| Title: | Lattice Options and Add-Ins |
|---|---|
| Description: | Various plots and functions that make use of the lattice/trellis plotting framework. The plots, which include loaPlot(), loaMapPlot() and trianglePlot(), and use panelPal(), a function that extends 'lattice' and 'hexbin' package methods to automate plot subscript and panel-to-panel and panel-to-key synchronization/management. |
| Authors: | Karl Ropkins [aut, cre] |
| Maintainer: | Karl Ropkins <[email protected]> |
| License: | GPL (>= 2) |
| Version: | 0.3.1.1 |
| Built: | 2024-12-21 13:23:37 UTC |
| Source: | https://github.com/r-forge/loa |
The loa package contains various plots, options and
add-ins for use with the lattice package.
| Package: | loa |
| Type: | Package |
| Version: | 0.3.1.1 |
| Date: | 2024-12-20 |
| License: | GPL (>= 2) |
| LazyLoad: | yes |
lattice provides an elegant and highly powerful implementation
of the Trellis plotting structure described by Cleveland and colleagues.
In particular the combination of panel... functions, which can be
layered within plots to generate novel visualisations, and simple-to-use
conditioning make it a hugely effective tool when working with data.
The loa package contains a number of plot functions developed to make
use of this framework. These are summarized in section 1 of this manual, and include:
1.1. loaPlot for various XYZ plots.
1.2. loaMapPlot and associated geoplotting functions.
1.3. trianglePlot and associated functions.
1.4. stackPlot and associated functions.
1.5. loaBarPlot and associated functions.
Other panel... functions and example data are summarized in sections 2 and
3, respectively:
2.1. Specialist panels, e.g. panel.kernelDensity,
2.2. Specialist panels for polar plotting, e.g. panel.polarPlot.
3.1. Example data, e.g. lat.lon.meuse.
While such 'stand alone' plot functions are of obvious value, the code framework is of possibly wider interest because it provides a template for the rapid third-party development of novel visualization functions and a highly flexible 'test bed' for the comparison of different data handling strategies.
Therefore, the functions in this package have been written in a relatively dissaggregated
fashion so code can be easily rearranged or modified by others to quickly develop
alternative plots within the lattice framework. Firstly, plot functions
in section 1 have where possible been supplied as main plot functions and plot component
functions that handle data, axes, panels, etc. Secondly, the workhorse functions, those common
functions used through-out the package to simplify many routine operations have been grouped
together and summarized in section 4:
4.1. panelPal
4.2. plot structure handlers: formulaHandler, etc.
4.3. Plot lim(s) and scale(s) handlers: limsHandler, localScalesHandler, etc.
4.4. Plot conditioning handlers: condsPanelHandler, etc.
4.5. Common plot argument handlers: cexHandler, colHandler,
zHandler, etc.
4.6. Key handlers: keyHandler, etc.
4.7. Other panel functions: getArgs, etc.
4.8. List handlers: listHandler, etc.
And, finally, functions used for working with data post-plotting, are summarized in section 5:
5.1. Interactive functions for working with plot outputs: getXY, etc.
This package is very much intended to be an evolutionary exercise. I use it on a routine basis to develop plots for use elsewhere and compare data visualization methods. However, that working pattern can generate some very 'developer-centric' code. So, I would be very pleased to hear from others - what they did and did not like about the package; what they would have liked to have been different; and, perhaps most interesting for me what they are using it to do.
Karl Ropkins <[email protected]>
Functions in loa make extensive use of code developed by others.
In particular, I gratefully acknowledge the huge contributions of:
lattice: Sarkar, Deepayan (2008) Lattice: Multivariate Data Visualization with R. Springer, New York. ISBN 978-0-387-75968-5
Trellis Plotting: Becker, R. A., Cleveland, W. S., Shyu, M. J. (1996). The Visual Design and Control of Trellis Display, Journal of Computational and Graphical Statistics, 5(2), 123-155. Cleveland, W.S. (1993) Visualizing Data, Hobart Press, Summit, New Jersey.
loaPlot, loaMapPlot, trianglePlot
loaPlot is a standard XYZ plotting function, where X and Y are the axes of a conventional XY plot and Z is an element (or elements if supplied in the form Z1 + Z2 + Z3...) visualized at associated XY coordinates. By default, loaPlot links Z to plot point size and color to generate a bubbleplot style output, or using modified plot calls other plot types.
loaPlot(x, data = NULL, panel = panel.loaPlot, ..., local.scales = FALSE, reset.xylims = TRUE, load.lists = NULL, by.group = NULL, by.zcase = NULL, preprocess = TRUE) #standard panels panel.loaPlot(..., loa.settings = FALSE) panel.loaPlot2(..., loa.settings = FALSE) panel.loa(..., loa.settings = FALSE) #grids panel.loaGrid(grid.x = NULL, grid.y = NULL, xlim = NULL, ylim = NULL, ..., grid = NULL, panel.scales = NULL)loaPlot(x, data = NULL, panel = panel.loaPlot, ..., local.scales = FALSE, reset.xylims = TRUE, load.lists = NULL, by.group = NULL, by.zcase = NULL, preprocess = TRUE) #standard panels panel.loaPlot(..., loa.settings = FALSE) panel.loaPlot2(..., loa.settings = FALSE) panel.loa(..., loa.settings = FALSE) #grids panel.loaGrid(grid.x = NULL, grid.y = NULL, xlim = NULL, ylim = NULL, ..., grid = NULL, panel.scales = NULL)
x |
A formula with the general structure
|
data |
If supplied, the assumed source of elements of |
panel |
|
... |
Additional arguments are passed on to related functions. For This mechanism provides access to most common plot parameters, e.g. |
local.scales |
For |
reset.xylims |
For |
load.lists |
For |
by.group, by.zcase
|
For |
preprocess |
For |
loa.settings |
For |
grid.x, grid.y, xlim, ylim, grid, panel.scales
|
For |
loaPlot provides lattice-style conditioning/handling for a range of
commonly used XYZ plotting options. It is perhaps easiest pictured as a
'mid point' alternative somewhere between the standard lattice
plot functions xyplot and levelplot.
The default form of the plot uses an extension of the subscripting methods described by Deepayan Sarkar in Chapter 5 of Lattice (see sections on scatterplots and extensions). The default output is a bubble plot (see example 1 below).
loaPlot returns a trellis object, much like a conventional lattice
plot function.
panel.loaPlot2 and panel.loaPlot2 are alternative versions of
panel.loaPlot that is currently under revision.
loaPlot arguments by.group and by.zcase are currently in
revision. Please use with care.
Karl Ropkins
These functions make extensive use of code developed by others.
lattice: Sarkar, Deepayan (2008) Lattice: Multivariate Data Visualization with R. Springer, New York. ISBN 978-0-387-75968-5
RColorBrewer: Erich Neuwirth <[email protected]> (2011). RColorBrewer: ColorBrewer palettes. R package version 1.0-5. http://CRAN.R-project.org/package=RColorBrewer
In loa: panelPal
In other packages, see
lattice: xyplot; and levelplot.
## Example 1 ## Basic usage loaPlot(Ozone~Solar.R*Temp|Wind>8, data=airquality, col.regions="Blues") # Notes: # Formula structure z ~ x * y |cond like levelplot. # Data (and groups) assignment like in standard lattice plots. # By default z is linked to col and cex. # Unless overridden by user inputs or group or zcase setting. # Plot passed via ...Handler functions to provide shortcut plot # reworking, e.g. here colHandler handles color scales # using col.region to generate a color range. # (Here, arguments like "Blues" and c("green", "red") are # allowed and handled using functions in the RColorBrewer # package.) # Formula stuctures: # ~ x * y like xyplot y ~ x # ~ x * y | cond like xyplot y ~ x | cond # z ~ x * y like xyplot y ~ x, col=f(z), cex=f(z) # z ~ x * y | cond like xyplot y ~ x | cond, col=f(z), cex=f(z) # z ~ x * y, groups = g like xyplot y ~ x, groups=g, cex=f(z) # z1 + z2 ~ x * y (zcases) # etc ## Example 2 ## Basic modifications loaPlot(Ozone~Solar.R*Temp, groups=airquality$Wind>8, data=airquality) # When groups are applied, by default group id is linked to col. # The follow example illustrates three options: loaPlot(Ozone~Solar.R*Temp, groups=airquality$Wind>8, data=airquality, group.args=c("pch"), pch=c(1,4), col="blue") # notes: # Here, group.args is used to change the default group arguments. # (So, pch rather than col is used to identify groups.) # pch is then assigned by group rather than by (x,y) case or z case. # (See panelPal Help further further details of assignments in loa.) # col supplied by the user supercedes the default z linkage. # (So, here cex remains z scales but col is fixed as blue.) ## Example 3 ## Key handling loaPlot(Ozone~Solar.R*Temp, data=airquality, col.regions=c("green", "red")) # Key settings are by the key argument (as in lattice) # or key... arguments via keyHandler and listLoad, so e.g.: loaPlot(Ozone~Solar.R*Temp, data=airquality, col.regions=c("green", "red"), key.fun = draw.loaColorKey) # Notes: # By default the loaPlot uses draw.loaPlotZKey to generate # its color key unless an alternative is supplied via key.fun. # (Here, the draw.colorKey wrapper draw.loaColorKey is used to # generate a color bar similar to that in levelplot.) ## Example 4 ## panels loaPlot(Ozone~Solar.R*Temp|Wind>8, data=airquality, col.regions="Reds") # The combined use of loaPlot, panelPal and appropriately configured # panel functions provides automatical handling of a range of plot # elements, e.g.: loaPlot(Ozone~Solar.R*Temp|Wind>8, data=airquality, col.regions="Reds", panel=panel.binPlot) # Notes: # Here, the choice of default key is set by the panel... function; # the panel by default bins data by location and for each bin cell # calculates the mean Ozone concentration just like a standard # lattice panel would, but it also tracks these values (calculated # within the panels) and scales panel-to-panel and panel-to-key # so users do not have to do that retrospectively; and, finally, # it retains in-panel calculations so users can recover them. # (See associated helps for further details: ?panelPal about methods; # and ?panel.binPlot about the panel function.)## Example 1 ## Basic usage loaPlot(Ozone~Solar.R*Temp|Wind>8, data=airquality, col.regions="Blues") # Notes: # Formula structure z ~ x * y |cond like levelplot. # Data (and groups) assignment like in standard lattice plots. # By default z is linked to col and cex. # Unless overridden by user inputs or group or zcase setting. # Plot passed via ...Handler functions to provide shortcut plot # reworking, e.g. here colHandler handles color scales # using col.region to generate a color range. # (Here, arguments like "Blues" and c("green", "red") are # allowed and handled using functions in the RColorBrewer # package.) # Formula stuctures: # ~ x * y like xyplot y ~ x # ~ x * y | cond like xyplot y ~ x | cond # z ~ x * y like xyplot y ~ x, col=f(z), cex=f(z) # z ~ x * y | cond like xyplot y ~ x | cond, col=f(z), cex=f(z) # z ~ x * y, groups = g like xyplot y ~ x, groups=g, cex=f(z) # z1 + z2 ~ x * y (zcases) # etc ## Example 2 ## Basic modifications loaPlot(Ozone~Solar.R*Temp, groups=airquality$Wind>8, data=airquality) # When groups are applied, by default group id is linked to col. # The follow example illustrates three options: loaPlot(Ozone~Solar.R*Temp, groups=airquality$Wind>8, data=airquality, group.args=c("pch"), pch=c(1,4), col="blue") # notes: # Here, group.args is used to change the default group arguments. # (So, pch rather than col is used to identify groups.) # pch is then assigned by group rather than by (x,y) case or z case. # (See panelPal Help further further details of assignments in loa.) # col supplied by the user supercedes the default z linkage. # (So, here cex remains z scales but col is fixed as blue.) ## Example 3 ## Key handling loaPlot(Ozone~Solar.R*Temp, data=airquality, col.regions=c("green", "red")) # Key settings are by the key argument (as in lattice) # or key... arguments via keyHandler and listLoad, so e.g.: loaPlot(Ozone~Solar.R*Temp, data=airquality, col.regions=c("green", "red"), key.fun = draw.loaColorKey) # Notes: # By default the loaPlot uses draw.loaPlotZKey to generate # its color key unless an alternative is supplied via key.fun. # (Here, the draw.colorKey wrapper draw.loaColorKey is used to # generate a color bar similar to that in levelplot.) ## Example 4 ## panels loaPlot(Ozone~Solar.R*Temp|Wind>8, data=airquality, col.regions="Reds") # The combined use of loaPlot, panelPal and appropriately configured # panel functions provides automatical handling of a range of plot # elements, e.g.: loaPlot(Ozone~Solar.R*Temp|Wind>8, data=airquality, col.regions="Reds", panel=panel.binPlot) # Notes: # Here, the choice of default key is set by the panel... function; # the panel by default bins data by location and for each bin cell # calculates the mean Ozone concentration just like a standard # lattice panel would, but it also tracks these values (calculated # within the panels) and scales panel-to-panel and panel-to-key # so users do not have to do that retrospectively; and, finally, # it retains in-panel calculations so users can recover them. # (See associated helps for further details: ?panelPal about methods; # and ?panel.binPlot about the panel function.)
