hs_SCA_conv_itol: Calculate the spectral conrast angle (SCA) and generate an...
In CMET-UGent/MicroRaman: Phenotyping of microbial Raman spectroscopy data

Description Usage Arguments Value References

The SCA measures the angle between two vectors corresponding to closely related spectra to measure whether they are the same or not (Wan *et al.*, 2002). This function returns an iTol (Letunic & Bork, 2016)

hs_SCA_conv_itol(
  x,
  Factor1 = c("LB", "NB", "LB"),
  Factor1Name = "Medium",
  Factor2 = c("rep1", "rep2", "rep3"),
  Factor2Name = "Replicate",
  clusMethod = "ward.D2"
)

`x`	a hyperSpec object containing the cells in the rows, and wavenumbers (features) in columns
`Factor1`	a character vector containing treatment levels (defaults to different media)
`Factor1Name`	a string naming Factor 1 (defaults to "Medium")
`Factor2`	a character vector containing "treatment" levels (defaults to different replicates)
`Factor2Name`	a string naming Factor 2 (defautls to "Replicate")
`clusMethod`	a string showing which stats::hclust linkage method should be chosen

an ape::phylo object based upon hclust of SCA distances of the hyperSpec object's cells

Wan, K. X., Vidavsky, I., & Gross, M. L. (2002). Comparing similar spectra: from similarity index to spectral contrast angle. Journal of the American Society for Mass Spectrometry, 13(1), 85-88.

Letunic, I., & Bork, P. (2016). Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic acids research, 44(W1), W242-W245.

CMET-UGent/MicroRaman documentation built on July 25, 2020, 6:20 p.m.