the rggobi package - university of...
TRANSCRIPT
The rggobi PackageApril 6, 2006
Version 2.1.1
Date 2006/3/23
Title Interface between R and GGobi
Author Duncan Temple Lang <[email protected]>, Debby Swayne<[email protected]>,
Depends R (>= 2.2.0)
SystemRequirements GGobi
Maintainer Hadley Wickham <[email protected]>
Description An interface from R to ggobi for programmatic dynamic, interactive visualization.
License BSD
LazyData true
URL http://www.ggobi.org/
Acknowledgements Di Cook, Nicholas Lewin-Koh, Xuejing Chen.
R topics documented:.GGobiCall . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2addVariable.ggobiDataset . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3"as.data.frame.ggobiDataset" . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4clean.ggobi . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5close.ggobi . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5"colorscheme<-" . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6colorscheme . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7connecting_edges . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7create_time_edges_for_unit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8create_time_edges . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8dataset . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9dim.ggobiDataset . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10dimnames.ggobiDataset . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10"edges<-" . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11edges . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12"excluded<-.ggobiDataset" . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
1
2 .GGobiCall
excluded.ggobiDataset . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13"[.ggobiDataset" . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14"$.ggobi" . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15ggobi_check_structs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15ggobi_count . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16ggobi_data_set_variables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17ggobi.find.file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17ggobi . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18ggobi_get . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19ggobi_longitudinal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20ggobi_set_data_file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20ggobi_set_data_frame . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21.ggobi.symbol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22ggobi_version . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22"glyph_colour<-.ggobiDataset" . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23glyph_colour.ggobiDataset . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24"glyph_size<-.ggobiDataset" . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24glyph_size.ggobiDataset . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25"glyph_type<-.ggobiDataset" . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26glyph_type.ggobiDataset . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26"ids<-.ggobiDataset" . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27ids.ggobiDataset . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28mapGlyphType . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28"names<-.ggobiDataset" . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29names.ggobi . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29names.ggobiDataset . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30ncol.ggobiDataset . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31nrow.ggobiDataset . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31print.ggobi . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32print.ggobiDataset . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32"rownames<-.ggobiDataset" . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33rownames.ggobiDataset . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34selected.ggobiDataset . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34"[<-.ggobi" . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35"[<-.ggobiDataset" . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36"shadowed<-.ggobiDataset" . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37shadowed.ggobiDataset . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37summary.ggobi . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38summary.ggobiDataset . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39valid_ggobi . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39variable_index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
Index 41
.GGobiCall Wrappers for calling C routines in the R-ggobi library.
Description
addVariable.ggobiDataset 3
Usage
.GGobiCall(.name, ..., .gobi = ggobi_get(), .test=TRUE)
Arguments
.name the simple name of the C routine to be resolved
... the arguments that to be passed to the .C or .Call
.gobi the ggobi instance identifier that is to be passed to the C routine as its last argu-ment
.test
Details
.GGobiC and .GGobiCall convert the name and then call their C invocation counterparts.
These functions map the simple name of a C routine into the package-specific version of that name.These allow use to hide the use a name mangling scheme of our choosing for the C level routines inthe shared library/DLL that provides the glue between R and ggobi. This is useful for avoiding nameconflicts with other C code in R or other packages. These are only of relevance to the developers ofthis package and those working with its C code.
The mapping of the name to its corresponding C routine name is done in conjunction with thepre-processor macro RS_GGOBI. These must be synchronized.
Value
the same result as the corresponding .C and .Call
Author(s)
Hadley Wickham <[email protected]>
See Also
.C, .Call
Examples
addVariable.ggobiDatasetAdd variable
Description
Add variable to a ggobiDataset
Usage
addVariable.ggobiDataset(x, vals, name, ...)
4 "as.data.frame.ggobiDataset"
Arguments
x ggobiDataset
vals values to add
name name of column to add
...
Details
Author(s)
Hadley Wickham <[email protected]>
Examples
"as.data.frame.ggobiDataset"Conversion methods
Description
Convert a ggobiDataset to a regular R data.frame or matrix
Usage
"as.data.frame.ggobiDataset"(x, ...)