Plotting georeferenced data on maps using lattice, RgoogleMaps and OpenStreetMap
loaMapPlot(x, data = NULL, panel = panel.loaPlot, map = NULL, map.panel = panel.loaBGMapPlotRaster, recolor.map = FALSE, show.axes = FALSE, ..., map.source = getOSMapArg, lon.lat = FALSE) RgoogleMapsPlot(x, data = NULL, ...) OpenStreetMapPlot(x, data = NULL, ...) #map handlers getRGMapArg(ylim, xlim, ..., lim.borders = 0.1) getOSMapArg(ylim, xlim, ..., lim.borders = 0.1) loaMapArg(object = NULL) #map panels panel.loaBGMapPlotRaster(map) panel.loaBGMapPlot(map) #scaling and axis handlers LatLon2MercatorXY(latitude, longitude, ...) MercatorXY2LatLon(mx, my, ...) axis.components.loaMap(map, xlim = NULL, ylim = NULL, ...) xscale.components.loaMap(lim, ..., map = map) yscale.components.loaMap(lim, ..., map = map) #legacy functions googleMap(...) GoogleMap(...) makeMapArg(...) getMapArg(object = NULL)loaMapPlot(x, data = NULL, panel = panel.loaPlot, map = NULL, map.panel = panel.loaBGMapPlotRaster, recolor.map = FALSE, show.axes = FALSE, ..., map.source = getOSMapArg, lon.lat = FALSE) RgoogleMapsPlot(x, data = NULL, ...) OpenStreetMapPlot(x, data = NULL, ...) #map handlers getRGMapArg(ylim, xlim, ..., lim.borders = 0.1) getOSMapArg(ylim, xlim, ..., lim.borders = 0.1) loaMapArg(object = NULL) #map panels panel.loaBGMapPlotRaster(map) panel.loaBGMapPlot(map) #scaling and axis handlers LatLon2MercatorXY(latitude, longitude, ...) MercatorXY2LatLon(mx, my, ...) axis.components.loaMap(map, xlim = NULL, ylim = NULL, ...) xscale.components.loaMap(lim, ..., map = map) yscale.components.loaMap(lim, ..., map = map) #legacy functions googleMap(...) GoogleMap(...) makeMapArg(...) getMapArg(object = NULL)
x |
For |
data |
For |
panel, map.panel
|
For |
map, map.source
|
For |
recolor.map |
For |
show.axes |
For |
... |
Additional arguments are passed on to related functions. For By default both data point colour and size are Similarly, argument passing to
|
lon.lat |
For |
ylim, xlim, lim.borders, lim
|
The latitude and longitude plot ranges.
|
object |
For |
latitude, longitude
|
For |
mx, my
|
For |
loaMapPlot provides lattice-style conditioning/handling for
RgoogleMaps and OpenStreetMap outputs. This uses
loaPlot and panelPal to manage default
panel and key settings.
RgoogleMapsPlot is a shortcut for using loaMapPlot with
maps produced by RgoogleMaps.
OpenStreetMapPlot is a shortcut for using loaMapPlot with
maps produced by OpenStreetMap.
getMap... functions accept latitude and longitude ranges and
related RgoogleMaps or OpenStreetMap function arguments,
and produces an output suitable for use as the map argument in
subsequent (same area) MapPlots or in panel.loaBGMapPlotRaster
or panel.loaBGMapPlot panel function calls.
LatLon2MercatorXY converts supplied latitude and longitude time-series
to Mercator X and Y time-series. MercatorXY2LatLon converts supplied
Mercator X and Y time-series to latitude and longitude time-series. Both output
results as lists containing newX and newY elements.
panel.loaBGMapPlotRaster and panel.loaBGMapPlotMaps are
lattice panel functions that generate map layers for a lattice
plot using getMap... function outputs.
yscale.components.loaMap and xscale.components.loaMap
are y- and x-axis handlers for use with the above panels.
axis.components.loaMap is a wrapper that combines
yscale.components.loaMap and xscale.components.loaMap
and allows both axis to be set from the lattice function
argument axis rather than each individually, via
yscale.components and xscale.components.
NOTE: The MapPlots and related panel and axis handling functions
are in development functions that have been subject to changes.
googleMap and GoogleMap are RgoogleMapsPlot wrappers,
included these were names of earlier versions of this function, that have
been documented in previously published code.
getMapArg was the earlier name for loaMapArg.
quickMap, a crude map plot function intended to demonstrate the use
of the 'handler' functions, is no longer packaged but the code is included
in the examples below.
MapPlots return trellis objects,
much like conventional lattice plot functions.
get...MapArgs return lists for use as maps
in ...MapPlot calls.
getMapArg recovers the map from an existing
GoogleMap output.
panel.GoogleMapsRaster and panel.GoogleMaps
generate panel outputs suitable for use in standard lattice
panel functions.
yscale.components.GoogleMaps, xscale.components.GoogleMaps
generate suitable latitude, longitude scales for use with map layers.
axis.components.GoogleMaps is a wrapper for their routine use.
Google Maps outputs are 2D projections of curve sections of the Earth's surface. Therefore, the assignment of points within panels and the annotation of latitudes and longitudes along axis needs to be locally handled to account for this.
LatLon2MercatorXY and MercatorXY2LatLon are
used to locally scale both axis and data in these plots. These
apply methods and code in the "sp" package.
Important: Users wanting to add data to these plots, e.g. using
update or layers in latticeExtra,
should first rescale the data. Likewise, users wanting to add
maps to other plots will need to rescale plotted data to use these
maps. See Example 1 below.
Important: map APIs often return a map panel larger than the
data (latitude, longitude) range requested. This means you may get back
a map that is large than necessary. As xlim and ylim
are passed to the API when they are called reseting these can
produce similar effects (so you may not get exactly the map range
you ask for! If you want to manually optimise an RgoogleMapsPlot
map range, the best option is currently to start with:
RgoogleMapsPlot(..., size=c(640,640))
...and then change either or both size values until you generate
an appropriate map size.
Karl Ropkins
This function makes extensive use of code developed by others.
lattice: Sarkar, Deepayan (2008) Lattice: Multivariate Data Visualization with R. Springer, New York. ISBN 978-0-387-75968-5
RColorBrewer: Erich Neuwirth <[email protected]> (2011). RColorBrewer: ColorBrewer palettes. R package version 1.0-5. http://CRAN.R-project.org/package=RColorBrewer
RgoogleMaps: Markus Loecher and Sense Networks (2011). RgoogleMaps: Overlays on Google map tiles in R. R package version 1.1.9.6. http://CRAN.R-project.org/package=RgoogleMaps
OpenStreetMap: Ian Fellows and using the JMapViewer library by Jan Peter Stotz (2019). OpenStreetMap: Access to Open Street Map Raster Images. R package version 0.3.4. https://CRAN.R-project.org/package=OpenStreetMap
sp: Pebesma, E.J., R.S. Bivand, 2005. Classes and methods for spatial data in R. R News 5 (2). https://cran.r-project.org/doc/Rnews/.
Roger S. Bivand, Edzer Pebesma, Virgilio Gomez-Rubio, 2013. Applied spatial data analysis with R, Second edition. Springer, NY. http://www.asdar-book.org/
Users should also always cite map sources when using outputs from
these MapPlots:
For GoogleMaps: Map layer: Map data (c) [year] Google
For OpenStreetMap Map layer (c) OpenStreetMap contributors
In other packages, see
RgoogleMaps: GetMap.
OpenStreetMap: openmap.
sp: coordinates; proj4string; and,
spTransform.
lattice: xyplot; panel.xyplot; and
panel.levelplot.
## Example 1 ## quickMap code ## as example of third-party use of functions quickMap <- function(lat, lon, show.data = FALSE, ...){ #get map map <- getRGMapArg(lat, lon, ...) #scale axis for map projection map.axis.comps <- axis.components.loaMap(map) map.axis <- function(components, ...) axis.default(components = map.axis.comps, ...) #scale data for map projection temp <- LatLon2MercaptorXY(lat, lon) lat <- temp$newY lon <- temp$newX #plot data on map xyplot(lat~lon, xlim = map$xlim, ylim = map$ylim, aspect = map$aspect, axis = map.axis, panel = function(...){ panel.loaGBMapPlotRaster(map) if(show.data) panel.xyplot(...) }, ...) } ## Example 2 ## Off-line loaMapPlot example: loaMapPlot(zinc~latitude*longitude, col.regions=c("grey", "darkred"), data=lat.lon.meuse, map=roadmap.meuse) # Note 1: # Here, the map argument is supplied so example works off-line. # If not supplied and R is on-line, the MapPlots will get map # from either Google or OpenStreetMap API. Repeat any of above # without map argument when on-line. For example: ## Not run: loaMapPlot(zinc~latitude*longitude, col.regions=c("grey", "darkred"), data=lat.lon.meuse) ## End(Not run) # (The map will appear slightly different because non-default # size and maptype settings were used to make roadmap.meuse. See # ?roadmap.meuse for details.) # Note 2: # To make a map for use with panel.loaBGMapPlotRaster or panel.loaBGMapPlotRaster # without plotting use makeRGMapArg() or makeOSMapArg(). # To recover a map from a previously plotted loa MapPloy use loaMapArg(). # Note 3: # Other example loaMapPlots (also not run): # using panel.binPlot to change data layer ## Not run: loaMapPlot(zinc~latitude*longitude, col.regions=c("grey", "darkred"), panel=panel.binPlot, data=lat.lon.meuse) ## End(Not run) # using zcase panelling to handle multiple z terms ## Not run: loaMapPlot(cadmium*50+copper*10+lead*2+zinc~latitude*longitude, col.regions=c("grey", "darkred"), key.z.main="Concentrations", panel.zcases = TRUE, data=lat.lon.meuse) ## End(Not run) # using a specialist panel to handle multiple z terms # (Please note: This will take a while...) ## Not run: loaMapPlot(cadmium*50+copper*10+lead*2+zinc~latitude*longitude, col.regions=c("grey", "darkred"), panel=panel.zcasePiePlot, data=lat.lon.meuse) ## End(Not run) # Note 4: # For all maps generated in above examples, the Map layer is # (c) OpenStreetMap contributors## Example 1 ## quickMap code ## as example of third-party use of functions quickMap <- function(lat, lon, show.data = FALSE, ...){ #get map map <- getRGMapArg(lat, lon, ...) #scale axis for map projection map.axis.comps <- axis.components.loaMap(map) map.axis <- function(components, ...) axis.default(components = map.axis.comps, ...) #scale data for map projection temp <- LatLon2MercaptorXY(lat, lon) lat <- temp$newY lon <- temp$newX #plot data on map xyplot(lat~lon, xlim = map$xlim, ylim = map$ylim, aspect = map$aspect, axis = map.axis, panel = function(...){ panel.loaGBMapPlotRaster(map) if(show.data) panel.xyplot(...) }, ...) } ## Example 2 ## Off-line loaMapPlot example: loaMapPlot(zinc~latitude*longitude, col.regions=c("grey", "darkred"), data=lat.lon.meuse, map=roadmap.meuse) # Note 1: # Here, the map argument is supplied so example works off-line. # If not supplied and R is on-line, the MapPlots will get map # from either Google or OpenStreetMap API. Repeat any of above # without map argument when on-line. For example: ## Not run: loaMapPlot(zinc~latitude*longitude, col.regions=c("grey", "darkred"), data=lat.lon.meuse) ## End(Not run) # (The map will appear slightly different because non-default # size and maptype settings were used to make roadmap.meuse. See # ?roadmap.meuse for details.) # Note 2: # To make a map for use with panel.loaBGMapPlotRaster or panel.loaBGMapPlotRaster # without plotting use makeRGMapArg() or makeOSMapArg(). # To recover a map from a previously plotted loa MapPloy use loaMapArg(). # Note 3: # Other example loaMapPlots (also not run): # using panel.binPlot to change data layer ## Not run: loaMapPlot(zinc~latitude*longitude, col.regions=c("grey", "darkred"), panel=panel.binPlot, data=lat.lon.meuse) ## End(Not run) # using zcase panelling to handle multiple z terms ## Not run: loaMapPlot(cadmium*50+copper*10+lead*2+zinc~latitude*longitude, col.regions=c("grey", "darkred"), key.z.main="Concentrations", panel.zcases = TRUE, data=lat.lon.meuse) ## End(Not run) # using a specialist panel to handle multiple z terms # (Please note: This will take a while...) ## Not run: loaMapPlot(cadmium*50+copper*10+lead*2+zinc~latitude*longitude, col.regions=c("grey", "darkred"), panel=panel.zcasePiePlot, data=lat.lon.meuse) ## End(Not run) # Note 4: # For all maps generated in above examples, the Map layer is # (c) OpenStreetMap contributors
Triangle plot functions for Lattice.
trianglePlot(x, data = NULL, ..., ref.cols = TRUE) #standard panels panel.trianglePlot(x = NULL, y = NULL, a0 = NULL, b0 = NULL, c0 = NULL, ..., loa.settings = FALSE, plot = TRUE, process = TRUE) panel.trianglePlotFrame(..., grid = NULL, axes = NULL) panel.trianglePlotGrid(alim = NULL, blim = NULL, clim = NULL, ..., grid = TRUE, panel.scales = NULL) panel.trianglePlotAxes(alim = NULL, blim = NULL, clim = NULL, ..., axes = TRUE, ticks=TRUE, annotation=TRUE, panel.scales = NULL) #other panels panel.triangleByGroupPolygon(x = NULL, y = NULL, a0 = NULL, b0 = NULL, c0 = NULL, ..., loa.settings = FALSE, plot = TRUE, process = TRUE) panel.triangleKernelDensity(x = NULL, y = NULL, a0 = NULL, b0 = NULL, c0 = NULL, ..., loa.settings = FALSE, plot = TRUE, process = TRUE) panel.triangleSurfaceSmooth(x = NULL, y = NULL, z = NULL, a0 = NULL, b0 = NULL, c0 = NULL, ..., loa.settings = FALSE, plot = TRUE, process = TRUE) #data handlers triABC2XY(a, b = NULL, c = NULL, ..., force.abc = TRUE, if.na = "remove.row", if.neg = "remove.row", verbose = FALSE) triXY2ABC(x, y = NULL, ..., force.xy = TRUE, verbose = FALSE) triLimsReset(ans) triABCSquareGrid(a, b = NULL, c = NULL, ..., n=100)trianglePlot(x, data = NULL, ..., ref.cols = TRUE) #standard panels panel.trianglePlot(x = NULL, y = NULL, a0 = NULL, b0 = NULL, c0 = NULL, ..., loa.settings = FALSE, plot = TRUE, process = TRUE) panel.trianglePlotFrame(..., grid = NULL, axes = NULL) panel.trianglePlotGrid(alim = NULL, blim = NULL, clim = NULL, ..., grid = TRUE, panel.scales = NULL) panel.trianglePlotAxes(alim = NULL, blim = NULL, clim = NULL, ..., axes = TRUE, ticks=TRUE, annotation=TRUE, panel.scales = NULL) #other panels panel.triangleByGroupPolygon(x = NULL, y = NULL, a0 = NULL, b0 = NULL, c0 = NULL, ..., loa.settings = FALSE, plot = TRUE, process = TRUE) panel.triangleKernelDensity(x = NULL, y = NULL, a0 = NULL, b0 = NULL, c0 = NULL, ..., loa.settings = FALSE, plot = TRUE, process = TRUE) panel.triangleSurfaceSmooth(x = NULL, y = NULL, z = NULL, a0 = NULL, b0 = NULL, c0 = NULL, ..., loa.settings = FALSE, plot = TRUE, process = TRUE) #data handlers triABC2XY(a, b = NULL, c = NULL, ..., force.abc = TRUE, if.na = "remove.row", if.neg = "remove.row", verbose = FALSE) triXY2ABC(x, y = NULL, ..., force.xy = TRUE, verbose = FALSE) triLimsReset(ans) triABCSquareGrid(a, b = NULL, c = NULL, ..., n=100)
x |
For |
data |
For |
... |
Additional arguments. |
ref.cols |
Either a logical to turn off/on grid color-coding or a
vector of colors to be applied to a0, b0 and c0 axes and grids. These are
applied to the grid lines and axes tick and annotation components. Some users,
particularly those less familiar with triangle plots, can find such color
referencing helpful when analyzing such plots. By default, the colorings are
quite subtle, so users can see the effect if them look for it but it does not
take over the plot when it is not focused on. Finer control can be achieved using
|
y, a, a0, b, b0, c, c0, z
|
(and |
loa.settings, plot, process
|
|
grid, axes, ticks, annotation
|
User-resets for the axes, grid, tick and annotation
elements of the plots. These can be |
alim, blim, clim
|
Delimiters for a, b and c scales, equivalent to |
panel.scales |
A local argument, typically a list, that controls the
appearance of the a0/b0/c0 axes. This is roughly equivalent to the |
force.abc, force.xy
|
Logicals. If a list or data.frame is supplied
to |
if.na |
Character. Handling method to be used if |
if.neg |
Character. Like |
verbose |
Logical, default |
ans |
For |
n |
For |
trianglePlot generates a triangle plot using the lattice framework.
