Plots a spot matrix.
Usage
plot_spot(object, ...)
# S4 method for matrix
plot_spot(
object,
type = c("ring", "plain"),
threshold = NULL,
diag = TRUE,
upper = TRUE,
lower = TRUE,
freq = FALSE,
...
)
# S4 method for data.frame
plot_spot(
object,
type = c("ring", "plain"),
threshold = NULL,
diag = TRUE,
upper = TRUE,
lower = TRUE,
freq = FALSE,
...
)
# S4 method for dist
plot_spot(
object,
type = c("ring", "plain"),
diag = FALSE,
upper = FALSE,
lower = !upper,
...
)
Arguments
- object
A \(m \times p\)
numeric
matrix
ordata.frame
of count data (absolute frequencies giving the number of individuals for each class).- ...
Extra parameters to be passed to
threshold
.- type
A
character
string specifying the graph to be plotted. It must be one of "ring
" (the default) or "plain
". Any unambiguous substring can be given.- threshold
A
function
that takes a numeric vector as argument and returns a numeric threshold value. IfNULL
(the default), no threshold is computed.- diag
A
logical
scalar indicating whether the diagonal of the matrix should be plotted. Only used ifobject
is a symmetric matrix.- upper
A
logical
scalar indicating whether the upper triangle of the matrix should be plotted. Only used ifobject
is a symmetric matrix.- lower
A
logical
scalar indicating whether the lower triangle of the matrix should be plotted. Only used ifobject
is a symmetric matrix.- freq
A
logical
scalar indicating whether relative frequency should be used instead of counts (absolute frequency).
Value
A ggplot2::ggplot object.
Details
The spot matrix can be considered as a variant of the Bertin diagram where the data are first transformed to relative frequencies.
Note
Adapted from Dan Gopstein's original idea.
See also
Other plot methods:
matrigraph()
,
plot_bertin()
,
plot_diceleraas()
,
plot_diversity
,
plot_ford()
,
plot_heatmap()
,
plot_rank()
,
seriograph()
Examples
## Data from Conkey 1980, Kintigh 1989
data("cantabria")
## Plot spot diagram of count data...
### ...without threshod
plot_spot(cantabria)
### ...with the column means as threshold
plot_spot(cantabria, threshold = mean)
### ...with the column medians as threshold
plot_spot(cantabria, threshold = median)