R: Level plot

level_plot {opm}

R Documentation

Level plot

Description

Level plot for OPM and OPMS objects using the function from the lattice package.

Usage

  ## S4 method for signature 'MOPMX'
level_plot(x, ...) 
  ## S4 method for signature 'OPM'
level_plot(x, main = list(),
    colors = opm_opt("color.borders"), panel.headers = FALSE, cex = NULL,
    strip.fmt = list(), striptext.fmt = list(), legend.sep = " ",
    space = "Lab", bias = 0.5, num.colors = 200L, ...) 
  ## S4 method for signature 'OPMS'
level_plot(x, main = list(),
    colors = opm_opt("color.borders"), panel.headers = TRUE, cex = NULL,
    strip.fmt = list(), striptext.fmt = list(), legend.sep = " ",
    space = "Lab", bias = 0.5, num.colors = 200L, ...)

Arguments

`x`	`OPM`, `OPMS` or `MOPMX` object.
`main`	The settings controlling the construction of the main title. Works like the `main` argument of `xy_plot`.
`colors`	Character vector indicating the colours (at least two).
`panel.headers`	`NULL`, logical scalar, expression or character vector. `NULL` and `FALSE` turn panel headers off. `TRUE` causes the panel headers to be constructed from the plate numbers or those metadata that were included by `flatten` (see there). Character vectors and expressions are directly used for the text within these panel headers. Currently ignored by the `OPM` method.
`cex`	Numeric scalar. Magnification of axis annotation. If `NULL`, automatically adapted to the number of wells (at least a good guess is made).
`strip.fmt`	List controlling the format of the description strip above each panel. For instance, the background colour is set using the `bg` key. For further details, see `strip.custom` from the lattice package. `strip.fmt` is ignored if panel.headers is `FALSE` and currently always ignored by the `OPM` method.
`striptext.fmt`	List controlling the format of the text within the strip above each panel. See `xy_plot` for details, which has an argument of the same name.
`legend.sep`	Character scalar. This works like the eponymous argument to `flatten` (see there); it is ignored unless metadata are chosen for constructing the panel headers.
`space`	Character scalar passed to `colorRampPalette` from the grDevices package. These and the following arguments are for fine-tuning the colour palette used for plotting.
`bias`	Numeric scalar also passed to `colorRampPalette`.
`num.colors`	Numeric scalar passed to the function returned by `colorRampPalette`.
`...`	Arguments that are passed between the methods or to `flatten`.

Value

An object of class ‘trellis’ or a list if such objects. See levelplot from the lattice package for details.

References

Jacobsen, J. S., Joyner, D. C., Borglin, S. E., Hazen, T. C., Arkin, A. P. et al. 2007 Visualization of growth curve data from phenotype microarray experiments. 11th International Conference on Information Visualization (IV07). Zuerich, Switzerland, July 4-6 2007. Published by the IEEE Computer Society.

Sarkar, D. 2008 Lattice: Multivariate Data Visualization with R. New York: Springer, 265 p.

Vaas, L. A. I., Sikorski, J., Michael, V., Goeker, M., Klenk H.-P. 2012 Visualization and curve parameter estimation strategies for efficient exploration of Phenotype Microarray kinetics. PLoS ONE 7, e34846.

Examples

# OPM method
level_plot(vaas_1, main = "Levelplot example")

plot of chunk unnamed-chunk-1

# OPMS method
## Not run: 
##D # headers include species and strain
##D level_plot(vaas_4, include = c("Species", "Strain"))
## End(Not run)

[Package opm version 1.3.63 Index]