panel.trianglePlot... functions handle the appearance of triangle plot
outputs.
panel.trianglePlot, which is assigned as the default panel
manages both the data layer of the plot and the plot frame (axes, grid, annotation,
etc).
panel.trianglePlotAxes and panel.trianglePlotGrid generate
axes and grid componets of the plot, and panel.trianglePlotFrame is
a wrapper for these. The data layer, which by default is panel.loaPlot,
can be accessed separately using the data.panel argument.
triangleKernelDensity generates a kernel density surface for supplied a0,
b0 and c0 cases.
triangleSurfaceSmooth generates a smoothed surface for supplied a0,
b0, c0 and z cases.
triABC2XY converts supplied (a, b, c) coordinates to an (x, y) scale suitable
for use with triangle plot functions.
triXY2ABC converts supplied (x,y) coordinates from triangle plots to the associated
proportional (a, b, c) scale.
There are various options for range limiting with triABC2XY, triXY2ABC,
and therefore triangle plots. Firstly, limits can be set individually with
alim, blim and clim, much like with xlim and ylim for
conventional plots. However, they can also be set at once using lims, as in e.g.
lims = c(0, 1) to set all axes to full ranges, or on the basis of minimum and maximum
cut-offs using abc.mins and abc.maxs, respectively.
trianglePlot uses localScalesHandler to override normal
lattice handling of scales. This allows parameters for axes other
than 'x' and 'y' to be passed via the scales argument for
axis generation within the plot panel itself. The function does this by recovering
the information for each of the local axes (here a0, b0 and c0)
from scales, and passing this on to the plot as the argument
panel.scales which can then be evaluated by an appropriate panel...
function like panel.trianglePlotAxes. At the same time it also resets
scales to stop the standard axes being generated. The intention here is two-fold.
Firstly, to provide plot users with an axes control mechanism like the standard
scales control of x and y that they already know. And, secondly,
to provide developers with a simple framework for the quick addition of non-standard axes
or scales. See localScalesHandler and panel.localScale for
further details.
trianglePlot uses getPlotArgs to manage lattice defaults and
plot developer and user resets for the different plot components (axes, ticks, grid,
annotation). As with localScalesHandler, the intention here is to provide more
routine access to higher level plot control.
trianglePlot returns trellis objects, much like
conventional lattice plot functions.
panel.trianglePlot... functions are intended for use
within a trianglePlot function call.
triABC2XY returns a list containing the named
components x and y, which are the 2-D (x,y) transformations
of supplied (a,b,c) trianglePlot elements.
triXY2ABC returns a list containing the named
components a, b and c, which are the (a,b,c)
triangle plot coordinates associated with supplied 2-D (x, y) that
trianglePlot would generate.
resetTriLims returns a supplied trellis object, rescaled
based on the assumption that it is a triangle plot.
General:
With triangle plots, the (a0, b0, c0) scales are proportional. So regardless of the
absolute sizes of a coordinate set (a,b,c), values are plotted and handled
as proportions, i.e. a/(a+b+c), b/(a+b+c) and c/(a+b+c), respectively. This means
that absolute values of a, b and c are lost when points are
plotted on these axes. So, the function triXY2ABC returns the relative proportions
of a, b and c, not the absolute amounts, when translating a 2-D
(x,y) coordinates into the associated (a, b, c) coordinates.
Development:
This is an in-development plot, and 'best handling' strategies have not been decided for several elements. So, future versions of these functions may differ significantly from the current version.
In particular:
Current axes assignments, e.g. (a, b, c) versus (a0, b0, c0), etc., have not be finalised. So, these may change in future versions of the function.
Currently, trianglePlot scale adjustment options have been limited. Options under
evaluation include: (1) by alim, blim, clim setting, equivalent to
xlim and ylim, (2) by lims to set all axes ranges the same, and
(3) by maxs to setting all axes range maximums and mins to set all axes
range minimums, etc.
These options are currently only avialable via the data converters.
One of the issues here is that the axes ranges are all inter-linked. The range of one axes
is a function of the other two axes ranges. So, setting these can generate contradictions.
For example, lims=c(0,0.1) should in theory set all ranges to (0, 0.1). But, the triangle
a = b = c = c(0, 0.1) cannot exist. Therefore, the plot would attempt to recover
the extended range that includes all the requested ranges (a = c(0, 0.1),
b = c(0, 0.1) and c = c(0, 0.1)), which in this case is the full
range: a = b = c = c(0, 1). Suggestions on this topic are very welcome.
trianglePlot:
As part of the loa version 0.2.19 update, trianglePlot was rewritten to run
with the most recent version of panelPal function. This means all plot
functions in loa now use the most recent version of panelPal.
This update should provide improved plot handling similar to recent versions of loaPlot
and GoogleMap functions which both already (from versions 0.2.0 onwards) use the latest
version of panelPal.
panel.trianglePlotAxes:
Code currently in revision. Please handle with care.
triABC2XY, triABCSquareGrid:
Code currently in revision. Please handle with care.
Karl Ropkins
These function makes extensive use of code developed by others.
Currently, several triangle plotting methods are under evaluation for use within this package. These are:
The tri-plot method of Graham and Mudgley:
Graham, David J. and Mudgley, Nicholas, G. Graphical representation of particle shape using triangular diagrams: An Excel spreadsheet method. Earth Surface Processes and Landforms, 25, 1473-1477, 2000.
The triangle.param method of Chessel (as coded in R package 'ade4')
Dray, S. and Dufour, A.B.(2007). The ade4 package: implementing the duality diagram for ecologists. Journal of Statistical, Software. 22(4): 1-20.
Chessel, D. and Dufour, A.B. and Thioulouse, J. (2004). The ade4 package - I - One-table methods. R News. 4: 5-10.
Dray, S. and Dufour, A.B. and Chessel, D. (2007). The ade4 package-II: Two-table and K-table methods. R News. 7(2): 47-52.
And the trilinear plot of Allen as reported by Zhu:
Zhu, M. (2008). How to draw a trilinear Plot. Statistical Computing & Graphics, 19(1), June, 2008.
In this version of the package tri-plot methods are used for the triABC2XY and
triXY2ABC transforms and a modification triangle.param methods is used
to calculate suitable values for alim, blim and clim.
As elsewhere, the use of lattice is also gratefully acknowledged:
lattice: Sarkar, Deepayan (2008). Lattice: Multivariate Data Visualization with R. Springer, New York. ISBN 978-0-387-75968-5
In loa: For in-panel axis/scale generation, see loaPlot, panelPal,
localScalesHandler and panel.localScale.
In other packages: xyplot in lattice.
## Example 1 ## Basic triangle plot usage trianglePlot(cadmium~copper+lead+zinc|lime, data=lat.lon.meuse) # Notes: # Formula structure z ~ a0 + b0 + c0 |cond, where a0, b0 and # c0 are the three axes of the triangle plot # Data (and groups) assignment like in standard lattice plots. # By default z is linked to col and cex. # Unless overridden by user inputs or group or zcase setting. # Plot handling is similar to loaPlot # (So, see ?loaPlot and ?panelPal for further details.) # Formula variations: # basic triangle plot without z values assignment # trianglePlot(~a0+b0+c0, ...) # ... with z values set # trianglePlot(z~a0+b0+c0, ...) # ... with grouping # trianglePlot(z~a0+b0+c0, groups=grps, ...) ## Example 2 ## Basic frame (axes, grid, tick, annotation) management trianglePlot(~1+1+1, type="n", grid.alpha = 0.2, ticks.alpha = 0.2) ## grid and tick alpha reset # notes: # Here, grid and ticks arguments are used to remove or modify these # elements of the plot frame individually. # Setting can be management in list form like in normal lattice or # in a loa shorthand where e.g. the argument grid.a0.lty = 1 is equivalent # to grid = list(a0 = list(lty = 1)) # (So, quicker if you are only changing a small number of elements.)## Example 1 ## Basic triangle plot usage trianglePlot(cadmium~copper+lead+zinc|lime, data=lat.lon.meuse) # Notes: # Formula structure z ~ a0 + b0 + c0 |cond, where a0, b0 and # c0 are the three axes of the triangle plot # Data (and groups) assignment like in standard lattice plots. # By default z is linked to col and cex. # Unless overridden by user inputs or group or zcase setting. # Plot handling is similar to loaPlot # (So, see ?loaPlot and ?panelPal for further details.) # Formula variations: # basic triangle plot without z values assignment # trianglePlot(~a0+b0+c0, ...) # ... with z values set # trianglePlot(z~a0+b0+c0, ...) # ... with grouping # trianglePlot(z~a0+b0+c0, groups=grps, ...) ## Example 2 ## Basic frame (axes, grid, tick, annotation) management trianglePlot(~1+1+1, type="n", grid.alpha = 0.2, ticks.alpha = 0.2) ## grid and tick alpha reset # notes: # Here, grid and ticks arguments are used to remove or modify these # elements of the plot frame individually. # Setting can be management in list form like in normal lattice or # in a loa shorthand where e.g. the argument grid.a0.lty = 1 is equivalent # to grid = list(a0 = list(lty = 1)) # (So, quicker if you are only changing a small number of elements.)
Stack plot functions for Lattice.
stackPlot(x, data = NULL, ...) #standard panels panel.stackPlot(..., process=TRUE, plot=TRUE, loa.settings = FALSE) #data handlers ##currently not exportedstackPlot(x, data = NULL, ...) #standard panels panel.stackPlot(..., process=TRUE, plot=TRUE, loa.settings = FALSE) #data handlers ##currently not exported
x |
For |
data |
For |
... |
Additional arguments. |
loa.settings, plot, process
|
stackPlot generates a stack plot using the lattice framework.
panel.stackPlot handles the appearance of triangle plot
outputs.
stackPlot returns trellis objects, much like
conventional lattice plot functions.
panel.stackPlot is intended for use
within a trianglePlot function call.
Development:
This is an in-development plot, and 'best handling' strategies have not been decided for several elements. So, future versions of these functions may differ significantly from the current version.
In particular:
stackPlot:
The stackPlot argument x may include conditioning in the form
y ~ x | cond. However, exact handling is has not been defined, so may
subject to change.
To generate the stacks, stackPlot resets y values by applying
y - min(y) to each layer and then stacks them. It also generates a
second element y0 of asociated baselines. This is then used in
the form x = c(x, rev(x)), y = c(y, rev(y0)) with
panel.polygon to generate the stack layers.
panel.stackPlot:
Code currently in revision. Please handle with care.
Karl Ropkins
These function makes extensive use of code developed by others.
As elsewhere, the use of lattice is also gratefully acknowledged:
lattice: Sarkar, Deepayan (2008). Lattice: Multivariate Data Visualization with R. Springer, New York. ISBN 978-0-387-75968-5
In other packages: xyplot and
panel.polygon in lattice.
## Example 1 ## Basic stack plot usage ## Not run: stackPlot(lead~dist.m, data=lat.lon.meuse) stackPlot(cadmium+copper+lead+zinc~dist.m, data=lat.lon.meuse) ## End(Not run) stackPlot(cadmium*40+copper*5+lead+zinc~dist.m, data=lat.lon.meuse)## Example 1 ## Basic stack plot usage ## Not run: stackPlot(lead~dist.m, data=lat.lon.meuse) stackPlot(cadmium+copper+lead+zinc~dist.m, data=lat.lon.meuse) ## End(Not run) stackPlot(cadmium*40+copper*5+lead+zinc~dist.m, data=lat.lon.meuse)
Bar plot variation using for Student Project.
loaBarPlot(x, y=NULL, groups=NULL, cond=NULL, data=NULL, ..., drop.nas=TRUE, stat=NULL)loaBarPlot(x, y=NULL, groups=NULL, cond=NULL, data=NULL, ..., drop.nas=TRUE, stat=NULL)
x |
Either the x case for the bar plot or a plot formula. If the x case, typically a vector of factor or grouping terms, used to assign x positions in bar plot. If a plot formula, a plot description in the format y~x|cond, where x is a factor or grouping term and y and cond are optional. |
y |
(Optional) The y case for the bar plot, typically a vector of numeric
terms, used with |
groups, cond
|
(Optional) The group case for the bar plot, typically a vector of factor or grouping terms. |
data |
(Optional) if supplied, the assumed source
of the plot elements, |
... |
Additional arguments, passed on to |
drop.nas |
Option to drop |
stat |
If supplied, the function used to summarise |
loaBarPlot summarises supplied plot data and generates a bar plot using the
lattice framework.
loaBarPlot returns trellis objects, much like
conventional lattice plot functions.
