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Affinity rankings for groups of species.
rank.affinity(aout, groups, percent = TRUE)The average rankings are inserted into the values element of aout, and the names of the groups are inserted into the species element.
The result can be used by diagram to make line plots or predominance diagrams (the predominance fields correspond to the groups with highest average ranking of affinity).
list, output of affinity
named list of indices (integer or numeric) for species in each group
return average rank percentage for each group
The affinities for all species are ranked, then the mean ranking for the species in each group is calculated.
The mean rankings of groups are converted to a percentage, or returned as-is if percent is FALSE.
Note that the calculations are applied to each set of conditions individually (i.e., each grid point in the affinity affinity calculation).
demo("rank.affinity")
reset()# Compare Rubisco proteins from three domains
datfile <- system.file("extdata/cpetc/rubisco.csv", package = "CHNOSZ")
fastafile <- system.file("extdata/protein/rubisco.fasta", package = "CHNOSZ")
dat <- read.csv(datfile)
aa <- read.fasta(fastafile)
groups <- sapply(c("A", "B", "E"), "==", dat$domain, simplify = FALSE)
names(groups) <- c("Archaea", "Bacteria", "Eukaryota")
ip <- add.protein(aa, as.residue = TRUE)
basis("QEC")
aout <- affinity(O2 = c(-74, -66, 100), H2O = c(-4, 4, 100), iprotein = ip)
arank <- rank.affinity(aout, groups = groups)
nspecies <- sapply(groups, sum)
names <- paste0(names(groups), " (", nspecies, ")")
diagram(arank, fill = "terrain", font = 2, names = names, format.names = FALSE)
title("Average affinity ranking of Rubisco proteins")
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