rank.affinity: Normalized Sums of Ranks of Chemical Affinities

Description

Affinity ranking for groups of species.

Usage

rank.affinity(aout, groups)

Value

The normalized sum of ranks 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 show the groups with the highest normalized sum of ranks.

Arguments

aout: list, output of affinity
groups: named list of indices (integer or numeric) for species in each group

Details

The following calculations are applied to each set of conditions (i.e., grid point if affinity was called with two variables). The ranks of affinities for all species are first computed. Then, the ranks for the species in each group are summed and divided by the number of species in that group (this is the normalization step).

Examples

Run this code

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")