadth of native features, simplicity, and speed of the autoimage package make it a unique contribution to the R user community in comparison with other R tools that can be used for creating heat maps. We note however that the autoimage package is a specialized tool and is limited to the construction of heat maps. This is in contrast to other plotting packages mentioned earlier, such as the lattice, sp, and ggplot2 packages, which have many plotting capabilities unrelated to heat maps.
A number of additional features and heat map customizations are
available in the autoimage package, but were not discussed in order to
shorten the length of this article. Additional discussion and examples
may be found in the documentation of the autoimage package. A more
detailed introduction to the capabilities of the autoimage package can
be accessed by executing the command vignette(’autoimage’).
Additionally, a vignette comparing some of the heat map capabilities of
the autoimage and ggplot2 packages can be accessed be executing the
command vignette(’ggplot2-comparison’).
The source code for the autoimage package is publicly hosted at https://github.com/jpfrench81/autoimage. Bugs and other issues may be reported there. Additionally, interested parties are encouraged to submit improvements for the autoimage package at the GitHub repository listed above.
5 Acknowledgments
This autoimage package was created for research supported by NSF Grant
DMS-1463642 and NIH Grant R01 CA157528. This package would not have been
created without inspiration from the internals of the image.plot
function in the fields package written by Doug Nychka and from the
image.scale.2 function written by Marc Taylor and discussed at
http://menugget.blogspot.com/2013/12/new-version-of-imagescale-function.html.
CRAN packages used
autoimage, fields, lattice, sp, ggplot2, spatstat, gridExtra, cowplot, akima, mapproj, gear, viridisLite, maps
CRAN Task Views implied by cited packages
NumericalMathematics, Phylogenetics, Spatial, SpatioTemporal, Survival, TeachingStatistics
Note
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