Arguments
x ggobiDataset
...
Details
Author(s)
Hadley Wickham <[email protected]>
Examples
clean.ggobi 5
clean.ggobi Clean ggobi
Description
Clean arguments for ggobi
Usage
clean.ggobi(x)
Arguments
x vector
Details
Arguments for ggobi need to be in specific format. This function helps ensure that.
Author(s)
Hadley Wickham <[email protected]>
Examples
close.ggobi Close GGobi instance
Description
Terminates and discards a ggobi instance
Usage
close.ggobi(con, ...)
Arguments
con ggobi object to close
... ignored and for compatability generic function.
Details
This allows the caller to close a ggobi instance and discard the resources it uses. The function closesthe display windows and variable panel window associated with this ggobi instance. It also resetsthe default ggobi instance to be the last one created.
@arguments ggobi object to close @arguments ignored and for compatability generic function.@keyword dynamic
6 "colorscheme<-"
Author(s)
Hadley Wickham <[email protected]>
Examples
g1 <- ggobi(mtcars)g2 <- ggobi(mtcars)close(g2)close(ggobi_get())
"colorscheme<-" Set active colour scheme.
Description
Specify the active color scheme in a GGobi instance or the session options.
Usage
"colorscheme<-"(x, value)
Arguments
x GGobi object
value colour scheme to make active
Details
This makes a particular color scheme active within a GGobi instance.
Value
The name of the previously active color scheme.
Author(s)
Hadley Wickham <[email protected]>
Examples
g <- ggobi(mtcars)colorscheme(g) <- "Set1 8"colorscheme(g) <- 1
colorscheme 7
colorscheme Get active colour scheme
Description
Get name of the active colour scheme
Usage
colorscheme(x)
Arguments
x GGobi object
Details
Author(s)
Hadley Wickham <[email protected]>
Examples
g <- ggobi(mtcars)colorscheme(g)
connecting_edges Get connecting edges
Description
Get actual edges from application of edges dataset to target dataset.
Usage
connecting_edges(x, y)
Arguments
x target ggobi dataset
y ggobi dataset containing edges
Details
Author(s)
Hadley Wickham <[email protected]>
8 create_time_edges
Examples
create_time_edges_for_unitCreate time edges for a unit
Description
Create time edges for a unit
Usage
create_time_edges_for_unit(d, time)
Arguments
d data frame of observations from one unit
time time variable
Details
Author(s)
Hadley Wickham <[email protected]>
Examples
create_time_edges Create time edges
Description
Generate the connecting edges for longitudinal data
Usage
create_time_edges(data, time = "Time", obsUnit = "ID")
Arguments
data the dataset from which to compute the edge connections.
time name/index of time variable
obsUnit name/index of ID variable
dataset 9
Details
This function takes a data frame containing records with repeated measurements for a given ob-servational unit and generates the appropriate edge information so that consecutive time points canbe connected in a GGobi display. The output of this function can be given to setEdges to enableviewing these time series plots for individuals.
Currently this only works if the data are sorted by ID. This will be fixed in the future as it requiresre-ordering the records from the original dataset.
Value
A matrix with 2 columns and as many rows as in original data. Each row in this matrix gives adirected line segment connecting one point in time to the next point in time
Author(s)
Hadley Wickham <[email protected]>
Examples
dataset Get ggobi dataset.
Description
Get an object representing an internal ggobi dataset
Usage
dataset(which, .gobi = ggobi_get())
Arguments
which which dataset to retrieve, an integer for positional matching or a character tomatch by name
.gobi GGobi instance
Details
It is convenient to be able to refer to and operate on a ggobi dataset as if it were a regular R dataset.This function allows one to get an ggobiDataset object that represents a particular dataset.