Development:
This is an in-development plot, and 'best handling' strategies have not been decided for several elements. So, future versions of these functions may differ significantly from the current version.
In particular:
loaBarPlot:
This is for student project, may not be staying.
Code currently in revision. Please handle with care.
Karl Ropkins
These function makes extensive use of code developed by others.
As elsewhere, the use of lattice is also gratefully acknowledged:
lattice: Sarkar, Deepayan (2008). Lattice: Multivariate Data Visualization with R. Springer, New York. ISBN 978-0-387-75968-5
In loa: listUpdate and colHandler.
In other packages: barchart in lattice.
## Example 1 ## Basic bar plot usage loaBarPlot(Species, Sepal.Width, data=iris, stat=mean) #or equivalent using formula ## Not run: loaBarPlot(Sepal.Width~Species, data=iris, stat=mean) ## End(Not run)## Example 1 ## Basic bar plot usage loaBarPlot(Species, Sepal.Width, data=iris, stat=mean) #or equivalent using formula ## Not run: loaBarPlot(Sepal.Width~Species, data=iris, stat=mean) ## End(Not run)
Specialist panel functions for use with lattice and loa plots.
panel.loaLevelPlot(x = NULL, y = NULL, z = NULL, ..., loa.settings = FALSE) panel.surfaceSmooth(x = NULL, y = NULL, z = NULL, breaks = 200, x.breaks = breaks, y.breaks = breaks, smooth.fun = NULL, too.far=0, ..., plot = TRUE, process = TRUE, loa.settings = FALSE) panel.kernelDensity(x, y, z = NULL, ..., n = 20, local.wt = TRUE, kernel.fun = NULL, too.far = 0, panel.range = TRUE, process = TRUE, plot = TRUE, loa.settings = FALSE) panel.binPlot(x = NULL, y = NULL, z = NULL, breaks=20, x.breaks = breaks, y.breaks = breaks, x1=NULL, x2=NULL, y1=NULL, y2=NULL, statistic = NULL, pad.grid = FALSE, ..., plot = TRUE, process = TRUE, loa.settings = FALSE)panel.loaLevelPlot(x = NULL, y = NULL, z = NULL, ..., loa.settings = FALSE) panel.surfaceSmooth(x = NULL, y = NULL, z = NULL, breaks = 200, x.breaks = breaks, y.breaks = breaks, smooth.fun = NULL, too.far=0, ..., plot = TRUE, process = TRUE, loa.settings = FALSE) panel.kernelDensity(x, y, z = NULL, ..., n = 20, local.wt = TRUE, kernel.fun = NULL, too.far = 0, panel.range = TRUE, process = TRUE, plot = TRUE, loa.settings = FALSE) panel.binPlot(x = NULL, y = NULL, z = NULL, breaks=20, x.breaks = breaks, y.breaks = breaks, x1=NULL, x2=NULL, y1=NULL, y2=NULL, statistic = NULL, pad.grid = FALSE, ..., plot = TRUE, process = TRUE, loa.settings = FALSE)
x, y, z
|
|
... |
Additional arguments, typically passed on. See below. |
loa.settings, process, plot
|
For |
breaks, x.breaks, y.breaks
|
(For |
smooth.fun |
(For |
too.far |
(For |
n |
(For |
local.wt |
(For |
kernel.fun |
(For |
panel.range |
(For |
x1, x2, y1, y2
|
(For |
statistic |
(For |
pad.grid |
For |
panel.loaLevelPlot is intended for plot data structured
for use with the lattice function levelplot,
e.g. regularised (x,y,z) or a matrix:
loaPlot(..., panel = panel.loaLevelPlot)levelplot(...) #in lattice
Other specialist panel... functions can be used with the
lattice function xyplot:
xyplot(..., panel = panel.kernelDensity)xyplot(..., n = 50, panel = panel.kernelDensity)xyplot(..., panel = function(...) panel.kernelDensity(..., n = 50))#etc
However, they are intended for use with loa plots that incorporate
panelPal. This combination provides a mechanism for the
routine preprocessing of panel data, the association of specialist keys,
and the routine alignment of panel and legend settings in cases where
values are reworked within the panel function call:
loaPlot(..., panel = panel.kernelDensity)#etc
panel.surfaceSmooth and other similar panel... functions
generate smoothed surfaces using supplied (x,y,z) data and pass
this to panel.loaLevelPlot to plot.
By default, panel.surfaceSmooth uses stats function
loess to generate a surface. Alternative smooths
can be set using the smooth.fun argument, and the surface
range can to controlled using the too.far argument.
panel.kernelDensity generates kernel density estimations
based on the supplied x and y data ranges. Because it is
density plot, it counts the number of z values. So, z values
are ignored. It is intended to be used in the form:
loaPlot(~x*y, ..., panel = panel.kernelDensity)
So, if any z information is supplied, users are warned that it has
been ignored, e.g:
loaPlot(z~x*y, ..., panel = panel.kernelDensity)#warning generated
panel.binPlot bins supplied z data according to x and
y values and associated break points (set by break arguments),
and then calculates the required statistic for each of these. By default,
this is mean, but alternative functions can be set using the
statistic argument. It is intended to be used in form:
loaPlot(z~x*y, ..., panel = panel.binPlot)
If no z values are supplied, as in:
loaPlot(~x*y, ..., panel = panel.binPlot)
... panel.binPlot resets statistic to length
(again with a warning) and gives a count of the number of elements in
each bin.
As with other panel... functions in this package, output are suitable
for use as the panel argument in loa (and sometimes
lattice) plot calls.
All these panel... functions treat col and col.regions,
etc, as discrete arguments. Typically, col links to lines (contour
lines for surfaces, bin borders for binned data) and col.regions
links any generates surface region.
panel.surfaceSmooth passes additional arguments on to the
smooth.fun to estimate surface smooths and the lattice
function panel.levelplot to generate the associated plot.
If no kernel.fun is supplied in the panel call, the
stats function loess is used to estimate surface smooth.
The too.far argument is based on same in vis.gam
function in the mgcv package.
panel.kernelDensity passes additional arguments on to the
kernel.fun to estimate kerenel density and the lattice
function panel.contourplot to generate the associated plot.
If no kernel.fun is supplied in the panel call, the
MASS function kde2d is used to estimate kernel density.
panel.binPlot passes limited arguments on to lrect.
panel.kernelDensity and panel.binPlot are currently under
review.
Karl Ropkins
These function makes extensive use of code developed by others.
lattice: Sarkar, Deepayan (2008) Lattice: Multivariate Data Visualization with R. Springer, New York. ISBN 978-0-387-75968-5
(for panel.kernelDensity) MASS package:
Venables, W. N. and Ripley, B. D. (2002) Modern Applied Statistics
with S. Fourth edition. Springer.
(for panel.surfaceSmooth) mgcv package and too.far argument:
Wood, S.N. (2004) Stable and efficient multiple smoothing parameter
estimation for generalized additive models.Journal of the American
Statistical Association. 99:673-686.
Also http://www.maths.bath.ac.uk/~sw283/
In loa: panelPal
In lattice: xyplot,
levelplot,
panel.contourplot, lrect
## Example 1 ## for data already set up for levelplot loaPlot(volcano, panel=panel.loaLevelPlot) ## Example 2 ## Surface smooth loaPlot(copper~longitude*latitude, data= lat.lon.meuse, panel=panel.surfaceSmooth, grid=TRUE, too.far=0.1, col.regions=3:2)## Example 1 ## for data already set up for levelplot loaPlot(volcano, panel=panel.loaLevelPlot) ## Example 2 ## Surface smooth loaPlot(copper~longitude*latitude, data= lat.lon.meuse, panel=panel.surfaceSmooth, grid=TRUE, too.far=0.1, col.regions=3:2)
In development specialist panel functions for polar plotting
panel.polarPlot(x = NULL, y = NULL, r = NULL, theta = NULL, ..., data.panel = panel.loaPlot, loa.settings = FALSE, plot = TRUE, process = TRUE) #grid, axes and axes labelling panel.polarFrame(..., grid = TRUE, axes = TRUE, labels = TRUE, panel.scales = NULL, grid.panel = panel.polarGrid, axes.panel = panel.polarAxes, labels.panel = panel.polarLabels) panel.polarAxes(axes.theta = NULL, axes.r = NULL, thetalim = NULL, rlim = NULL, ..., axes = NULL, panel.scales = NULL) panel.polarGrid(grid.theta = NULL, grid.r = NULL, thetalim = NULL, rlim = NULL, ..., grid = NULL, panel.scales = NULL) panel.polarLabels(labels.theta = NULL, labels.r = NULL, thetalim = NULL, rlim = NULL, ..., labels = NULL, panel.scales = NULL)panel.polarPlot(x = NULL, y = NULL, r = NULL, theta = NULL, ..., data.panel = panel.loaPlot, loa.settings = FALSE, plot = TRUE, process = TRUE) #grid, axes and axes labelling panel.polarFrame(..., grid = TRUE, axes = TRUE, labels = TRUE, panel.scales = NULL, grid.panel = panel.polarGrid, axes.panel = panel.polarAxes, labels.panel = panel.polarLabels) panel.polarAxes(axes.theta = NULL, axes.r = NULL, thetalim = NULL, rlim = NULL, ..., axes = NULL, panel.scales = NULL) panel.polarGrid(grid.theta = NULL, grid.r = NULL, thetalim = NULL, rlim = NULL, ..., grid = NULL, panel.scales = NULL) panel.polarLabels(labels.theta = NULL, labels.r = NULL, thetalim = NULL, rlim = NULL, ..., labels = NULL, panel.scales = NULL)
x, y
|
The |
r, theta
|
The equivalent polar coordinates of the plot
points. If these are not supplied, |
... |
Additional arguments, typically passed on. For
|
data.panel |
The panel to use to handle data once polar
coordinates have been checked for or generated. For
|
loa.settings, plot, process
|
|
grid, axes, labels
|
plot management options for the grid, axis
and axis label elements of the plot. These can be logicals ( |
panel.scales |
|
grid.panel, axes.panel, labels.panel
|
Used by the |
axes.theta, axes.r, thetalim, rlim
|
For |
grid.theta, grid.r
|
Like |
labels.theta, labels.r
|
Like |
The panel.polar... series of the functions are intended for
use with loaPlot.
panel.polarPlot generates a 'bubble plot' style output on
polar coordinates. It generates axes and annonation within each
plot panel using the other panel functions.
panel.polarGrids, panel.polarAxes and panel.polarLabels
generate plot grid, axes and axes labelling elements of the plot.
panel.polarFrame provides a wrapper for these plot elements.
Users can fine-tune axes, grids and labels by supplying additional arguments in plot calls, or replace these elements with purpose written functions to more completely modify plot appearance.
The panel.polar... functions are intended to be used as the
panel argument in loa plot calls. So, e.g.:
a <- 1:360loaPlot(a~a*a, panel=panel.polarPlot)
They can also be used with relatively simple lattice plots.
However, some features of loa plots managed by
panelPal, e.g. default plot appearance management,
automatic grouping and panel and key alignment will not be available.
panel.polarPlot is in-development. Function arguments may change.
Karl Ropkins
These function makes extensive use of code developed by others.
lattice: Sarkar, Deepayan (2008) Lattice: Multivariate Data Visualization with R. Springer, New York. ISBN 978-0-387-75968-5
In loa: loaPlot; and panelPal.
In other packages: xyplot in lattice.
In development specialist panel functions for generating zcase glyph structures.
panel.zcasePiePlot(..., loa.settings = FALSE) panel.zcasePieSegmentPlot(..., zcase.rescale=TRUE, loa.settings = FALSE)panel.zcasePiePlot(..., loa.settings = FALSE) panel.zcasePieSegmentPlot(..., zcase.rescale=TRUE, loa.settings = FALSE)
... |
Additional arguments, typically setting the color and properties of the plotted glyphs. See below. |
zcase.rescale |
Should the glyph element be rescaled? See below. |
loa.settings |
loa options, to be handled by |
All these panel... functions generate glyphs using z inputs and plot these
at the associated (x, y) location. So, for example a called which used one of the panels
and the plot formula:
z1 + z2+ z3 + z4 ~ x * y
... would plot a series of glyphs, each containing four elements that would be scaled
according to z1, z2, z3 and z4, and each at the associated
(x, y) location. This means there will be one discrete glyph for each row of data supplied
to the plot call.
panel.zcasePiePlot generates a series of x/y referenced pie graphs. By default, pie
dimensions are assigned as: Pie size (radius) proportional to sum of z cases and scaled using
cexHandler (z1 + z2 + z3 + z4 for the above formula); Number of Pie segments
equal to number of z cases (so, 4 for the above formula); Pie segment width (phi) proportional to
the individual zcase (so, z1 / (z1 + z2 + z3 + z4) * 360 for first pie segment for the above
formula).
panel.zcasePieSegmentPlot is a variation on the conventional pie plot where segement radius
rather than segment width is varying by zcase.
These panel... functions are intended to be used as the
panel argument in loa plot calls. So, e.g.:
a <- 1:10b <- 10:1loaPlot(a+b~a*a, panel=panel.zcasePiePlot)loaPlot(a+b~a*a, panel=panel.zcasePieSegmentPlot)
Functions in development. Arguments may change, e.g.:
panel.zcasePieSegmentPlot includes the argument zcase.rescale.
This normalises data within each zcase before generating the pie segments. This
might not stay.
Karl Ropkins
These function makes extensive use of code developed by others.
lattice: Sarkar, Deepayan (2008) Lattice: Multivariate Data Visualization with R. Springer, New York. ISBN 978-0-387-75968-5
In other packages: xyplot in lattice.
