- x
Numeric vector or matrix/data.frame; x values to 2D bin. If x is a two (or more) column matrix or data.frame and y/z is missing as an argument, then the first column is used for x and the second/third column for y/z.
- y
Numeric vector; the y coordinates of points in the plot, optional if x is an appropriate structure.
- z
Numeric vector; the z coordinates of points in the plot (optional), optional if x is an appropriate structure.
- xlim
Numeric vector; the x limits to use for the data. Default of NULL calculates the range based on the provided x data vector. If length equals 1 then the argument is taken to mean the sigma range to select for plotting and the clipping is done by magclip.
- ylim
Numeric vector; the y limits to use for the data. Default of NULL calculates the range based on the provided y data vector. If length equals 1 then the argument is taken to mean the sigma range to select for plotting and the clipping is done by magclip.
- zlim
Numeric vector; the z limits to use for the data. Default of NULL calculates the range based on the provided z data vector. If length equals 1 then the argument is taken to mean the sigma range to select for plotting and the clipping is done by magclip.
- Nbin
Integer vector; The number of bins to (approximately) split the x/y axes into. If length 1 then this value is used by both (default is 50 bin in x/y), if length 2 then Nbin[1] is used for the x-axis and Nbin[2] is used for the y-axis.
- step
Numeric vector; grid steps in x and y directions. If NULL then this is c(diff(xlim), diff(ylim))/Nbin. If length 1, then this value is repeated. Overrides Nbin if supplied.
- log
Character scalar; log axis arguments to be passed to used. E.g. use 'x', 'y', 'xy' or 'yx' as appropriate. Default '' assumes no logging of any axes. For convenience you can specify the 'z' axis too, which somewhat replaces the colstretch argument. Note that in all cases the x/y/z data is explictly logged, which means the plotting window does not know it is in logged space (via the par()$xlag and par()$ylog structures). This means is you want to add points etc to the plot you will need to apply log10 yourself, so a point with coordinates [10^2,10^-3] should be plotted at [2,-3].
- unlog
Character scalar; determines if x/y axis labels should be unlogged (z is ignored here). By default inherits log, since that is usually what you would want.
- clustering
Numeric scalar; excess counts in densist bin relative to Uniform data. This is to optimise the binning, so can probably be ignored.
- dustlim
Numeric scalar; if between 0 and 1 then the 2D bin count quantile to switch to showing the individual points (which visually look like 'dust'), if larger than 1 then the exact counts threshold. If this is NA or 0 then all cells are shown.
- shape
Character scalar; type of binning, either hex/hexagon; sq/square; tri/triangle or trihex. 'trihex' is a triangle tessellation that is also arranged to have hexagonal packing (so 6 triangles can form a hexagon).
- plot
Logical; create a plot? If FALSE then just the binning output list is created.
- colramp
Vector; a colour scaling to use. Must be a vector and not a function.
- colstretch
Character scalar; colour stretch, either linear (lin, default) or logarithmic (log, good for large dynamic ranges).
- sizestretch
Character scalar; size stretch, either linear (lin, default) or logarithmic (log, good for large dynamic ranges).
- colref
Character scalar; colour reference for call, either it should be based on the counts (count, default) or the z-axis statistic (zstat)?
- sizeref
Character scalar; size reference for call, either it should be ignored (none, so all are the same size and closely packed), based on the counts (count) or the z-axis statistic (zstat)?
- funstat
Function; function to use to compute a statistic over the z axis. The default is median, but other good options might be mean, sd, mad. Note, to change default arguments you might need to send through a new function, e.g. funstat = function(x) median(x, na.rm=TRUE) and similar, but if you are happy with the defaults then you can use the simpler funstat = mean etc.
- direction
Character scalar; should there be a shape side aligned horizontally ('h', the default) or vertically ('v')? This is only relevant for hexagon and triangle bin shapes, and has the effect of leading the eye differently with some scatter structures.
- offset
Numeric/character scalar; only relevant for shape='sq' or shape='tri'. Either a numeric value specifying the offset (relative to step) to apply to alternating rows (direction='h') or columns (direction='v'); or 'jitter' which means the rows or columns are randomly jittered (only used for shape='sq' bins. This option is useful for visually breaking up strong patterns in certain types of data.
- jitterseed
Integer scalar; the random seed to use for jittering (means you can recreate your plots exactly if the seed is the same). This argument is only used for shape='sq' bins.
- projden
Logical; do you want projected density PDFs to be displayed above and to the side of the standard plot.magbin plot? If so you also need to pass the same xdata and ydata that you originally sent to magbin, since this is not stored in the object output from magbin.
- projsig
Logical; if projden = TRUE then this will optionally add lines to show the pseudo 1-sigma range (15.9% to 84.1% quantiles).
- ...
Dots to be passed to magplot, magmap and magbar. Relevant arguments are matched, so look in those functions for optional arguments to pass.