forams (version 2.0-6)

plot.fi: Custom plot function for FORAM Index results

Description

This function generates custom plots for FI objects.

Usage

# S4 method for fi
plot(x, ylim = c(1, 10), yaxp = c(1, 10, 9), xlab = 'Samples',
  ylab = 'FORAM Index', pch.urg = 25, pch.mrg = 21, pch.crg = 24,
  bg.urg = 'red', bg.mrg = 'yellow', bg.crg = 'green', pt.cex = 1,
  limits = TRUE, ...)

Arguments

x

an object of class fi.

ylim

the y limits (x1, x2) of the plot, defaults to c(1, 10)

yaxp

a vector of the form c(y1, y2, n) giving the coordinates of the extreme tick marks and the number of intervals between tick-marks, defaults to c(1, 10, 9).

xlab

a label for the x axis, defaults to "Samples".

ylab

a label for the y axis, defaults to "FORAM Index".

pch.urg

plotting 'character', i.e., symbol to use, prefer one between 21:25, defaults to 25

pch.mrg

plotting 'character', i.e., symbol to use, prefer one between 21:25, defaults to 21

pch.crg

plotting 'character', i.e., symbol to use, prefer one between 21:25, defaults to 24

bg.urg

background (fill) color for the open plot symbols given by pch=21:25, defaults to "red".

bg.mrg

background (fill) color for the open plot symbols given by pch=21:25, defaults to "yellow".

bg.crg

background (fill) color for the open plot symbols given by pch=21:25, defaults to "green".

pt.cex

character (or symbol) expansion: a numerical vector, defaults to 1.

limits

logical; if TRUE, draws lines limiting the three FORAM Index classes and identifies them, defaults to TRUE.

...

other graphical parameters, see par for details.

Author

Rodrigo Aluizio

Details

The plot uses the axis function, so a complete customization (i.e. side) of the axes is not possible at this moment, and some other parameters may show improperly if changed.

References

Hallock, P., Lidz, B.H., Cockey-Burkhard, E.M. & Donnelly, K.B. (2003). Foraminifera as bioindicators in coral reef assessment and monitoring: The foram index. Environmental monitoring and assessment 81, 221-238.

Examples

data(LF)
data(Factors)
MyFI <- fi(LF, Factors)
plot(MyFI)