## Example 1 ## plotting georeferenced pie plots # Using a subsample of lat.lon.meuse temp <- lat.lon.meuse[sample(1:155, 15),] ## Not run: # plot Cu/Pb/Zn pie plots at sampling locations loaPlot(copper+lead+zinc~longitude*latitude, panel=panel.zcasePiePlot, data=temp) # then rescale smaller pie segments on the fly ## End(Not run) loaPlot(copper*10+lead*4+zinc~longitude*latitude, panel=panel.zcasePiePlot, data=temp)## Example 1 ## plotting georeferenced pie plots # Using a subsample of lat.lon.meuse temp <- lat.lon.meuse[sample(1:155, 15),] ## Not run: # plot Cu/Pb/Zn pie plots at sampling locations loaPlot(copper+lead+zinc~longitude*latitude, panel=panel.zcasePiePlot, data=temp) # then rescale smaller pie segments on the fly ## End(Not run) loaPlot(copper*10+lead*4+zinc~longitude*latitude, panel=panel.zcasePiePlot, data=temp)
In development specialist panel functions
panel.compareZcases(x=x, y=y, z=NULL, ..., loa.settings = FALSE)panel.compareZcases(x=x, y=y, z=NULL, ..., loa.settings = FALSE)
x, y, z
|
Standard plot data series, typically vectors. |
... |
Additional arguments, typically passed on. |
loa.settings |
loa options, to be handled by |
The panel.compareZcases generates a simple plot which
compares z and y elements.
These panel... functions are intended to be used as the
panel argument in loa plot calls. So, e.g.:
x <- 1:10y <- 1:10z <- y + rnorm(10)loaPlot(z~x*y, panel=panel.compareZcases, col.regions="Reds")
These are ad hoc panel... functions. Not sure of their
life expectancy...
Karl Ropkins
These function makes extensive use of code developed by others.
lattice: Sarkar, Deepayan (2008) Lattice: Multivariate Data Visualization with R. Springer, New York. ISBN 978-0-387-75968-5
In other packages: xyplot in lattice.
Example data intended for use with examples in loa.
lat.lon.meuse roadmap.meuselat.lon.meuse roadmap.meuse
lat.lon.meuse is a modified form of the meuse data set
taken from the sp package. Here, coordinate (x,y) elements
have been transformed to latitudes and longtiudes and the object
class has been converted from SpatialPointsDataFrame to
data.frame.
roadmap.meuse is a previously downloaded map intended for
use with off-line plot examples using lat.lon.meuse.
lat.lon.meuse was generated using method based on mzn object
production in https://github.com/etes/Geoprocessing/blob/master/heatmap.R.
library(sp); library(gstat); library(rgdal) data(meuse) coordinates(meuse) =~ x + y proj4string(meuse) = CRS("+init=epsg:28992") meuse1 = spTransform(meuse, CRS("+init=epsg:4326")) meuse2=as.data.frame(meuse1) mzn=meuse2[,c(14,13,4)] names(mzn)<-c("Latitude","Longitude","zinc")
roadmap.meuse was generated using:
RgoogleMapsPlot(zinc~latitude*longitude, data=lat.lon.meuse, size=c(450,500), maptype="roadmap") roadmap.meuse <- loaMapArg()
For meuse:
M G J Rikken and R P G Van Rijn, 1993. Soil pollution with heavy metals - an inquiry into spatial variation, cost of mapping and the risk evaluation of copper, cadmium, lead and zinc in the floodplains of the Meuse west of Stein, the Netherlands. Doctoraalveldwerkverslag, Dept. of Physical Geography, Utrecht University
P.A. Burrough, R.A. McDonnell, 1998. Principles of Geographical Information Systems. Oxford University Press.
Stichting voor Bodemkartering (Stiboka), 1970. Bodemkaart van Nederland : Blad 59 Peer, Blad 60 West en 60 Oost Sittard: schaal 1 : 50 000. Wageningen, Stiboka.
For sp:
Roger S. Bivand, Edzer J. Pebesma, Virgilio Gomez-Rubio, 2008. Applied spatial data analysis with R. Springer, NY. http://www.asdar-book.org/
Pebesma, E.J., R.S. Bivand, 2005. Classes and methods for spatial data in R. R News 5 (2), http://cran.r-project.org/doc/Rnews/.
## data structure of lat.lon.meuse head(lat.lon.meuse) ## Use a subsample of lat.lon.meuse temp <- lat.lon.meuse[sample(1:155, 15),] ## various loaPlot examples ## using lat.lon.meuse loaPlot(~longitude*latitude, data=temp) loaPlot(cadmium~longitude*latitude, data=temp) loaPlot(cadmium~longitude*latitude, col.regions=c("green", "red"), data=temp) loaPlot(cadmium*50+copper*10+lead*2+zinc~longitude*latitude, panel.zcases = TRUE, col.regions=c("green", "red"), key.z.main="Concentrations", data=temp) ## (off line) GoogleMap example ## using lat.lon.meuse and roadmap.meuse GoogleMap(zinc~latitude*longitude, data=temp, map=roadmap.meuse, col.regions=c("grey", "darkred")) # Note 1: # With loaPlot and GoogleMap, note latitude, longitude axes # assignments: # loaPlot plots z ~ x * y | cond. # GoogleMap plots z ~ lat * lon | cond (z ~ y * x | cond) # Note 2: # Here, the map argument is supplied so example works off-line. # If not supplied and R is on-line, GoogleMap will (try to) get map # from the Google API. Look at: ## Not run: GoogleMap(zinc~latitude*longitude, data=lat.lon.meuse, col.regions=c("grey", "darkred")) ## End(Not run) # (The map will appear slightly different, because non-default # size and maptype settings were used to make roadmap.meuse. See above.)## data structure of lat.lon.meuse head(lat.lon.meuse) ## Use a subsample of lat.lon.meuse temp <- lat.lon.meuse[sample(1:155, 15),] ## various loaPlot examples ## using lat.lon.meuse loaPlot(~longitude*latitude, data=temp) loaPlot(cadmium~longitude*latitude, data=temp) loaPlot(cadmium~longitude*latitude, col.regions=c("green", "red"), data=temp) loaPlot(cadmium*50+copper*10+lead*2+zinc~longitude*latitude, panel.zcases = TRUE, col.regions=c("green", "red"), key.z.main="Concentrations", data=temp) ## (off line) GoogleMap example ## using lat.lon.meuse and roadmap.meuse GoogleMap(zinc~latitude*longitude, data=temp, map=roadmap.meuse, col.regions=c("grey", "darkred")) # Note 1: # With loaPlot and GoogleMap, note latitude, longitude axes # assignments: # loaPlot plots z ~ x * y | cond. # GoogleMap plots z ~ lat * lon | cond (z ~ y * x | cond) # Note 2: # Here, the map argument is supplied so example works off-line. # If not supplied and R is on-line, GoogleMap will (try to) get map # from the Google API. Look at: ## Not run: GoogleMap(zinc~latitude*longitude, data=lat.lon.meuse, col.regions=c("grey", "darkred")) ## End(Not run) # (The map will appear slightly different, because non-default # size and maptype settings were used to make roadmap.meuse. See above.)
lattice plot management using the loa function panelPal
panelPal(ans, panel = NULL, preprocess = FALSE, reset.xylims = FALSE, legend = NULL, by.group = NULL, by.zcase = NULL, ...) panelPal.old(x, y, subscripts, at, col.regions, ..., panel = panel.xyplot, ignore = NULL, group.fun = NULL) loaHandler(panel = NULL,...)panelPal(ans, panel = NULL, preprocess = FALSE, reset.xylims = FALSE, legend = NULL, by.group = NULL, by.zcase = NULL, ...) panelPal.old(x, y, subscripts, at, col.regions, ..., panel = panel.xyplot, ignore = NULL, group.fun = NULL) loaHandler(panel = NULL,...)
ans |
For |
panel |
A panel function, e.g. |
preprocess, reset.xylims, legend, by.group, by.zcase
|
For
|
... |
Additional arguments, typically passed on. |
x, y, subscripts, at, col.regions
|
For |
ignore |
Any additional arguments that |
group.fun |
Fine control of the standard |
panelPal provides a range of generic plot management features.
Firstly, it allows plot as well as panel defaults to be managed by the
panel... function. This allows the panel developer to control
plot-level components of the plot output, e.g. which key to use with the
plot and what default settings to apply to it. See example 1 below.
Secondly, it uses a generalised extension of the subscripting methods described by Deepayan Sarkar in Chapter 5 of Lattice (see sections on scatterplots and extensions) to automatically handle plot argument subscripting, demonstrated in example 2 below.
Thirdly, it applies an extension of the method used by the hexbin lattice panel to pass hex cell counts (calculated in panels) to the plot key and standardise the assignment of associated parameters within all panels to provide more general panel-to-panel and panel-to-scale. The method is briefly discussed in Chapter 14 of Sarkar.
This method has also been extended by isolating processing and plot components
of the panel... function operation allowing results of any calculations
made in-panel to be retained rather than lost when plot is generated.
Fourly, group... and zcase... arguments can used to manage plot
group and zcase based plot outputs.
Some panelPal are implemented if specially structured (or loa-friendly)
panel... functions are supplied. These are illustrated in the final
example below.
loaHandler is a workhorse that assesses information in 'loa' friendly
panel... functions. As well as checking this, loaHandler also
checks the supplied panel for any default plot settings. This allows users to
manage the appearance of a plot from the panel or automatically associated
color keys.
Both panelPal and panelPal.old are intended to be used with
trellis plot outputs.
panelPal should be employed retrospectively. So, for example:
p1 <- xyplot(...)panelPanel(p1, ...)
The previous version, currently retained as panelPal.old, was employed
developed as a panel... function wrapper and intended to be employed
within the plot call. So, for example:
xyplot(..., panel = function(...) panelPal(..., panel=panel))
Because it is run within the plot call, and therefore within each panel called, it does not provide features that require panel-to-plot, panel-to-key or panel-to-panel communication.
loaHandler returns either a logical (FALSE if not loa 'friendly';
TRUE if loa 'friendly') or a list of default arguments to be used when
plotting.
The by.group and by.zcase arguments of panelPal and
the group.fun argument of panelPal.old are all currently
under review. Please do not use these.
Karl Ropkins
These function makes extensive use of code developed by others.
lattice:
Sarkar, Deepayan (2008) Lattice: Multivariate Data
Visualization with R. Springer, New York. ISBN
978-0-387-75968-5
hexbin:
Dan Carr, ported by Nicholas Lewin-Koh and Martin Maechler (2013).
hexbin: Hexagonal Binning Routines. R package version 1.26.2.
http://CRAN.R-project.org/package=hexbin
panelPal.old and panelPal both apply an extension
of the subscripting methods described by Deepayan Sarkar in Chapter
5 of Lattice (see sections on scatterplots and extensions) to
automatically handle plot argument subscripting.
panelPal applies an extension of the method used by
hex bin lattice panel to comunicate hex cell counts (calculated
in panels) panel-to-panel and panel-to-scale. The method is
briefly discussed in Chapter 14 of Sarkar.
## the combination of panelPal and specially ## structured panel... functions provides ## several additional plot features: require(lattice) ## example 1 ## plot management from the panel... functions. # loaHandler can used to see if a panel is loa-friendly loaHandler(panel.xyplot) #FALSE loaHandler(panel.loaPlot) #panel defaults # note that these include a list called # default.settings. These are settings that are # automatically added to the plot call. # Here this assigns a specialist key to that # panel. However, the same mechanism can also # be used to turn off plot elements like the # standard lattice axes, when using in panel # alternatives # first some silly data a <- rnorm(1000) b <- rnorm(1000) # now compare: # default plot # note bubble plot style key loaPlot(a~a*b) # bin plot # with classic color key loaPlot(a~a*b, panel = panel.binPlot) ## example 2 ## automatic subscripting with loa # Other arguments are not automatically # aligned with the main plots. # For example, consider the data: a <- 1:10 ref <- rep(1:2, each=5) # and associated lattice xyplot output: xyplot(a~a|ref, col=ref, pch=19) # Here, the 'col' argument does not # automatically track plot conditioning. # With lattice plots you need to assign # arguments you want to track in this # manner using subscripts, as discussed # in Lattice Chapter 5. # Now compare a similar loaPlot: loaPlot(~a*a|ref, col=ref, pch=19) # Here, panelPal automatically handles # such subscripting. It extends this # assumption to all supplied arguments. # For example, try ## Not run: loaPlot(~a*a|ref, col=ref, pch=ref) loaPlot(~a*a|ref, col=ref, pch=1:10) ## End(Not run)## the combination of panelPal and specially ## structured panel... functions provides ## several additional plot features: require(lattice) ## example 1 ## plot management from the panel... functions. # loaHandler can used to see if a panel is loa-friendly loaHandler(panel.xyplot) #FALSE loaHandler(panel.loaPlot) #panel defaults # note that these include a list called # default.settings. These are settings that are # automatically added to the plot call. # Here this assigns a specialist key to that # panel. However, the same mechanism can also # be used to turn off plot elements like the # standard lattice axes, when using in panel # alternatives # first some silly data a <- rnorm(1000) b <- rnorm(1000) # now compare: # default plot # note bubble plot style key loaPlot(a~a*b) # bin plot # with classic color key loaPlot(a~a*b, panel = panel.binPlot) ## example 2 ## automatic subscripting with loa # Other arguments are not automatically # aligned with the main plots. # For example, consider the data: a <- 1:10 ref <- rep(1:2, each=5) # and associated lattice xyplot output: xyplot(a~a|ref, col=ref, pch=19) # Here, the 'col' argument does not # automatically track plot conditioning. # With lattice plots you need to assign # arguments you want to track in this # manner using subscripts, as discussed # in Lattice Chapter 5. # Now compare a similar loaPlot: loaPlot(~a*a|ref, col=ref, pch=19) # Here, panelPal automatically handles # such subscripting. It extends this # assumption to all supplied arguments. # For example, try ## Not run: loaPlot(~a*a|ref, col=ref, pch=ref) loaPlot(~a*a|ref, col=ref, pch=1:10) ## End(Not run)
Function(s) for handling (front end) plot arguments like x and strip that manage the plot structure.
formulaHandler(x, data = NULL, groups = NULL, ..., expand.plot.args = TRUE, formula.type = "z~x*y|cond", panel.zcases = FALSE, coord.conversion = NULL, lattice.like = NULL, check.xy.dimensions = TRUE, check.coord.dimensions = TRUE, get.zcase.dimensions = TRUE, output = "extra.args") matrixHandler(x, data = NULL, row.values=NULL, column.values=NULL, ...) stripHandler(..., striplab=NULL) getZcaseDimensions(...)formulaHandler(x, data = NULL, groups = NULL, ..., expand.plot.args = TRUE, formula.type = "z~x*y|cond", panel.zcases = FALSE, coord.conversion = NULL, lattice.like = NULL, check.xy.dimensions = TRUE, check.coord.dimensions = TRUE, get.zcase.dimensions = TRUE, output = "extra.args") matrixHandler(x, data = NULL, row.values=NULL, column.values=NULL, ...) stripHandler(..., striplab=NULL) getZcaseDimensions(...)
x |
(For |
data |
If supplied, the assumed source of the elements of formula
|
groups |
If supplied, the grouping argument to be used with
|
... |
Additional arguments are passed on to related functions. |
expand.plot.args |
For |
formula.type |
For |
panel.zcases |
For |
coord.conversion |
For |
lattice.like |
For |
check.xy.dimensions, check.coord.dimensions
|
For |
get.zcase.dimensions |
For |
output |
For |
row.values, column.values
|
For |
striplab |
For |
formulaHandler manages the formula component or x element of
of loa plot functions.