Value
A list of ggobiDataset objects
Author(s)
Hadley Wickham <[email protected]>
10 dimnames.ggobiDataset
See Also
link{.ggobi}
Examples
dim.ggobiDataset ggobiDataset dimensions
Description
Retrieve the dimension of an ggobi dataset
Usage
dim.ggobiDataset(x)
Arguments
x dataset
Details
Author(s)
Hadley Wickham <[email protected]>
Examples
dimnames.ggobiDatasetGet dimension names
Description
Get row and column names for a ggobiDataget
Usage
dimnames.ggobiDataset(x)
Arguments
x ggobiDataget
"edges<-" 11
Details
Author(s)
Hadley Wickham <[email protected]>
Examples
"edges<-" Set edges
Description
Set edges for a dataset.
Usage
"edges<-"(x, value)
Arguments
x ggobiDataset
value matrix or data frame of edges. First column should be from edge, second columnto edge.
Details
To remove edges, set edges to NULL.
@arguments ggobiDataset @arguments matrix or data frame of edges. First column should be fromedge, second column to edge. @keyword manip
Author(s)
Hadley Wickham <[email protected]>
Examples
cc<-cor(t(swiss),use="p", method="s")ccd<-sqrt(2*(1-cc))a <- which(lower.tri(ccd), arr.ind=TRUE)src <- row.names(swiss)[a[,2]]dest <- row.names(swiss)[a[,1]]weight <- as.vector(as.dist(ccd))gg <- ggobi(swiss)gg$cor <- data.frame(weight)edges(gg$cor) <- cbind(src, dest)edges(gg$cor)edges(gg$cor) <- NULL
12 "excluded<-.ggobiDataset"
edges Get edges
Description
Get edges for a dataset
Usage
edges(x)
Arguments
x ggobi dataset
Details
Value
A matrix of edge pairs
Author(s)
Hadley Wickham <[email protected]>
Examples
"excluded<-.ggobiDataset"Set excluded status
Description
Set the exclusion status of points.
Usage
"excluded<-.ggobiDataset"(x, value)
Arguments
x ggobiDataset
value logical vector
Details
If a point is excluded it is not drawn.
excluded.ggobiDataset 13
Author(s)
Hadley Wickham <[email protected]>
See Also
excluded
Examples
excluded.ggobiDatasetGet excluded status
Description
Get the exclusion status of points.
Usage
excluded.ggobiDataset(x)
Arguments
x ggobiDataget
Details
If a point is excluded it is not drawn.
Author(s)
Hadley Wickham <[email protected]>
See Also
excluded<-
Examples
14 "[.ggobiDataset"
"[.ggobiDataset" Subsettting
Description
Subsetting for ggobi datasets
Usage
"[.ggobiDataset"(x, i, j, drop=FALSE)
Arguments
x arguments for generic data.frame subset function
i drop dimensions?
j
drop
Details
This functions allow one to treat a ggobi dataset as if it were a local data.frame. One can extractand assign elements within the dataset.
This method works by retrieving the entire dataset into R, and then subsetting with R.
Value
desired subset from data.frame
Author(s)
Hadley Wickham <[email protected]>
Examples
g <- ggobi(mtcars)x <- g$mtcarsx[1:5, 1:5]x[[1]]x$cyl
"$.ggobi" 15
"$.ggobi" Get ggobi data.
Description
Conveniently retrieve ggobi dataset.
Usage
"$.ggobi"(x, i)
Arguments
x GGobi object
i name of dataset to retrive
Details
It is convenient to be able to refer to and operate on a ggobi dataset as if it were a regular R dataset.This function allows one to get an ggobiDataset object that represents a particular dataset.
Author(s)
Hadley Wickham <[email protected]>
Examples
g <- ggobi(ChickWeight)g["cars"] <- mtcarsg[1:2]g["ChickWeight"]g["cars"]g$cars
ggobi_check_structsCheck structs
Description
Validates GGobi and Rggobi views of internal data structures
Usage
ggobi_check_structs()
Arguments
16 ggobi_count
Details
This function is called when the Rggobi library is loaded and it verifies that the sizes of the differentinternal data structures for GGobi are the same for both the GGobi shared library/DLL and theRggobi package. This is important as the two shared libraries are compiled separately and mayhave different compilation flags, etc. that make them incompatible. This function simply comparesthe sizes of the two views of the structures and raises a warning if they do not agree.
