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hyperSpec 🔵 ➡️ 🟠 ChemoSpec

Source: R/to_ChemoSpec.R
hyperSpec_to_ChemoSpec.Rd

ChemoSpec requires that the hyperSpec object meets the following conditions:

  • Wavelengths must be unique.

  • Spectra must not contain NAs.

Usage

hyperSpec_to_ChemoSpec(hySpc, names, groups = "{missing group}", ...)

Arguments

hySpc

hyperSpec::hyperSpec object.

names

Character vector with unique sample names. Length must match nrow(data). Defaults to rownames(data).

groups

Factor with sample class assignments or single integer or string value. Length of factor must match nrow(data). A single value is treated as setting the same group for all samples. Defaults to "{missing group}"

...

Arguments passed on to to_ChemoSpec

desc

Optional description for plots generated with ChemoSpec.

colors_set,sym_set,alt.sym_set

Character vector with group colors, Numeric vector with group symbol numbers, Character vector with alternative group symbols. Their length must match at least the number of levels in groups. Groups are assigned colors based on their numeric factor level. Defaults to ChemoSpecUtils::Col8, ChemoSpecUtils::Sym8 and base::letters. A color-blind friendly palette is available in ChemoSpecUtils::Col7. Extended palettes are available at ChemoSpecUtils::Col12, ChemoSpecUtils::Sym12, and using other packages, like RColorBrewer.

.strict_extra_data_names

(Default: TRUE) Set this to FALSE to allow columns from extra_data to overwrite values on the Spectra object.

See also

to_ChemoSpec(), ChemoSpec_to_hyperSpec()

Examples

suppressPackageStartupMessages(library(hyperSpec))
data(flu)
hyperSpec_to_ChemoSpec(
  flu,
  names = 1:6 |> as.character(),
  groups = LETTERS[1:6] |> as.factor()
) |> str()
#> 	Additional data was found: filename
#> 	Additional data was found: c
#> List of 11
#>  $ data    : num [1:6, 1:181] 27.1 66.8 93.1 130.7 167.3 ...
#>   ..- attr(*, "dimnames")=List of 2
#>   .. ..$ : NULL
#>   .. ..$ : chr [1:181] "405" "405.5" "406" "406.5" ...
#>  $ freq    : num [1:181] 405 406 406 406 407 ...
#>  $ unit    : chr [1:2] "lambda/nm" "I[fl]/\"a.u.\""
#>  $ desc    : chr "{missing description}"
#>  $ groups  : Factor w/ 6 levels "A","B","C","D",..: 1 2 3 4 5 6
#>  $ names   : chr [1:6] "1" "2" "3" "4" ...
#>  $ colors  : chr [1:6] "#511CFCFF" "#FB0D16FF" "#2AA30DFF" "#700D87FF" ...
#>  $ sym     : num [1:6] 0 1 2 3 15 16
#>  $ alt.sym : chr [1:6] "a" "b" "c" "d" ...
#>  $ filename: chr [1:6] "rawdata/flu1.txt" "rawdata/flu2.txt" "rawdata/flu3.txt" "rawdata/flu4.txt" ...
#>  $ c       : num [1:6] 0.05 0.1 0.15 0.2 0.25 0.3
#>  - attr(*, "class")= chr "Spectra"