Functions show(), print(), summary(), and as.character() calculate
and show a basic summary of a hyperSpec object.
# S4 method for hyperSpec
show(object)
# S4 method for hyperSpec
print(x, range = FALSE, include = "main", ...)
# S4 method for hyperSpec
summary(object, ..., include = "all", range = TRUE)
# S4 method for hyperSpec
as.character(
x,
digits = getOption("digits"),
range = FALSE,
max.print = 5,
shorten.to = c(2, 1),
include = c("all", "main", "wl", "data")
)A hyperSpec object.
Should the values be indicated as a range (from the smallest to the largest value) rather than as first and last elements?
Character vector that contains at least one (but usually
several) of "all", "main","wl", or "data":
"all": the same as c("main", "wl", "data").
"main": the output includes the number of spectra, as well as the number
rows an columns in @data field of hyperSpec object.
"wl": the output includes the summary of @wavelength field.
"data: the output includes the summary of each column in @data field.
print() and summary() hand further arguments to
as.character().
Number of digits handed over to format.
Maximum number of elements to be printed (of a variable).
If a vector is longer than max.print, only the
first shorten.to[1] and the last shorten.to[2] elements are
printed.
After printing:
show() invisibly returns NULL,
print() and summary() invisibly returns x.
Function as.character() returns a character vector with summary of
hyperSpec.
Function as.character() does the main calculations. Functions show(),
print(), and summary() use as.character() and print their results with
different defaults:
show() prints the summary with the most basic information on hyperSpec
object (number of rows, columns and spectra),
print()has the same default output show(),
summary() prints a bit larger summary of hyperSpec, that includes
the number of rows, columns and spectra, the information on
@wavelengths, lists column names of @data as well as a preview of
the smallest and the largest values.
# show()
faux_cell # Implicitly prints the object. The same as show(faux_cell)
#> hyperSpec object
#> 875 spectra
#> 4 data columns
#> 300 data points / spectrum
show(faux_cell)
#> hyperSpec object
#> 875 spectra
#> 4 data columns
#> 300 data points / spectrum
# print()
print(faux_cell)
#> hyperSpec object
#> 875 spectra
#> 4 data columns
#> 300 data points / spectrum
print(faux_cell, include = "data")
#> data: (875 rows x 4 columns)
#> 1. x: x position [numeric] -11.55 -10.55 ... 22.45
#> 2. y: y position [numeric] -4.77 -4.77 ... 19.23
#> 3. region: [factor] matrix matrix ... matrix
#> 4. spc: intensity (arbitrary units) [matrix, array300] 15 168 ... 93
print(faux_cell, range = TRUE, include = "data")
#> data: (875 rows x 4 columns)
#> 1. x: x position [numeric] range -11.55 -10.55 ... 22.45
#> 2. y: y position [numeric] range -4.77 -3.77 ... 19.23
#> 3. region: [factor] range cell matrix nucleus
#> 4. spc: intensity (arbitrary units) [matrix, array300] range 0 1 ... 448
# The difference between range = TRUE and FALSE
# is evident only when data is not sorted.
set.seed(1)
faux_cell_2 <- sample(faux_cell)
print(faux_cell_2, include = "data")
#> data: (875 rows x 4 columns)
#> 1. x: x position [numeric] 18.45 1.45 ... -8.55
#> 2. y: y position [numeric] 18.23 14.23 ... 2.23
#> 3. region: [factor] matrix matrix ... matrix
#> 4. spc: intensity (arbitrary units) [matrix, array300] 72 136 ... 128
print(faux_cell_2, range = TRUE, include = "data")
#> data: (875 rows x 4 columns)
#> 1. x: x position [numeric] range -11.55 -10.55 ... 22.45
#> 2. y: y position [numeric] range -4.77 -3.77 ... 19.23
#> 3. region: [factor] range cell matrix nucleus
#> 4. spc: intensity (arbitrary units) [matrix, array300] range 0 1 ... 448
# summary()
summary(faux_cell)
#> hyperSpec object
#> 875 spectra
#> 4 data columns
#> 300 data points / spectrum
#> wavelength: Delta * tilde(nu)/cm^-1 [numeric] 602 606 ... 1798
#> data: (875 rows x 4 columns)
#> 1. x: x position [numeric] range -11.55 -10.55 ... 22.45
#> 2. y: y position [numeric] range -4.77 -3.77 ... 19.23
#> 3. region: [factor] range cell matrix nucleus
#> 4. spc: intensity (arbitrary units) [matrix, array300] range 0 1 ... 448
summary(faux_cell, include = c("wl", "data"))
#> wavelength: Delta * tilde(nu)/cm^-1 [numeric] 602 606 ... 1798
#> data: (875 rows x 4 columns)
#> 1. x: x position [numeric] range -11.55 -10.55 ... 22.45
#> 2. y: y position [numeric] range -4.77 -3.77 ... 19.23
#> 3. region: [factor] range cell matrix nucleus
#> 4. spc: intensity (arbitrary units) [matrix, array300] range 0 1 ... 448
as.character(faux_cell)
#> [1] "hyperSpec object"
#> [2] " 875 spectra"
#> [3] " 4 data columns"
#> [4] " 300 data points / spectrum"
#> [5] "wavelength: Delta * tilde(nu)/cm^-1 [numeric] 602 606 ... 1798 "
#> [6] "data: (875 rows x 4 columns)"
#> [7] " 1. x: x position [numeric] -11.55 -10.55 ... 22.45 "
#> [8] " 2. y: y position [numeric] -4.77 -4.77 ... 19.23 "
#> [9] " 3. region: [factor] matrix matrix ... matrix "
#> [10] " 4. spc: intensity (arbitrary units) [matrix, array300] 15 168 ... 93 "
as.character(faux_cell, include = c("wl", "data"))
#> [1] "wavelength: Delta * tilde(nu)/cm^-1 [numeric] 602 606 ... 1798 "
#> [2] "data: (875 rows x 4 columns)"
#> [3] " 1. x: x position [numeric] -11.55 -10.55 ... 22.45 "
#> [4] " 2. y: y position [numeric] -4.77 -4.77 ... 19.23 "
#> [5] " 3. region: [factor] matrix matrix ... matrix "
#> [6] " 4. spc: intensity (arbitrary units) [matrix, array300] 15 168 ... 93 "