Essentially, you should never notice this function. A warning implies that you need to re-installRggobi against the version of GGobi you are using.
@value TRUE if the sizes in the two libraries are the same, otherwise a named logical vectorindicating which structures are different
Value
TRUE if the sizes in the two libraries are the same, otherwise a named logical vector indicatingwhich structures are different
Author(s)
Hadley Wickham <[email protected]>
Examples
ggobi_count Get number of GGobis
Description
Retrieves the number of ggobi instances within this session
Usage
ggobi_count()
Arguments
Details
One or more ggobi instances can be created within an R session so that one can simultaneously lookat different datasets or have different views of the same dataset. This function returns the numberof ggobis in existence.
The different ggobi instances are maintained as C level structures. This function accesses a variablethat stores how many are in existence when the function is invoked.
Author(s)
Hadley Wickham <[email protected]>
ggobi_data_set_variables 17
Examples
ggobi_count()
ggobi_data_set_variablesSet variable values
Description
Set the variable values for a column in a ggobiDataset
Usage
ggobi_data_set_variables(x, values, var, update = TRUE)
Arguments
x ggobiDataset
values values of new variable
var variable name
update update?
Details
Author(s)
Hadley Wickham <[email protected]>
Examples
ggobi.find.file Find GGobi file.
Description
Finds a file stored somewhere in the ggobi installation.
Usage
ggobi.find.file(..., check = F)
Arguments
... bits of the path to join together
check
18 ggobi
Details
Author(s)
Hadley Wickham <[email protected]>
Examples
ggobi.find.file("data","tips.xml")
ggobi New ggobi
Description
Creates a new ggobi instance
Usage
ggobi(data, args=character(0), mode=character(0), name = deparse(sys.call()[[2]]), ...)
Arguments
data the name of a file containing the data, or a data frame or matrix containing thevalues
args a character vector of command-line arguments
mode data format GGobi should expect to read the data from, if reading from a file.
name the name to use in GGobi for the dataset, if one is specified
...
Details
Create a new instance of GGobi with or without new data. Use function whenever you want tocreate a new GGobi indepdent of the others—they will not share linked plots. If you want to addanother dataset to an existing ggobi, please see [<-.ggobi
There are currently three basic types of functions that you can use with rggobi:
• Data getting and setting: see [.ggobi, and [.ggobiDataset
• "Automatic" brushing: see glyph_colour, glyph_size, glyph_type, shadowed,excluded, and the associated setter functions.
• Edge modifcation: see edges, edges<-, ggobi_longitudinal
You will generally spend most of your time working with ggobDatasets, you retrieve using$.ggobiDataset, [.ggobiDataset, or [[.ggobiDataset. Most of the time these willoperate like normal R datasets while pointing to the data in GGobi so that all changes are kept insync. If you need to force a ggobiDaataset to be an R data.frame use as.data.frame.
ggobi_get 19
Value
A ggobi object
Author(s)
Hadley Wickham <[email protected]>
Examples
ggobi(ggobi.find.file("data", "flea.csv"))ggobi(ggobi.find.file("data", "flea.xml"))ggobi(mtcars)mtcarsg <- ggobi_get()$mtcarsglyph_colour(mtcarsg)glyph_colour(mtcarsg) <- ifelse(mtcarsg$cyl < 4, 1, 2)glyph_size(mtcarsg) <- mtcarsg$cyl
ggobi_get Get GGobi
Description
Returns a ggobi reference
Usage
ggobi_get(id = ggobi_count(), drop=TRUE)
Arguments
id numeric vector indicating which ggobi instances to retrieve. Use default if nonespecified
drop
Details
This allows one to get a list of all the ggobi instances currently in existence in the R session. Also,one can fetch particular instances.
@arguments numeric vector indicating which ggobi instances to retrieve. Use default if none spec-ified @returns list of ggobi instances @keyword dynamic
Author(s)
Hadley Wickham <[email protected]>
Examples
ggobi(mtcars)ggobi(Nile)ggobi_get(1)ggobi_get(1:2)
20 ggobi_set_data_file
ggobi_longitudinal Create longitudinal dataset.
