as.data.frame {hyperSpec}

Conversion of a hyperSpec object into a data.frame or matrix as.data.frame returns x@data (as data.frame) as.matrix returns the spectra matrix x@data$spc as matrix

Description

The data.frame returned by as.long.df is guaranteed to have columns spc and .wavelength. If nwl (x) == 0 these columns will be NA.

Usage

## S3 method for class 'hyperSpec'
as.data.frame(x, row.names = TRUE, optional = NULL, ...)

## S3 method for class 'hyperSpec'
as.matrix(x, ...)

as.wide.df(x, wl.prefix = "")

as.long.df(x, rownames = FALSE, wl.factor = FALSE, na.rm = TRUE)

as.t.df(x)

Arguments

x

a hyperSpec object

row.names

if TRUE, a column .row is created containing row names or row indices if no rownames are set. If character vector, the rownames are set accordingly.

optional

ignored

...

ignored

wl.prefix

prefix to prepend wavelength column names

rownames

should the rownames be in column .rownames of the long-format data.frame?

wl.factor

should the wavelengths be returned as a factor (instead of numeric)?

na.rm

if TRUE, rows where spc is not NA are deleted.

Value

x@data and x@data$spc (== x$spc == x [[]]), respectively.

as.wide.df returns a data.frame that consists of the extra data and the spectra matrix converted to a data.frame. The spectra matrix is expanded in place.

as.long.df returns the stacked or molten version of x@data. The wavelengths are in column .wavelength.

as.t.df returns a data.frame similar to as.long.df, but each spectrum in its own column. This is useful for exporting summary spectra, see the example.

Author(s)

C. Beleites

See Also

as.data.frame

and base::as.matrix()

[[[()] (⁠[[]]⁠) for a shortcut to as.matrix

stack and melt or reshape2::melt() for other functions producing long-format data.frames.

Examples

as.data.frame (chondro [1:3,, 600 ~ 620])
as.matrix (chondro [1:3,, 600 ~ 620])
lm (c ~ spc, data = flu [,,450])

as.wide.df (chondro [1:5,, 600 ~ 610])
summary (as.wide.df (chondro [1:5,, 600 ~ 610]))

as.long.df (flu [,, 405 ~ 410])
summary (as.long.df (flu [,, 405 ~ 410]))
summary (as.long.df (flu [,, 405 ~ 410], rownames = TRUE))
summary (as.long.df (flu [,, 405 ~ 410], wl.factor = TRUE))

df <- as.t.df (apply (chondro, 2, mean_pm_sd))
head (df)

if (require (ggplot2)){
  ggplot (df, aes (x = .wavelength)) +
    geom_ribbon (aes (ymin = mean.minus.sd, ymax = mean.plus.sd),
      fill = "#00000040") +
    geom_line (aes (y = mean))
}