radial_plot {opm} | R Documentation |
A wrapper for radial.plot
from the plotrix
package with some adaptations likely to be useful for
OmniLog(R) data.
## S4 method for signature 'MOPMX' radial_plot(object, ...) ## S4 method for signature 'OPMS' radial_plot(object, as.labels, subset = opm_opt("curve.param"), sep = " ", extract.args = list(), ...) ## S4 method for signature 'data.frame' radial_plot(object, as.labels, subset = "numeric", sep = " ", extract.args = list(), ...) ## S4 method for signature 'matrix' radial_plot(object, as.labels = NULL, subset = TRUE, sep = " ", extract.args = list(), rp.type = "p", radlab = FALSE, show.centroid = TRUE, show.grid.labels = 1, lwd = 3, mar = c(2, 2, 2, 2), line.col = opm_opt("colors"), draw.legend = TRUE, x = "bottom", y = NULL, xpd = TRUE, pch = 15, legend.args = list(), group.col = FALSE, point.symbols = 15, point.col = opm_opt("colors"), poly.col = NA, main = paste0(as.labels, sep = sep), ...)
object |
|
as.labels |
For the |
subset |
For the |
sep |
Character scalar determining how to join row
names. See |
extract.args |
Optional list of arguments passed to
the |
rp.type |
Character scalar. Among the possible
values ‘p’ for polygons, ‘s’ for symbols
and ‘r’ for radial lines, the latter is not
recommended. These and the following arguments are passed
to |
radlab |
Logical scalar. Rotation of the outer labels to a radial orientation might safe some space in the graphic. |
show.centroid |
Logical scalar. |
show.grid.labels |
Logical scalar. Indicates whether and where display labels for the grid are shown. |
lwd |
Numeric scalar for the line width. |
mar |
Numeric vector of length 4 determining the margins of the plot. |
line.col |
Character or numeric vector for determining the line colour. |
point.symbols |
Like the following arguments, passed
to |
point.col |
Indicates the colour(s) of the symbols. |
poly.col |
Indicates the colour for filling the
drawn polygons, if any. Use |
group.col |
Logical scalar indicating whether or not wells from plates that belong to the same group shall have the same colour. |
main |
The main title of the plot. |
... |
Optional other arguments passed to
|
draw.legend |
Logical scalar. Whether to draw a
legend. Ignored unless |
x |
Legend position, passed to |
y |
Optional Second legend coordinate. Also passed to that function. |
xpd |
Logical scalar. Also passed to that function. |
pch |
Integer scalar. Also passed to that function. |
legend.args |
List of optional other arguments passed to that function. |
The default positioning of the legend is not necessarily
very useful, but suitable combinations of margin
,
x
and y
can be found for given data sizes.
Plotting entire plates usually makes not much sense (see
the examples).
The data frame and OPMS
methods extract a
numeric matrix from a given data frame or
OPMS
object and pass the result to the
matrix method.
A vector with the row names of object
as names and
the corresponding colours as values, equivalent to the
legend; NULL
if no row names are present. A list
of such objects in the case of the MOPMX
method.
Lea A.I. Vaas and Markus Goeker
plotrix::radial.plot graphics::legend
Other plotting-functions: ci_plot
,
heat_map
, level_plot
,
parallel_plot
, parallelplot
,
summary
, xy_plot
data("vaas_4")
## 'OPMS' method
# Note that this visualization is not useful when applied to too many wells.
# Thus, we here use only a subset of the wells for plotting.
(y <- radial_plot(vaas_4[, , 1:5], as.labels = list("Species", "Strain"),
main = "Test", x = 200, y = 200))
## Escherichia coli DSM18039 Escherichia coli DSM30083T
## "#008080" "#800080"
## Pseudomonas aeruginosa DSM1707 Pseudomonas aeruginosa 429SC1
## "#808000" "#000000"
# with some fine tuning; note the centroids
(y <-radial_plot(vaas_4[, , 1:5], as.labels = list("Species", "Strain"),
main = "Test", x = 200, y = 200, rp.type = "s", show.centroid = TRUE))
## Escherichia coli DSM18039 Escherichia coli DSM30083T
## "#008080" "#800080"
## Pseudomonas aeruginosa DSM1707 Pseudomonas aeruginosa 429SC1
## "#808000" "#000000"
# with the same colour for members of the same group
(xy <-radial_plot(vaas_4[, , 1:5], as.labels = list("Species"),
group.col = TRUE, main = "Test", x = 200, y = 200, rp.type = "s",
show.centroid = TRUE))
## Warning in .local(object, ...): duplicated label: Escherichia coli
## Escherichia coli Pseudomonas aeruginosa
## "#008080" "#800080"
## Data-frame method (rarely needed)
x <- extract(vaas_4, as.labels = list("Species", "Strain"), dataframe = TRUE)
(yy <- radial_plot(x[, 1:8], as.labels = c("Species", "Strain"),
main = "Test"))
## Escherichia coli DSM18039 Escherichia coli DSM30083T
## "#008080" "#800080"
## Pseudomonas aeruginosa DSM1707 Pseudomonas aeruginosa 429SC1
## "#808000" "#000000"
stopifnot(identical(y, yy)) # should also yield the same picture than above
stopifnot(is.character(yy), names(yy) == paste(x$Species, x$Strain))
## Matrix method (rarely needed)
x <- extract(vaas_4, as.labels = list("Species", "Strain"))
(yy <- radial_plot(x[, 1:5], main = "Test"))
## Escherichia coli DSM18039 Escherichia coli DSM30083T
## "#008080" "#800080"
## Pseudomonas aeruginosa DSM1707 Pseudomonas aeruginosa 429SC1
## "#808000" "#000000"
stopifnot(identical(y, yy)) # should also yield the same picture than above
stopifnot(is.character(yy), names(yy) == rownames(x))