aplot: Scientific X-Y Plotting
In taranu/astro: Astronomy Functions, Tools and Routines

Description Usage Arguments Details Note Author(s) See Also Examples

Generic function for plotting of R objects.

aplot(x, y = NULL, z = NULL, xlim = NULL, ylim = NULL, zlim = NULL, 
      xlab = NULL, ylab = NULL, zlab = NULL, col = NULL, axes = TRUE, 
      side = 1:4, labels = TRUE, majticks = TRUE, minticks = TRUE, 
      nxmaj = NULL, nymaj = NULL, nxmin = NULL, nymin = NULL, xat = NULL, 
      yat = NULL, log = "", unlog = FALSE, xformat = NULL, yformat = NULL, 
      digits = 0, cex = 1, xlabpos = 1, ylabpos = 2, zcol = NULL, 
      cb = FALSE, cbpos = 4, cbsep = 1.5, cbspan = 2, cbinset = 1, 
      cbx1 = NULL, cbx2 = NULL, cby1 = NULL, cby2 = NULL, cblegend = NULL, 
      cbsteps = 250, las = 0, mgp = c(2.5,0.5,0), tcl = 0.5, dexcl = 0.2, 
      cex.axis = 1, cex.cb = 1, zline = mgp[1]+1, col.axes = "black", 
      col.axis = "black", add = FALSE, type = NULL, bgcol = NULL, ...)

`x,y,z`	the 'x', 'y' and 'z' arguments provide the x, y and z coordinates for the plot. Supplying the 'z' argument will colour each data point differently according to its z value.
`xlim,ylim,zlim`	the x, y and z limits of the plot in the form c(lower,upper)
`xlab,ylab,zlab`	the x, y and z axis labels
`col`	colour of the data points (will override z)
`axes`	plot axes
`side`	sides to plot axes [T/F or 1:4]
`labels`	sides to plot axes labels [T/F or 1:4]
`majticks`	plot major tick marks
`minticks`	plot minor tick marks
`nxmaj`	number of major tick marks on the x-axis
`nymaj`	number of major tick marks on the y-axis
`nxmin`	number of minor tick marks between major ticks (x)
`nymin`	number of minor tick marks between major ticks (y)
`xat`	position of x-axes major tick marks
`yat`	position of y-axes major tick marks
`log`	logged axes
`unlog`	unlog axes plotting logged data
`xformat`	format for x-axes labelling (see 'formatC')
`yformat`	format for y-axes labelling (see 'formatC')
`digits`	number of digits for axes labels
`cex`	expansion factor
`xlabpos`	label position (x)
`ylabpos`	label position (y)
`zcol`	z-axis colour palette
`cb`	plot colourbar
`cbpos`	position of colourbar
`cbsep`	separation of colourbar from plot
`cbspan`	width/height of colourbar
`cbinset`	size of inset of colourbar on axis parallel to plotting side
`cbx1,cbx2,cby1,cby2`	manual colourbar positioning (xlower, xupper, ylower, yupper
`cblegend`	colourbar legend
`cbsteps`	colourbar resolution
`las,mgp,tcl`	standard 'par' plotting parameters
`dexcl`	distance from major tick marks within which no minor tick labels should be plotted
`cex.axis`	expansion factor for axis annotation
`cex.cb`	expansion factor for colourbar annotation
`zline`	colourbar label line
`col.axes`	colour of axes
`col.axis`	colour of axes annotation
`add`	add the plot to an existing plot
`type`	plot type
`bgcol`	background colour
`...`	additional arguments to be passed to 'plot'

The top-level function 'aplot' (astro:plot) is a wrapper around the R function 'plot'. It provides significant additional features which trivially allow the creation of figures more suited for a scientific audience. Notably, 'aplot' allows z-axis information to be displayed through the use of colourbars and provides improved axes (including minor-tick marks) through the use of the 'aaxis' function.

Colourbar features are provided by the 'color.legend' function within the 'plotrix' package (author: Jim Lemon). 'aplot' provides a wrapper around this function, therefore, in order for colourbar features to function correctly, the 'plotrix' package must be installed.

Lee Kelvin <lee.kelvin@uibk.ac.at>

The astronomy package: astro.

# example #1
layout(1)
par("mar"=c(5.1,4.1,2.1,2.1))
par("oma"=c(0,0,0,0))
aplot(sin, xlim=c(0,2*pi), ylim=c(-1.1,1.1), bgcol="lightgoldenrodyellow")
abline(h=0, col="grey75")
label("top", txt="Sine Function", lwd=0, bgcol="grey25", col="white")
label("bottomleft", txt="astro:label (label)", cex=2, lwd=0, bgcol=NULL)

# example #2
layout(1)
par("mar"=c(5.1,4.1,2.1,4.1))
par("oma"=c(0,0,0,0))
aplot(1:1000, log10(1:1000), unlog="y", type="l", yformat="p", side=1:3, 
col="red", lwd=2)
aaxis(4, nmaj=4, nmin=9)
mtext(bquote(paste(log[10]," y ")), side=4, line=2.5)
label("bottomright", txt="astro:axis (aaxis)", cex=2, lwd=0, bgcol=NULL)

# example #3
layout(cbind(c(1,2),c(3,3)), widths=c(5,1))
par("mar"=c(0,0,0,1))
par("oma"=c(3.1,3.1,3.1,2.1))
aplot(rnorm(1000), rnorm(1000), rnorm(1000), pch=17, zlim=c(-1,1), xlim=c(-3,3), 
ylim=c(-3,3), labels=2:3)
grid()
label("topleft", txt="astro:colourbar (acb)", cex=2, lwd=0, bgcol=NULL)
aplot(rnorm(1000), rnorm(1000), rnorm(1000), pch=16, zlim=c(-1,1), xlim=c(-3,3), 
ylim=c(-3,3), labels=1:2)
grid()
acb(zlim=c(-1,1), zlab="z-axis label")

# example #4
layout(1)
par("mar"=c(5.1,4.1,4.1,5.1))
par("oma"=c(0,0,0,0))
aplot(rnorm(1000), rnorm(1000), rnorm(1000), cb=TRUE, zlim=c(-1,1), pch=16, 
xlab="x-axis label", ylab="y-axis label", zlab="z-axis label", bgcol="grey95")
label("topleft", txt="astro:plot (aplot)", cex=2, lwd=0, bgcol=NULL)