For example, for loaPlot it assumes the general formula structure
z ~ x * y | cond, and applies it in a similar fashion to the
lattice function levelplot.
Within the formula part of the plot call x and y are the
horizontal and vertical axes, z is any additional information to be
used in point, symbol, surface or glyph generation, and cond any
additional conditioning to be applied. (The coordinates, x and
y, are required elements; z and cond are typically
optional.)
matrixHandler converts a matrix supplied as x element of a
loa plot to a formula and associated data. If row.values and
column.values are supplied, these are used as (x,y)
values for the supplied matrix.
stripHandler manages the strip component of loa plot functions.
getZcaseDimensions tracks the dimensions of multiple z
formulaHandler returns a list, containing the plot elements
defined in the supplied formula.
matrixHandler returns a list containing all supplied arguments,
subject to the following modifications: matrix x converted to formula
(z~x*y); data, replaced with supplied matrix content;
xlim and ylim, added is not suppied.
stripHandler returns a list containing all supplied arguments,
subject to the following modifications: strip, Updated or generated
if not supplied; striplab, added to strip via the strip
argument var.name, if this is undeclared in call.
getZcaseDimensions returns a list containing all the supplied
arguments, plus two additions arguments (if supplied in the call):
zcase.zlim and z.rowsum.lim. zcase.zlim is a
list of lim values, one for each zcase.
z.rowsum.lim is the range of 'by-row' sums of zcases.
These are calculated using any zcase information supplied in
the call.
These function are in development and may be subject to changes.
The current version of formulaHandler includes code from the
stats function get_all_vars. It operates in a similar
fashion to the previous version but checks zcase dimensions.
The previous version of formulaHandler was a wrapper for
the lattice function latticeParseFormula. This
version of formulaHandler was updated to simplify multiple
z argument handling.
The latest version of formulaHandler includes more flexible
formula.type handling. For example, it can now handle formulas
that have more than two coordinates. As a result the
check.xy.dimensions argument was replaced with a
check.coord.dimensions argument. The previous argument
will however remain in the function formals and function as before
until all related code has been updated.
The latest version of formulaHandler uses getZcaseDimensions
to calculate the dimensions of z if it is multi-part, e.g.
z1 + z2 + etc ~ x * y rather than z ~ x * y.
The current version of matrixHandler is based on code from
levelplot.matrix in lattice. If used with x and
data arguments it will overwrite data with the matrix
content.
Karl Ropkins
This function makes extensive use of code developed by others.
lattice: Sarkar, Deepayan (2008) Lattice: Multivariate Data Visualization with R. Springer, New York. ISBN 978-0-387-75968-5
In other packages: levelplot in lattice.
In development functions for lims and scales handling with lattice plots.
limsHandler(x=NULL, y=NULL, z=NULL, ..., lim.borders = 0.05) localScalesHandler(scales = NULL, ..., allowed.scales =c("x", "y"), disallowed.scales = NULL, remove.box = FALSE) panel.localScale(x.loc, y.loc, lim, ..., panel.scale = NULL, label.before = TRUE, x.offset = NULL, y.offset = NULL, axis = TRUE, ticks = TRUE, annotation = TRUE) yscale.component.log10(...) xscale.component.log10(...)limsHandler(x=NULL, y=NULL, z=NULL, ..., lim.borders = 0.05) localScalesHandler(scales = NULL, ..., allowed.scales =c("x", "y"), disallowed.scales = NULL, remove.box = FALSE) panel.localScale(x.loc, y.loc, lim, ..., panel.scale = NULL, label.before = TRUE, x.offset = NULL, y.offset = NULL, axis = TRUE, ticks = TRUE, annotation = TRUE) yscale.component.log10(...) xscale.component.log10(...)
x, y, z
|
|
lim.borders |
numeric vector, giving the relative border to
extend |
scales, panel.scale
|
A list of elements like the |
... |
Additional arguments. |
allowed.scales |
A character vector containing the names of the axes to be generated for as part of a local axis. |
disallowed.scales |
A character vector containing the names
of any axes that are not required. Note: If found, these are
removed from |
remove.box |
A logical, default |
x.loc, y.loc, lim
|
two member vectors setting the |
label.before, x.offset, y.offset
|
Scale annotation overrides.
|
axis, ticks, annotation
|
If supplied, fine controls for the
appearance of the axis line, axis tick marks and axis annotation
on the generated scale. These can be vectors, in which they are
assumed to be color assignments, or lists of common plot parameters,
such as |
limsHander generates xlim, ylim and/or zlim
ranges for axes or color scales for use in a range of plots.
localScalesHandler provides a relatively crude mechanism
for the removal of conventional lattice plot axes and
the generation of alternative axes using a panel... function
like panel.localScale.
limsHandler returns a list containing ...lim ranges for
any of the elements x, y and/or z supplied to it.
localScalesHandler returns a list containing the
elements: scales, panel.scales and possibly
par.settings. scales turns off the standard
axes annotation. panel.scales is a list of named elements, one
per named axis, describing the axis layout. If
remove.box = TRUE, the additional argument par.settings
is also supplied.
All arguments should be passed on to the associated plot.
panel.scales or axis-specific elements in panel.scales
can then be evaluated by an associated panel... function run
from within the lattice plot call. This would typically
take the form:
panel.my.axis(panel.scale = panel.scale$axis, ...)
panel.localScale is a local axis/scale plotter. It can be used
in combination with localScalesHandler, and should called
once for each axis that is required, or it can be used 'stand alone'
panel to add a local scale to a lattice plot.
yscale.component.log10 and xscale.component.log10 are
simple axis transforms for use with log to the base 10 transformed
plot axes.
panel.localScale is currently in revision. Scale arrows are
currently not available.
Karl Ropkins
These function makes extensive use of code developed by others.
lattice: Sarkar, Deepayan (2008) Lattice: Multivariate Data Visualization with R. Springer, New York. ISBN 978-0-387-75968-5
In other packages: xyplot in lattice.
## See trianglePlot Example 2 for example application## See trianglePlot Example 2 for example application
Plot conditioning handling
condsPanelHandler(..., conds = NULL, panel = NULL, by.cond = NULL, process = TRUE, plot = TRUE) groupsPanelHandler(..., groups = NULL, panel = NULL, by.group = NULL, process = TRUE, plot = TRUE) zcasesPanelHandler(..., zcases = NULL, panel = NULL, by.zcase = NULL, process = TRUE, plot = TRUE) groupsAndZcasesPanelHandler(panel=NULL, ..., plot = TRUE, process = TRUE) groupsHandler(z = NULL, groups = NULL, ..., group.ids = NULL, handler = "zzz") zcasesHandler(z = NULL, zcases = NULL, ..., zcases.ids = NULL, handler = "zzz") groupsAndZcasesHandler(..., loa.settings = NULL) stepwiseZcasesGlyphHandler(zcases = NULL, ..., zcase.ids = NULL, panel.elements = NULL, loaGlyph = NULL)condsPanelHandler(..., conds = NULL, panel = NULL, by.cond = NULL, process = TRUE, plot = TRUE) groupsPanelHandler(..., groups = NULL, panel = NULL, by.group = NULL, process = TRUE, plot = TRUE) zcasesPanelHandler(..., zcases = NULL, panel = NULL, by.zcase = NULL, process = TRUE, plot = TRUE) groupsAndZcasesPanelHandler(panel=NULL, ..., plot = TRUE, process = TRUE) groupsHandler(z = NULL, groups = NULL, ..., group.ids = NULL, handler = "zzz") zcasesHandler(z = NULL, zcases = NULL, ..., zcases.ids = NULL, handler = "zzz") groupsAndZcasesHandler(..., loa.settings = NULL) stepwiseZcasesGlyphHandler(zcases = NULL, ..., zcase.ids = NULL, panel.elements = NULL, loaGlyph = NULL)
... |
Additional arguments. See Notes below. |
conds, panel, by.cond
|
For all supplied additional arguments,
|
plot, process, loa.settings
|
Passed to and handled by |
groups, by.group
|
As |
zcases, by.zcase
|
As |
z, handler
|
The |
group.ids, zcases.ids, zcase.ids
|
If given, vectors of the unique cases in
|
panel.elements |
If given, the names of all plot arguments that have been
vectorized by |
loaGlyph |
(For |
NOTE: These functions are currently in development and may be subject to changes.
condsPanelHandler is a general purpose function that can be used to routinely
manage plot conditioning within a panel... function call. It takes all undeclared
arguments are supplied to it, and subsets them by unique case in the supplied conds
argument. Then it modifies each of these based on the associated elements of by.cond
and processes and/or plots the results depending on process and plot settings.
groupsPanelHandler is similar but is intended for use with the plot call argument
groups.
zcasesPanelHandler is similar but is intended for use with arguments conditioned
within the z term of the plot formula. So, for example, for unique handling of z1
and z2 cases in the plot loaPlot(z1+z2~x*y).
groupsAndZcasesPanelHandler is a wrapper for groups and zcase that
allows users to simultaneously and uniquely handle both types of conditioning.
stepwiseZcasesGlyphHandler is a ...Handler function for generating gylph plots
based on multiple z inputs.
All ..PanelHandlers functions are intended for use with panelPal.
Using different combinations of these allows plot developers a high degree of
flexibility.
This function is in development and may be subject to changes.
Karl Ropkins
This function makes extensive use of code developed by others.
lattice: Sarkar, Deepayan (2008) Lattice: Multivariate Data Visualization with R. Springer, New York. ISBN 978-0-387-75968-5
For information on related functions in other packages, see
lattice: xyplot;
panel.xyplot; and
panel.levelplot.
Functions for use the routine handling of some common plot arguments.
cexHandler(z = NULL, cex = NULL, cex.range = NULL, expand.outputs = TRUE, ref = NULL, ..., zlim = NULL) colHandler(z = NULL, col = NULL, region = NULL, colorkey = FALSE, legend = NULL, pretty = FALSE, at = NULL, cuts = 20, col.regions = NULL, alpha.regions = NULL, expand.outputs = TRUE, ref = NULL, ..., zlim = NULL, output="col") colRegionsHandler(...) pchHandler(z = NULL, pch = NULL, pch.order = NULL, expand.outputs = TRUE, ref = NULL, ..., zlim = NULL) scalesHandler(...) zHandler(z = NULL, expand.outputs = TRUE, ref = NULL, ...)cexHandler(z = NULL, cex = NULL, cex.range = NULL, expand.outputs = TRUE, ref = NULL, ..., zlim = NULL) colHandler(z = NULL, col = NULL, region = NULL, colorkey = FALSE, legend = NULL, pretty = FALSE, at = NULL, cuts = 20, col.regions = NULL, alpha.regions = NULL, expand.outputs = TRUE, ref = NULL, ..., zlim = NULL, output="col") colRegionsHandler(...) pchHandler(z = NULL, pch = NULL, pch.order = NULL, expand.outputs = TRUE, ref = NULL, ..., zlim = NULL) scalesHandler(...) zHandler(z = NULL, expand.outputs = TRUE, ref = NULL, ...)
z |
If supplied, a vector of values intended to used as a scale when assigning a property. For For For For |
cex, col, pch
|
For associated handlers, the parameter value(s) to be managed (i.e.,
|
cex.range |
If supplied, the range for |
region, colorkey, legend, pretty, at, cuts, col.regions, alpha.regions
|
The
colorscale settings to be used when generating a colorkey. The most useful of
these are probably |
pch.order |
A vector of symbol ids (typically the numbers 1 to 24) to used
when plotting points if, e.g. using a scatter plot. By default, all points are
plotted using the first of these pch ids unless any conditioning (e.g. grouping or
zcase handling) is declared and linked to |
expand.outputs, ref
|
|
zlim |
The range over which the scale is to be applied if not |
output |
For |
... |
Additional arguments, often ignored. |
The ...Handler functions are argument handlers intended to
routinely handle some common activities associated with plotting
data.
cexHandler manages symbol sizes. It generates a (hopefully)
sensible cex scale for handling plot symbol size based on
a supplied input (z).
colHandler manages colors. It works like the colorkey in
levelplot in lattice, to generate a
colorscale based on a supplied input (z).
colRegionsHandler is a wrapper for colHandler that
can be used to with the col.regions argument.
scalesHandler is a crude method to avoid scales argument
list structures.
zHandler expands (by wrapping) or foreshortens vectors.
cexHandler returns a vector, which can be used as
the cex argument in many common plotting functions
(e.g. plot, xyplot).
colHandler depending on output setting returns
either the col vector or a list containing elements (z,
col, legend, at, col.regions and
alpha.regions), which can be used to create a col
series scaled by z and an associated colorkey
like that generated by levelplot for other
lattice functions (e.g. xyplot).
colRegionsHandler returns a vector of color values suitable
for use with the col.regions argument.
scalesHandler returns the supplied arguments modified as follows:
all scales... arguments are converted into a single list(...); all
scales.x... and scales.y... argument are converted into
list(x=list(...)) and list(y=list(...)), respectively. so e.g.
scales.x.rot=45 generates scales=list(x=list(rot=45)).
pchHandler returns a vector of pch values of an
appropriate length, depending on expand.outputs and ref
settings.
cexHandler recently revised. Default cex range now smaller, in line
with feedback.
scalesHandler might not be staying.
