caroline (version 0.7.4)

pies: Pie chart scatterplot

Description

Plot pie charts in an XY scatterplot. An overhauled wrapper of the original pie plot function. It is currently very slow: a recommened work around is to plot to something other than the default device (aka png, pdf, etc).

Usage

pies(x, show.labels = FALSE, show.slice.labels = FALSE, color.table = NULL, 
		radii = rep(2,length(x)), x0=NULL, y0=NULL, 
		edges = 200,  clockwise = FALSE, 
                init.angle = if (clockwise) 90 else 0, density = NULL, angle = 45, 
                border = NULL, lty = NULL, 
                other.color='gray', na.color='white', ...)

Arguments

x

a list of named vectors.

show.labels

boolean specifying if the pie point lables should be plotted.

show.slice.labels

boolean specifying if the pie slice labels should be plotted.

color.table

a named vector of colors. names should correspond to all possible levels of x

radii

a vector of radii used to size the pie points.

x0,y0

a vector of x and y positions for the pie points.

edges

the circular outline of the pie is approximated by a polygon with this many edges.

clockwise

logical indicating if slices are drawn clockwise or counter clockwise (i.e., mathematically positive direction), the latter is default.

init.angle

number specifying the starting angle (in degrees) for the slices. Defaults to 0 (i.e., 3 o'clock) unless clockwise is true where init.angle defaults to 90 (degrees), (i.e., 12 o'clock).

density

the density of shading lines, in lines per inch. The default value of NULL means that no shading lines are drawn. Non-positive values of density also inhibit the drawing of shading lines.

angle

the slope of shading lines, given as an angle in degrees (counter-clockwise).

border

(possibly vectors) arguments passed to polygon which draws each slice.

lty

(possibly vectors) arguments passed to polygon which draws each slice.

other.color

color used for x vector elements for names without corresponding names in the color table

na.color

color used for x vector elements with missing names

...

other arguments passed to polygon

Value

• Pie charts as points on a plot

See Also

pie

Examples

## these examples are to the default plot window, which can be slow
## try instead to plot to png or pdf for example

## example 1
  pies(
       list(
            a=nv(c(1,2,3),c('one','two','thre')),
            b=nv(c(2,2,3),c('one','two','thre')),
            c=nv(c(1,2,3),c('one','two','thre'))
            ),
       x0=c(0,.5,1),
       y0=c(0,.5,1), radii=6, border=c('gray', 'black', 'red')
       )


## example 2
n <- 200
n.groups <- 10
n.subgroups <-  6

grps <- paste('gene',seq(1,n.groups), sep='')[round(runif(n,1,n.groups))]
subgrps <- paste('species',seq(1,n.subgroups), sep='')[round(runif(n,1,n.subgroups))]
group.df <- cbind.data.frame(grps,subgrps)
subgroup.list <- by(group.df, group.df$grps, function(x) x$subgrps)

pie.list <- lapply(subgroup.list, table)
col.tab <- nv(rainbow(6), unique(subgrps))

pies(x=pie.list, x0=rnorm(n.groups), y0=rnorm(n.groups), radii=10, show.labels=TRUE, show.slice.labels=TRUE, color.table=col.tab)


## example 3  reading from external flat file
## salt.df <- read.delim('/path/to/my/file.tab')
## create a dummy dataset that might live inside the above file
salt.df <- data.frame(salinity=rnorm(25,5), temperature=rnorm(25,25), spec_a=rpois(25,4), 
							   spec_b=rpois(25,4), 
							   spec_c=rpois(25,4), 
							   spec_d=rpois(25,4),
							   spec_e=rpois(25,4)
							   )
## pull out the colnumn names that are specific to pie wedge numbers	
salt.spec.nms <- names(salt.df)[grep('spec',names(salt.df))]
## turn them into a list
pie.list <- lapply(1:nrow(salt.df), function(i) as.table(nv(as.vector(as.matrix(salt.df[i,salt.spec.nms])), salt.spec.nms)))
names(pie.list)<- letters[1:25]
with(salt.df, pies(x=pie.list, x0=salinity, y0=temperature, radii=2))