Description
Instantiate new ggobi with a longitudinal data set.
Usage
ggobi_longitudinal(data, time = "Time", obsUnit = "ID")
Arguments
data data frame
time time variable
obsUnit id variable
Details
@arguments data frame @arguments time variable @arguments id variable @keyword dynamic
Author(s)
Hadley Wickham <[email protected]>
Examples
data(Oxboys, package="nlme")ggobi_longitudinal(Oxboys, "Occasion", "Subject")
ggobi_set_data_fileSet data file.
Description
Open data file and add to ggobi datasets.
Usage
ggobi_set_data_file(file, mode = "unknown", add = TRUE, .gobi = ggobi_get())
Arguments
file path to file
mode mode of file
add add?
.gobi ggobi instance
ggobi_set_data_frame 21
Details
Author(s)
Hadley Wickham <[email protected]>
Examples
ggobi_set_data_frameSet data frame.
Description
Add data.frame to ggobi instance.
Usage
ggobi_set_data_frame(data, name = deparse(sys.call()[[2]]), description = paste("R data frame", name), id = rownames(data), .gobi = ggobi_get())
Arguments
data data frame to add
name data set name (appears on tabs in ggobi)
description description of data frame
id rownames
.gobi ggobi instance
Details
Author(s)
Hadley Wickham <[email protected]>
Examples
22 ggobi_version
.ggobi.symbol Ggobi symbol
Description
Usage
.ggobi.symbol(name)
Arguments
name
Details
Used entirely within R to map the given name to the name of the corresponding C routine.
A simple way of generating the prefix for a symbol used in this package/library so that we can hideit from other packages and avoid conflicts.
Value
the name of the C routine corresponding to its argument
Author(s)
Hadley Wickham <[email protected]>
Examples
ggobi_version Get version
Description
GGobi version information
Usage
ggobi_version()
Arguments
"glyph_colour<-.ggobiDataset" 23
Details
Return an object that describes the version of the ggobi library being used. This allows code toexecute conditionally on certain version numbers, etc.
@value the release date of the ggobi library @value a vector of 3 integers containing the major, mi-nor and patch-level numbers. @value a string version of the major, minor and patch-level numbers,@keyword dynamic
Valuethe release date of the ggobi library
a vector of 3 integers containing the major, minor and patch-level numbers.
a string version of the major, minor and patch-level numbers,
Author(s)
Hadley Wickham <[email protected]>
Examples
ggobi_version()
"glyph_colour<-.ggobiDataset"Set glyph colour
Description
Set glyph colour
Usage
"glyph_colour<-.ggobiDataset"(x, value)
Arguments
x ggobiDataset
value vector of new colours
Details
Author(s)
Hadley Wickham <[email protected]>
See Also
glyph_colour
24 "glyph_size<-.ggobiDataset"
Examples
glyph_colour.ggobiDatasetGet glyph colour
Description
Get glyph colour
Usage
glyph_colour.ggobiDataset(x)
Arguments
x ggobiDataset
Details
Author(s)
Hadley Wickham <[email protected]>
See Also
glyph_colour<-
Examples
"glyph_size<-.ggobiDataset"Set glyph size
Description
Set glyph size
Usage
"glyph_size<-.ggobiDataset"(x, value)
Arguments
x ggobiDataset
value vector of new sizes
glyph_size.ggobiDataset 25
Details
Author(s)
Hadley Wickham <[email protected]>
See Also
glyph_size
Examples
glyph_size.ggobiDatasetGet glyph size
Description
Get glyph size
Usage
glyph_size.ggobiDataset(x, value)
Arguments
x ggobiDataset
value
Details
Author(s)
Hadley Wickham <[email protected]>
See Also
glyph_size<-
Examples
26 glyph_type.ggobiDataset
"glyph_type<-.ggobiDataset"Set glyph type
Description
Set glyph type
Usage
"glyph_type<-.ggobiDataset"(x, value)
Arguments
x ggobiDataset
value vector of new types
Details
Author(s)
Hadley Wickham <[email protected]>
See Also
glyph_type
Examples
glyph_type.ggobiDatasetGet glyph type.