Karl Ropkins
These function makes extensive use of code developed by others.
lattice: Sarkar, Deepayan (2008) Lattice: Multivariate Data Visualization with R. Springer, New York. ISBN 978-0-387-75968-5
RColorBrewer: Erich Neuwirth <[email protected]> (2011). RColorBrewer: ColorBrewer palettes. R package version 1.0-5. http://CRAN.R-project.org/package=RColorBrewer
In other packages: See xyplot in lattice.
#some trivial data a <- 1:10 ## Example 1 ## Simple plot with cex handling myplot1 <- function(x, y, z = NULL, cex = NULL, cex.range = NULL, ...){ #set cex cex <- cexHandler(z, cex, cex.range) #plot (xyplot in lattice) lattice::xyplot(y~x, cex = cex,...) } myplot1(a, a, a) # compare ## Not run: myplot1(a, a) #like plot(x, y) myplot1(a, a, a*100) #as myplot1(a, a, a) #because cex scaled by range myplot1(a, b, c, cex.range = c(1,5)) #cex range reset myplot1(a, b, c, cex.range = c(10,50), cex = 1) #cex supersedes all else if supplied ## End(Not run) ## Example2 ## plot function using lists/listUpdates myplot2 <- function(x, y, z = NULL, ...){ #my default plot default.args <- list(x = y~x, z = z, pch = 20, cex = 4) #update with whatever user supplied plot.args <- listUpdate(default.args, list(...)) #col Management plot.args$col <- do.call(colHandler, plot.args) do.call(lattice::xyplot, plot.args) } #with colorkey based on z case myplot2(a, a, a) # compare ## Not run: myplot2(a, b, c, col.regions = "Blues") #col.regions recoloring myplot2(a, b, c, col = "red") ##but (again) col supersedes if supplied ## End(Not run) # Note: # See also example in ?listUpdate#some trivial data a <- 1:10 ## Example 1 ## Simple plot with cex handling myplot1 <- function(x, y, z = NULL, cex = NULL, cex.range = NULL, ...){ #set cex cex <- cexHandler(z, cex, cex.range) #plot (xyplot in lattice) lattice::xyplot(y~x, cex = cex,...) } myplot1(a, a, a) # compare ## Not run: myplot1(a, a) #like plot(x, y) myplot1(a, a, a*100) #as myplot1(a, a, a) #because cex scaled by range myplot1(a, b, c, cex.range = c(1,5)) #cex range reset myplot1(a, b, c, cex.range = c(10,50), cex = 1) #cex supersedes all else if supplied ## End(Not run) ## Example2 ## plot function using lists/listUpdates myplot2 <- function(x, y, z = NULL, ...){ #my default plot default.args <- list(x = y~x, z = z, pch = 20, cex = 4) #update with whatever user supplied plot.args <- listUpdate(default.args, list(...)) #col Management plot.args$col <- do.call(colHandler, plot.args) do.call(lattice::xyplot, plot.args) } #with colorkey based on z case myplot2(a, a, a) # compare ## Not run: myplot2(a, b, c, col.regions = "Blues") #col.regions recoloring myplot2(a, b, c, col = "red") ##but (again) col supersedes if supplied ## End(Not run) # Note: # See also example in ?listUpdate
Workhorse functions for routine use of keys in plots.
keyHandler(key = NULL, ..., output = "key") #keys draw.loaPlotZKey(key = NULL, draw = FALSE, vp = NULL, ...) draw.loaKey02(key = NULL, draw = FALSE, vp = NULL, ...) draw.loaColorKey(key = NULL, draw = FALSE, vp = NULL, ...) draw.loaColorRegionsKey(key = NULL, draw = FALSE, vp = NULL, ...) draw.zcasePlotKey(key = NULL, draw = FALSE, vp = NULL, ...) draw.ycasePlotKey(key = NULL, draw = FALSE, vp = NULL, ...) draw.groupPlotKey(key = NULL, draw = FALSE, vp = NULL, ...) draw.key.log10(key = NULL, draw = FALSE, vp = NULL, ...)keyHandler(key = NULL, ..., output = "key") #keys draw.loaPlotZKey(key = NULL, draw = FALSE, vp = NULL, ...) draw.loaKey02(key = NULL, draw = FALSE, vp = NULL, ...) draw.loaColorKey(key = NULL, draw = FALSE, vp = NULL, ...) draw.loaColorRegionsKey(key = NULL, draw = FALSE, vp = NULL, ...) draw.zcasePlotKey(key = NULL, draw = FALSE, vp = NULL, ...) draw.ycasePlotKey(key = NULL, draw = FALSE, vp = NULL, ...) draw.groupPlotKey(key = NULL, draw = FALSE, vp = NULL, ...) draw.key.log10(key = NULL, draw = FALSE, vp = NULL, ...)
key |
The key to be used. |
... |
Any additional arguments to be used to modify the
the |
output |
The format to return the function output in. This is
|
draw, vp
|
|
keyHandler is a general function that rotuine generates
defaults arguments for add a key to a plot.
draw...key functions are all specialist plots keys. They are
typically modifications of or variations on similar functions in
lattice, e.g. draw.key and draw.colorkey.
draw.loaPlotZKey is the default 'bubble plot' key used with
loaPlot.
draw.loaColorKey and draw.loaColorRegionsKey are variations
on the draw.colorkey function in lattice.
draw.zcasePlotKey, draw.ycasePlotKey and draw.groupPlotKey
are simple legends based on zcase, ycase and group
annotation.
draw.key.log10 is a simple legend for use with log to the base
10 transformed z scale.
keyHandler return a list of plot arguments to be used to generate
a key .
When run within plot calls, the draw...key functions associated
color keys. If they are used with loa plots and suitable
panel... functions, color scales are automatically aligned.
In Development: Function structures may change in future package updates.
Karl Ropkins
These functions make extensive use of code developed by others.
lattice: Sarkar, Deepayan (2008) Lattice: Multivariate Data Visualization with R. Springer, New York. ISBN 978-0-387-75968-5
In other packages: See xyplot in lattice.
In development panel functions for use with lattice
parHandler(scheme = NULL, ...) #related getArgs(source = TRUE, local.resets = TRUE, user.resets = TRUE, is.scales.lines = FALSE, elements = NULL, ..., defaults = list(), defaults.only = FALSE) getPlotArgs(defaults.as = "axis.line", source = TRUE, local.resets = TRUE, user.resets = TRUE, elements = NULL, ..., is.scales.lines = NULL, defaults.only = TRUE) isGood4LOA(arg)parHandler(scheme = NULL, ...) #related getArgs(source = TRUE, local.resets = TRUE, user.resets = TRUE, is.scales.lines = FALSE, elements = NULL, ..., defaults = list(), defaults.only = FALSE) getPlotArgs(defaults.as = "axis.line", source = TRUE, local.resets = TRUE, user.resets = TRUE, elements = NULL, ..., is.scales.lines = NULL, defaults.only = TRUE) isGood4LOA(arg)
scheme |
The color scheme to apply. This can be a list of parameters to apply
or a character vector for a pre-defined scheme. Current pre-defined schemes include
|
source, local.resets, user.resets
|
When recovering plot arguments
with |
is.scales.lines |
When recovering arguments with |
elements |
When recovering arguments with |
... |
Other arguments, often ignored. |
defaults, defaults.only, defaults.as
|
When recovering arguments with |
arg |
For |
getArgs returns a list of parameters/values based on
lattice, developer and user settings. If multiple
elements are identified as containing case-specific information,
the list will contain one list of plot parameters for each named
element.
getPlotArgs is a variation of getArgs
intended for use with panel... and l... type
lattice functions. It returns a list of plot parameters
for different plot components, e.g. symbols, lines, or text.
isGood4LOA is a simple workhorse that checks if a
supplied arg should be used by loa. (See value and
note below.)
parHandler manages the default appearance of plots.
getArgs and getPlotArgs return lists of located
parameters/values. For example, the call
getPlotArgs(default.as = "axis.line")
returns a list containing the lattice defaults for an axis
line (alpha, col, lty and lwd) These
can then be used in combination with appropriate x and
y values in llines, or panel.lines calls.
The arguments local.resets and user.resets can
be added into the call to provide developer and user overrides.
(See note below.)
isGood4LOA returns a logical (TRUE or FALSE),
depending on the type of a supplied argument. This returns
FALSE for NULL, for all FALSE logicals, and
any arg that has previously been tagged as 'not wanted'.
parHandler returns a list a list suitable for use as
par.settings with most lattice plots.
getPlotArgs is intended as a 'workhorse' for plot developers,
to recover lattice settings, impose their own preferences on
these, and in turn to provide users with similar options to quickly
override developer settings.
isGood4LOA only exists because I, perhaps wrongly,
equate arg = NULL with arg = FALSE when that
argument is a component of a plot defined in the plot formals.
For example, in trianglePlot I want
grids = NULL to turn off the plot grids much like
grids = FALSE, but got fed up always writing the same
everywhere. Does not mean it is right, particularly useful or
even clever...
The getPlotArgs/isGood4LOA combination is a first attempt
at providing plot developers with a simple tool to integrate plot argument
management by lattice, the plot developer and the plot user. It is intended
to be applied in the form shown in the Examples below.
Axis, tick, grid and annotation handling in trianglePlot is
intended to illustrate this type of application.
Karl Ropkins
These function makes extensive use of code developed by others.
lattice: Sarkar, Deepayan (2008) Lattice: Multivariate Data Visualization with R. Springer, New York. ISBN 978-0-387-75968-5
In other packages: See xyplot in lattice.
#getPlotArgs/isGood4LOA notes #in formals #my.plot <- function(..., user.reset = TRUE, ...) #in main code body #local.resets <- [what developer wants] #plot.arg <- getPlotArgs("[type]", source, local.reset, user.reset) #in panel call #(for panel off/on control) #if(isGood4LOA(plot.arg)) panel...(..., plot.arg,...) #in panel... function #for panel component off/on control) #if(isGood4LOA(plot.arg1)) panel...(..., plot.arg1,...) #if(isGood4LOA(plot.arg2)) l...(..., plot.arg2,...) #etc.#getPlotArgs/isGood4LOA notes #in formals #my.plot <- function(..., user.reset = TRUE, ...) #in main code body #local.resets <- [what developer wants] #plot.arg <- getPlotArgs("[type]", source, local.reset, user.reset) #in panel call #(for panel off/on control) #if(isGood4LOA(plot.arg)) panel...(..., plot.arg,...) #in panel... function #for panel component off/on control) #if(isGood4LOA(plot.arg1)) panel...(..., plot.arg1,...) #if(isGood4LOA(plot.arg2)) l...(..., plot.arg2,...) #etc.
Workhorse functions for routine list handling in loa and elsewhere.
listHandler(a, use = NULL, ignore = NULL, drop.dots=TRUE) listUpdate(a, b, use = NULL, ignore = NULL, use.a = use, use.b = use, ignore.a = ignore, ignore.b = ignore, drop.dots = TRUE) listExpand(a, ref = NULL, use = NULL, ignore = NULL, drop.dots = TRUE) listLoad(..., load = NULL)listHandler(a, use = NULL, ignore = NULL, drop.dots=TRUE) listUpdate(a, b, use = NULL, ignore = NULL, use.a = use, use.b = use, ignore.a = ignore, ignore.b = ignore, drop.dots = TRUE) listExpand(a, ref = NULL, use = NULL, ignore = NULL, drop.dots = TRUE) listLoad(..., load = NULL)
a |
A required list. The list to be modified. |
b |
For |
use, use.a, use.b
|
Vectors, all defaults |
ignore, ignore.a, ignore.b
|
Vectors, default |
ref |
For |
drop.dots |
Logical, default |
... |
For |
load |
For |
listHandler is a general function used by other list...
functions for routine list preprocessing.
listUpdate is a list handler intended for use when managing
user updates for default options (see examples).
listExpand is a list handler that expands vectors to
a given reference length, intended for use for data wrapping.
listLoad is a list generator. See Note below.
By default, all list... functions return results as lists.
listHandler, listUpdate and listExpand functions
all return a modified (or updated) version of supplied list a.
listLoad (in-development) returns modified (or updated) version
of additional arguments as a list. See Note below.
listLoad is an in-development workhorse function
that generates lists based on the supplied load argument.
It assumes each element of load is the name of an expected list
and searches the associated additional arguments for arguments to
populate it with using the rule '[load].[arg] is an element of list
[load]'. So, for example, for a call including the arguments
load = 'key' and key.fun = draw.colorkey, it would strip out
both arguments and return key = list(fun=draw.colorkey). Used in
functions, it allowed list-in-list args that can be commonplace
when modifying, for example, key elements of conventional lattice
plots to be simplified.