Description
Get glyph type.
Usage
glyph_type.ggobiDataset(x)
Arguments
x ggobiDataset
"ids<-.ggobiDataset" 27
Details
Author(s)
Hadley Wickham <[email protected]>
See Also
glyph_type<-
Examples
"ids<-.ggobiDataset"Set row ids
Description
Set row ids from a ggobiDataset
Usage
"ids<-.ggobiDataset"(x, value)
Arguments
x ggobiDataset
value new values
Details
Author(s)
Hadley Wickham <[email protected]>
See Also
ids
Examples
28 mapGlyphType
ids.ggobiDataset Row ids
Description
Retrive row ids from a ggobiDataset
Usage
ids.ggobiDataset(x)
Arguments
x ggobiDataset
Details
Author(s)
Hadley Wickham <[email protected]>
See Also
ids<-
Examples
mapGlyphType Map glyph type.
Description
Map glyph character code to number
Usage
mapGlyphType(types)
Arguments
types vector of glyph character codes
Details
"names<-.ggobiDataset" 29
Author(s)
Hadley Wickham <[email protected]>
Examples
"names<-.ggobiDataset"Set column names
Description
Set column names for a ggobiDataset
Usage
"names<-.ggobiDataset"(x, value)
Arguments
x ggobiDataset
value new names
Details
Author(s)
Hadley Wickham <[email protected]>
Examples
names.ggobi GGobi names
Description
Get dataset names
Usage
names.ggobi(x)
Arguments
x
30 names.ggobiDataset
Details
Author(s)
Hadley Wickham <[email protected]>
Examples
g <- ggobi(mtcars)names(g)
names.ggobiDataset ggobiDataset column names
Description
Get column names for a ggobiDataset
Usage
names.ggobiDataset(x, ...)
Arguments
x dataset
...
Details
Author(s)
Hadley Wickham <[email protected]>
Examples
ncol.ggobiDataset 31
ncol.ggobiDataset ggobiDataset columns
Description
Retrieve the number of columns in an ggobi dataset
Usage
ncol.ggobiDataset(d)
Arguments
d dataset
Details
Author(s)
Hadley Wickham <[email protected]>
Examples
nrow.ggobiDataset ggobiDataset rows
Description
Retrieve the number of row in an ggobi dataset
Usage
nrow.ggobiDataset(d)
Arguments
d dataset
Details
Author(s)
Hadley Wickham <[email protected]>
Examples
32 print.ggobiDataset
print.ggobi Print ggobi
Description
Prints summary of ggobi object by instance
Usage
print.ggobi(x, ...)
Arguments
x ggobi object
...
Details
Author(s)
Hadley Wickham <[email protected]>
See Also
summary.ggobi
Examples
print.ggobiDataset Print ggobiDataset
Description
Print ggobiDataset
Usage
print.ggobiDataset(x, ...)
Arguments
x GGobi dataset to retrieve
...
"rownames<-.ggobiDataset" 33
Details
By default printing a ggobiDataset acts like printing an R data.frame - ie. show all the data
Author(s)
Hadley Wickham <[email protected]>
Examples
"rownames<-.ggobiDataset"Set row names
Description
Set row names for a ggobiDataset
Usage
"rownames<-.ggobiDataset"(x, value)
Arguments
x ggobiDataset
value new names
Details
Author(s)
Hadley Wickham <[email protected]>
Examples
34 selected.ggobiDataset
rownames.ggobiDatasetGet row names
Description
Get row names for a ggobiDataget
Usage
rownames.ggobiDataset(x)
Arguments
x ggobiDataget
new names
Details
Author(s)
Hadley Wickham <[email protected]>
Examples
selected.ggobiDatasetGet selection status
Description
Returns logical vector indicating if each point is under the brush
Usage
selected.ggobiDataset(x)
Arguments
x ggobiDataset
logical vector
"[<-.ggobi" 35
Details
Author(s)
Hadley Wickham <[email protected]>
Examples
"[<-.ggobi" [<-.ggobi
Description
Add data to ggobi instance.
Usage
"[<-.ggobi"(x, i, value)
Arguments
x ggobi instance
i name of data frame
value data.frame, or string to path of file to load
Details
This function allows you to add (and eventually) replace ggobi to a ggobi instance.
Author(s)
Hadley Wickham <[email protected]>
Examples
g <- ggobi()g["a"] <- mtcarsg$b <- mtcars
36 "[<-.ggobiDataset"
"[<-.ggobiDataset" Assignments for ggobi datasets
Description
Usage
"[<-.ggobiDataset"(x, i, j, value)
Arguments
x row indices
i column indices
j new values
value
Details
This functions allow one to treat a ggobi dataset as if it were a local data.frame. One can extractand assign elements within the dataset.
This method works by retrieving the entire dataset into R, subsetting that copy, and then returningany changes.
@argument ggobi dataset @arguments row indices @arguments column indices @arguments newvalues @keyword manip @keyword internal
Author(s)
Hadley Wickham <[email protected]>
Examples
g <- ggobi(mtcars)x <- g["mtcars"]x[1:5, 1:5]x[1:5, 1] <- 1:5x[1:5, 1:5]
"shadowed<-.ggobiDataset" 37
"shadowed<-.ggobiDataset"Set shadowed status
Description
Set the exclusion status of points.
Usage
"shadowed<-.ggobiDataset"(x, value)
Arguments
x ggobiDataset
value logical vector
Details
If a point is shadowed it is drawn in a dark gray colour.
Author(s)
Hadley Wickham <[email protected]>
See Also
shadowed
Examples
shadowed.ggobiDatasetGet shadowed status
Description
Get the exclusion status of points.
Usage
shadowed.ggobiDataset(x)
Arguments
x ggobiDataget
38 summary.ggobi
Details
If a point is shadowed it is drawn in a dark gray colour.
Author(s)
Hadley Wickham <[email protected]>
See Also
shadowed<-
Examples
summary.ggobi GGobi summary
Description
Get a description of the global state of the GGobi session.
Usage
summary.ggobi(object, ...)
Arguments
object ggobi object
...
Details
Author(s)
Hadley Wickham <[email protected]>
Examples
g <- ggobi(mtcars)summary(g)
summary.ggobiDataset 39
summary.ggobiDatasetSummarise ggobiDataset.
Description
Summarise a ggobiDataset with dimensions, mode and variable names.
Usage
summary.ggobiDataset(object, ...)
Arguments
object ggobiDataset
...
Details
Author(s)
Hadley Wickham <[email protected]>
Examples
valid_ggobi Determines whether a reference to an internal ggobi object is valid
Description
Usage
valid_ggobi(.gobi)
Arguments
.gobi an object of class ggobi which refers to an internal ggobi instance.
40 variable_index
Details
One can create multiple, independent ggobi instances within a single R session and one can alsoremove them either programmatically or via the GUI. To be able to refer to these objects which areactually C-level internal objects, one has a reference or handle from an S object. Since the C levelobject can be destroyed while the S object still refers to them, this function allows one to checkwhether the internal object to which R refers is still in existence.