Karl Ropkins
These functions make extensive use of code developed by others.
lattice: Sarkar, Deepayan (2008) Lattice: Multivariate Data Visualization with R. Springer, New York. ISBN 978-0-387-75968-5
## Example 1 ## general # two lists list1 <- list(a = 1:10, b = FALSE) list2 <- list(b = TRUE, c = "new") # updating a with b # keeps unchanged list1 entry, a # updates changed list1 entry, b # adds new (list2) entry, c listUpdate(list1, list2) ## Example2 ## use in plot functions ## to simplify formals ## Not run: # some data a <- 1:10 b <- rnorm(10,5,2) #a bad plot function badplot <- function(x, ...){ #setting defaults in xyplot call itself xyplot(x = x, pch = 20, col = "red", panel = function(...){ panel.grid(-1, -1) panel.xyplot(...) panel.abline(0,1) }, ...) } badplot(a~b) #OK # compare with badplot(a~b, xlim = c(1,20)) #OK badplot(a~b, col = "blue") #not OK # because col hardcoded into badplot function # It is duplicated in call and '...' # so user cannot update col #a standard correction stdplot <- function(x, pch = 20, col = "red", ...){ #setting defaults in xyplot call itself xyplot(x = x, pch = 20, col = "red", panel = function(x=x, pch=pch, col=col, ...){ panel.grid(-1, -1) panel.xyplot(x=x, pch=pch, col=col, ...) panel.abline(0,1) }, ...) } stdplot(a~b) #OK stdplot(a~b, col = "blue", xlim=c(1:20)) #also OK # An alternative correction using lists and # listUpdate that removes the need for formal # definition of all modified plot arguments myplot <- function(x, ...){ #defaults I set for myplot form of xyplot mylist <- list(x = x, pch = 20, col = "red", panel = function(...){ panel.grid(-1, -1) panel.xyplot(...) panel.abline(0,1) }) #plot do.call(xyplot, listUpdate(mylist, list(...))) } myplot(a~b) #OK myplot(a~b, col = "blue", xlim = c(1,20)) #also OK ## End(Not run)## Example 1 ## general # two lists list1 <- list(a = 1:10, b = FALSE) list2 <- list(b = TRUE, c = "new") # updating a with b # keeps unchanged list1 entry, a # updates changed list1 entry, b # adds new (list2) entry, c listUpdate(list1, list2) ## Example2 ## use in plot functions ## to simplify formals ## Not run: # some data a <- 1:10 b <- rnorm(10,5,2) #a bad plot function badplot <- function(x, ...){ #setting defaults in xyplot call itself xyplot(x = x, pch = 20, col = "red", panel = function(...){ panel.grid(-1, -1) panel.xyplot(...) panel.abline(0,1) }, ...) } badplot(a~b) #OK # compare with badplot(a~b, xlim = c(1,20)) #OK badplot(a~b, col = "blue") #not OK # because col hardcoded into badplot function # It is duplicated in call and '...' # so user cannot update col #a standard correction stdplot <- function(x, pch = 20, col = "red", ...){ #setting defaults in xyplot call itself xyplot(x = x, pch = 20, col = "red", panel = function(x=x, pch=pch, col=col, ...){ panel.grid(-1, -1) panel.xyplot(x=x, pch=pch, col=col, ...) panel.abline(0,1) }, ...) } stdplot(a~b) #OK stdplot(a~b, col = "blue", xlim=c(1:20)) #also OK # An alternative correction using lists and # listUpdate that removes the need for formal # definition of all modified plot arguments myplot <- function(x, ...){ #defaults I set for myplot form of xyplot mylist <- list(x = x, pch = 20, col = "red", panel = function(...){ panel.grid(-1, -1) panel.xyplot(...) panel.abline(0,1) }) #plot do.call(xyplot, listUpdate(mylist, list(...))) } myplot(a~b) #OK myplot(a~b, col = "blue", xlim = c(1,20)) #also OK ## End(Not run)
Simple shapes.
loaPolygon(x, y, z=NULL, rot=NULL, ..., polygon = NULL, loa.scale = NULL) loaCircle(..., polygon = NULL, radius = 1) loaPieSegment(..., polygon = NULL, start = 0, angle=360, radius = 1, center=TRUE)loaPolygon(x, y, z=NULL, rot=NULL, ..., polygon = NULL, loa.scale = NULL) loaCircle(..., polygon = NULL, radius = 1) loaPieSegment(..., polygon = NULL, start = 0, angle=360, radius = 1, center=TRUE)
x, y
|
The |
z |
If supplied a |
rot |
The angle to rotate the polygon by before drawing it. |
... |
Any additional arguments, usually passed on. |
polygon |
A list with elements |
loa.scale |
A list of parameters that can be used to fine-tune the
|
radius |
The radius to used when drawing either circles or pie segments. |
start, angle
|
When drawing pie segments, |
center |
Should the segement begin and end at the center? |
loaPolygon is a general function for drawing polygons. It is
intended as an alternative to lpolygon, and other standard
loa... shapes are typically wrappers for this function.
loaCircle draws a circle with an origin at (x, y).
loaPieSegment draws a pie segment (or slice of cake) shape. It
is typically used as building block for pie plots and other similar
glyph structures.
All these functions generate simple shapes and are intended to be run
within panel... functions as building blocks for more complex
glyph type structures.
Karl Ropkins
These functions make extensive use of code developed by others.
lattice: Sarkar, Deepayan (2008) Lattice: Multivariate Data Visualization with R. Springer, New York. ISBN 978-0-387-75968-5
In other packages: See lrect, and similar, in lattice
Recovering information from existing lattice plots.
getXY(n = -1, ..., unit = "native", scale.correction = NULL) getLatLon(..., scale.correction = function(x) { temp <- MercatorXY2LatLon(x$x, x$y) as.list(as.data.frame(temp)) })getXY(n = -1, ..., unit = "native", scale.correction = NULL) getLatLon(..., scale.correction = function(x) { temp <- MercatorXY2LatLon(x$x, x$y) as.list(as.data.frame(temp)) })
n |
If positive, the maximum number of points to locate. If negative (default), unlimited. |
unit |
The unit to use when reporting located points, by
default |
scale.correction |
The correction to apply if the plot has locally scaled axes. See Note below. |
... |
Additional arguments, passed on to related functions. These may be subject to revision, but are currently:
|
getXY is an interactive function which returns
the locations of points on a plot selected using the
mouse (left click to select points; right click and
stop to end point collection; escape to abort without
returning any values).
It is a wrapper for the grid function
grid.locator that behaves more like
locator, the equivalent function intended
for use with plot outputs.
By default getXY selections are not automatically
marked. Adding common plot parameters to the function
call overrides this behaviour, e.g. to add red symbols
and lines.
ans <- getXY(col = "red", pch = 4, type = "b")
getXY also provides a mechanism to handle data plotted on
locally scaled axes. See Note below.
getLatLon is wrapper for getXY for use
with loaMapPlot and other similarly
georeferenced plots. See Note below.
getXY returns the x and y coordinates of
the selected points on a plot as a list containing two
components, x and y.
getLatLon returns the latitude and longitude
values of the selected points on a map as a list
containing two components, lat and lon.
getXY recovers the (x, y) coordinates of points selected
on a previously generated plot.
Some plots, use local scaling. For example, when plotting latitude, longitude data on a map a scale correction may be used to account for the curvature of the Earth. Similarly, if different data series are plotted on primary and secondary axes in a single plot, some or all data may be normalised. In such cases scaling may be local, i.e. what you actually plot may not be exactly what the annotation says it is.
Using getXY on such plots would recover the actual (x, y)
coordinates of the points selected.
However, corrections can be applied using scale.correction,
if it is supplied, to convert these to the same scale as the axes
annotation. The correction should be a function that can be
applied directly to a standard getXY output (a list of
x and y values) and rescale x and y to give
their 'corrected' values.
getLatLon provides an example of the mechanism, and is
for use with georeferenced plots that have been locally scaled
using LatLon2MercatorXY. getLatLon uses
MercatorXY2LatLon to rescale x and y
values and then as... functions to convert the outputs of
this step to a list format like that generated by locator,
grid.locator or getXY.
Karl Ropkins
This function makes extensive use of code developed by others.
lattice: Sarkar, Deepayan (2008) Lattice: Multivariate Data Visualization with R. Springer, New York. ISBN 978-0-387-75968-5
RgoogleMaps: Markus Loecher and Sense Networks (2011). RgoogleMaps: Overlays on Google map tiles in R. R package version 1.1.9.6. http://CRAN.R-project.org/package=RgoogleMaps
In other packages: See grid.locator;
trellis.focus and lpoints in lattice.
General functions for adding extra layers to existing plots.
add.XYZGhosts(object = NULL, ..., unit = "native", ghost.panel = panel.loaPlot) add.Y2Axis(object = NULL, ..., unit = "native", rescale = NULL) add.XYPolygon(object = NULL, x = NULL, y = NULL, data = NULL, ..., unit = "native", y2.scale=FALSE, first=FALSE) add.LonLatMap(object = NULL, ..., map = NULL, recolor.map=FALSE, show.axes = FALSE, unit = "native", first = TRUE)add.XYZGhosts(object = NULL, ..., unit = "native", ghost.panel = panel.loaPlot) add.Y2Axis(object = NULL, ..., unit = "native", rescale = NULL) add.XYPolygon(object = NULL, x = NULL, y = NULL, data = NULL, ..., unit = "native", y2.scale=FALSE, first=FALSE) add.LonLatMap(object = NULL, ..., map = NULL, recolor.map=FALSE, show.axes = FALSE, unit = "native", first = TRUE)
object |
The plot to add an extra plot layer or layers to. This defaults to last lattice plot produced if not set in call. |
... |
Additional arguments, passed on to related functions. |
unit |
The plot units, by default native. |
ghost.panel |
The plot panel to use when adding ghost points (lines, etc). |
rescale |
For |
x, y
|
x and y data-series to be used. |
data |
If supplied, the expected source of x and y data-series. |
y2.scale |
When building the Plot, use the second y axis if that exists, default FALSE. |
first |
When building the plot add the new plot layer first, default varies. |
map, recolor.map, show.axes
|
Options when adding a map layer, see loaMapPlot documentations. |
add.loaGhosts adds ghost points showing the
locations of all points in all panels.
add.Y2Axis adds a second y axis.
add.XYPolygon adds a supplied (x,y) polygon.
add.LonLatMap adds a map layer.
add... functions returns the supplied (or last)
lattice plot with an additional plot layer added.
add.XYZGhosts and add.LonLatMap are
in-development and may change significantly in
future package versions.
Karl Ropkins
These functions make extensive use of code developed by others.
lattice: Sarkar, Deepayan (2008) Lattice: Multivariate Data Visualization with R. Springer, New York. ISBN 978-0-387-75968-5
Grid (part of base R): R Core Team (2017). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.
Functions for adding XY fit model layers to existing plots.
#main functions add.loaPanel(lattice.plot = NULL, preprocess = NULL, panel = NULL, postprocess = NULL, ..., use = NULL, ignore = NULL) add.XYLMFit(lattice.plot = NULL, preprocess = add.XYFit_prep, panel = panel.loaXYFit, ...) add.XYLOESSFit(lattice.plot = NULL, preprocess = add.XYFit_prep, model.method = loaXYFit_loess, panel = panel.loaXYFit, ...) #others add.XYFit_prep(lattice.plot = NULL, model.method = loaXYFit_lm, ...) loaXYFit_lm(x, y, output.len = 25, formula.signif = 2, r2.digits = 3, group.id = NULL, ...) loaXYFit_loess(x, y, output.len = 25, r2.digits = 3, group.id = NULL, ...) panel.loaXYFit(...)#main functions add.loaPanel(lattice.plot = NULL, preprocess = NULL, panel = NULL, postprocess = NULL, ..., use = NULL, ignore = NULL) add.XYLMFit(lattice.plot = NULL, preprocess = add.XYFit_prep, panel = panel.loaXYFit, ...) add.XYLOESSFit(lattice.plot = NULL, preprocess = add.XYFit_prep, model.method = loaXYFit_loess, panel = panel.loaXYFit, ...) #others add.XYFit_prep(lattice.plot = NULL, model.method = loaXYFit_lm, ...) loaXYFit_lm(x, y, output.len = 25, formula.signif = 2, r2.digits = 3, group.id = NULL, ...) loaXYFit_loess(x, y, output.len = 25, r2.digits = 3, group.id = NULL, ...) panel.loaXYFit(...)
lattice.plot |
The plot to add an extra layer or layers to. This defaults to last lattice plot produced if not set in call. |
preprocess |
If set, a function to apply to
|
panel |
If set, a new |
postprocess |
If set, a function to apply to
|
... |
Additional arguments, passed on to daughter functions. |
model.method |
Function to use on XY data to generate fit reports. |
use, ignore
|
if set, the names of arguments supplied to the previous plot that should be used or ignored, respectively, by panel being added. |
x, y
|
XY data from plot, typically filtered by both panel and group. |
output.len |
Number of XY pairs to use when making fit line standard error bands. |
formula.signif, r2.digits
|
When number of significant numbers and digits to use when reporting the fit formula and r.squared, respectively. |
group.id |
When XY data is grouped, the group identity. |
add.loaPanel adds a plot panel to an existing
loaPlot output.
add.XYLMFit and add.XYLFit add linear
and loess model fit surfaces to exiting lattice plot.
Both functions are intended to be used in form:
[make plot, e.g. loaPlot(...) then] addXYLMFit(...)
loaXYFit_lm and loaXYFit_lm generate fit and
report information for linear and loess fit surfaces.
Other functions contain code structure common to all
addXYFit functions.
add.XYLMFit returns the supply (or last) lattice plot
with an added linear fit surface layer, generated using
lm().
add.XYLMFit returns the supply (or last) lattice plot
with an added linear fit surface layer, generated using
loess().
The elements of the XYFit layers are fit the fit line,
se the standard error bands, and report the
fit report panels. These track properties, e.g. col, etc,
of the plot they add to unless these terms are reset in the
addXYFit call. They can also be removed by setting to FALSE,
e.g. fit=FALSE, or updated individually using e.g.
fit.col=2 to change just the fit line color to red.
The report position within the plot panel can be set using report.position which uses a relative (x=0-1, y=0-1) scale to position the report.
These functions are in-development aand may change significantly in future pacakge versions.
Karl Ropkins
This function makes extensive use of code developed by others.
lattice: Sarkar, Deepayan (2008) Lattice: Multivariate Data Visualization with R. Springer, New York. ISBN 978-0-387-75968-5
lm() and loess() in stats (part of base R): R Core Team (2017). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.
# add lm fit a loaPlot add.XYLMFit(loaPlot(cadmium~copper*zinc, data=lat.lon.meuse)) ## Not run: loaPlot(cadmium~copper*zinc, data=lat.lon.meuse) add.XYLOESSFit(col="red") p <- loaPlot(cadmium~copper*zinc, data=lat.lon.meuse) add.XYLMFit(p, se.col="grey", report.position=c(0.95, 0.22)) ## End(Not run)# add lm fit a loaPlot add.XYLMFit(loaPlot(cadmium~copper*zinc, data=lat.lon.meuse)) ## Not run: loaPlot(cadmium~copper*zinc, data=lat.lon.meuse) add.XYLOESSFit(col="red") p <- loaPlot(cadmium~copper*zinc, data=lat.lon.meuse) add.XYLMFit(p, se.col="grey", report.position=c(0.95, 0.22)) ## End(Not run)