@arguments an object of class ggobi which refers to an internal ggobi instance. @value TRUE ifreal object still exist, FALSE otherwise @keyword dynamic
Value
TRUE if real object still exist, FALSE otherwise
Author(s)
Hadley Wickham <[email protected]>
Examples
g <- ggobi(mtcars)valid_ggobi(g)close(g)valid_ggobi(g)
variable_index Variable index
Description
Return indices corresponding to variable names
Usage
variable_index(x, names)
Arguments
x ggobiDataset
names variable names
Details
Author(s)
Hadley Wickham <[email protected]>
Examples
Index
∗Topic attributedim.ggobiDataset, 9dimnames.ggobiDataset, 9names.ggobiDataset, 29ncol.ggobiDataset, 30nrow.ggobiDataset, 30print.ggobiDataset, 31rownames.ggobiDataset, 33summary.ggobiDataset, 38variable_index, 39
∗Topic colorcolorscheme, 6
∗Topic dynamic.GGobiCall, 1.ggobi.symbol, 21clean.ggobi, 4close.ggobi, 4create_time_edges, 7create_time_edges_for_unit, 7excluded.ggobiDataset, 12ggobi, 17ggobi.find.file, 16ggobi_count, 15ggobi_get, 18ggobi_longitudinal, 19ggobi_version, 21glyph_colour.ggobiDataset, 23glyph_size.ggobiDataset, 24glyph_type.ggobiDataset, 25mapGlyphType, 27names.ggobi, 28print.ggobi, 31selected.ggobiDataset, 33shadowed.ggobiDataset, 36summary.ggobi, 37valid_ggobi, 38
∗Topic internal.GGobiCall, 1.ggobi.symbol, 21clean.ggobi, 4create_time_edges, 7create_time_edges_for_unit, 7dataset, 8
dim.ggobiDataset, 9dimnames.ggobiDataset, 9ggobi.find.file, 16ggobi_check_structs, 14ggobi_data_set_variables, 16ggobi_set_data_file, 19ggobi_set_data_frame, 20mapGlyphType, 27names.ggobiDataset, 29ncol.ggobiDataset, 30nrow.ggobiDataset, 30print.ggobi, 31print.ggobiDataset, 31rownames.ggobiDataset, 33valid_ggobi, 38variable_index, 39
∗Topic manipaddVariable.ggobiDataset, 2connecting_edges, 6dataset, 8edges, 11ggobi_data_set_variables, 16ggobi_set_data_file, 19ggobi_set_data_frame, 20ids.ggobiDataset, 27
∗Topic programmingggobi_check_structs, 14
.C, 2
.Call, 2
.GGobiC (.GGobiCall), 1
.GGobiCall, 1
.ggobi.symbol, 21[.ggobi, 17[.ggobiDataset, 17[<-.ggobi, 17[[.ggobiDataset, 17$.ggobiDataset, 17
addVariable(addVariable.ggobiDataset),2
addVariable.ggobiDataset, 2as.data.frame, 17
41
42 INDEX
clean.ggobi, 4close.ggobi, 4colorscheme, 6connecting_edges, 6create_time_edges, 7create_time_edges_for_unit, 7
dataset, 8dim.ggobiDataset, 9dimnames.ggobiDataset, 9
edges, 11, 17edges<-, 17excluded, 12, 17excluded (excluded.ggobiDataset),
12excluded.ggobiDataset, 12excluded<-, 12
ggobi, 17ggobi.find.file, 16ggobi_check_structs, 14ggobi_count, 15ggobi_data_set_variables, 16ggobi_get, 18ggobi_longitudinal, 17, 19ggobi_set_data_file, 19ggobi_set_data_frame, 20ggobi_version, 21glyph_color
(glyph_colour.ggobiDataset),23
glyph_colour, 17, 22glyph_colour
(glyph_colour.ggobiDataset),23
glyph_colour.ggobiDataset, 23glyph_colour<-, 23glyph_size, 17, 24glyph_size
(glyph_size.ggobiDataset),24
glyph_size.ggobiDataset, 24glyph_size<-, 24glyph_type, 17, 25glyph_type
(glyph_type.ggobiDataset),25
glyph_type.ggobiDataset, 25glyph_type<-, 26
ids, 26ids (ids.ggobiDataset), 27
ids.ggobiDataset, 27ids<-, 27
mapGlyphType, 27
names.ggobi, 28names.ggobiDataset, 29ncol.ggobiDataset, 30nrow.ggobiDataset, 30
print.ggobi, 31print.ggobiDataset, 31
rownames.ggobiDataset, 33
selected (selected.ggobiDataset),33
selected.ggobiDataset, 33shadowed, 17, 36shadowed (shadowed.ggobiDataset),
36shadowed.ggobiDataset, 36shadowed<-, 37summary.ggobi, 31, 37summary.ggobiDataset, 38
valid_ggobi, 38variable_index, 39