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\makeatletter
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%\VignetteIndexEntry{Hot-spring proteins in CHNOSZ}
%\VignetteEngine{knitr::knitr}

% so DOIs in bibliography show up as hyperlinks
\newcommand*{\doi}[1]{\href{https://doi.org/#1}{doi: #1}}

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\begin{document}
<<setup, include=FALSE, cache=FALSE>>=
library(knitr)
## set global chunk options
opts_chunk$set(fig.path='figure/hotspring-', cache.path='cache/hotspring-', fig.align='center', fig.show='hold', par=TRUE)
## set code/output width
options(width=85)
## set number of digits
options(digits=5)
## tune details of base graphics (http://yihui.name/knitr/hooks)
knit_hooks$set(par=function(before, options, envir){
if (before && options$fig.show!='none') par(mar=c(4,4,1,1),cex.lab=.95,cex.axis=.9,mgp=c(2,.7,0),tcl=-.3)
})
@

\title{Hot-spring proteins in CHNOSZ}

\author{Jeffrey M. Dick and Everett L. Shock}
\maketitle

\section{Introduction}

This document is intended to demonstrate the calculations described
in two recent papers \citep{DS11,DS13} dealing with the distribution
and abundances of proteins in ``Bison Pool'', a hot spring in Yellowstone
National Park. The calculations use metastable equilibrium to interrelate
the compositions of proteins (from metagenomic data) with environmental
conditions, particularly pH, temperature, and redox chemistry. This
document is focused on the details of the calculations and has little
in the way of introduction of concepts or interpretation and discussion;
please see the papers for more details.

There is no hidden code in this document; all code used to make the
figures is shown in the blocks, but much of the text output (particularly
in the figure-generating code) has been suppressed. The R code here
is based on the Supporting Information for the papers, with modifications.
In order to keep the code here as short and efficient as possible,
some aspects of the published figures including manual labeling and
higher resolution are not all reproduced; these changes are noted
where possible. Also, some shortcuts (e.g. using \texttt{xtabs()}
to create the BLAST frequency table, and \texttt{revisit()} to calculate
the $\Delta G_{tr}$) have been introduced here in order to streamline
the code.

Load CHNOSZ and the thermodynamic database. In order to reproduce
the calculations from the 2011 paper, we modify the methionine sidechain
group using old values of standard Gibbs energy and enthalpy from
\citep{DLH06}; these are inaccurate values that were updated by \citep{LD12}
and are available starting in CHNOSZ\_0.9-9 (the current values are
used further below).

<<libraryCHNOSZ>>=
library(CHNOSZ)
data(thermo)
mod.obigt("[Met]", G=-35245, H=-59310)
@

Some values that are shared among different calculations: measured
temperature ($^{\circ}$C) and pH. These are representative values
only; the actual values are not constant but vary due to water flow,
weather, animals, etc.

<<TpH>>=
bison.T <- c(93.3, 79.4, 67.5, 65.3, 57.1)
bison.pH <- c(7.350, 7.678, 7.933, 7.995, 8.257)
@

Now let's plot the measured temperature and pH in the hot spring.
Distances (in meters) of the sampling sites are measured from the
source of the hot spring. The \texttt{Tfun()} and \texttt{pHfun()}
are also used further below.

<<TpHplot, fig.width=6, fig.height=3>>=
distance <- c(0, 6, 11, 14, 22)
par(mfrow=c(1, 2), mar=c(4, 4, 3, 2))
xpoints <- seq(0, 22, length.out=128)
# T plot
plot(distance, bison.T, xlab="distance, m", ylab=axis.label("T"))
Tfun <- splinefun(distance, bison.T, method="mono")
lines(xpoints, Tfun(xpoints))

# pH plot
plot(distance, bison.pH, xlab="distance, m", ylab="pH")
pHfun <- splinefun(distance, bison.pH, method="mono")
lines(xpoints, pHfun(xpoints))
@

\href{https://doi.org/10.1371/journal.pone.0022782.g005}{DOI link}
to published figure (panels A and B). The length of \texttt{xpoints}
here, 128, is the resolution used for the figures in the 2011 paper
(defined in the \texttt{mkargs()} function of the Supporting Information).

\section{General setup}

Load the proteins. These are ``model proteins'', i.e. average amino
acid compositions of sequences classified according to their functional
annotation or by their phylum association, at each of the five sampling
sites located in the hot spring.

<<proteins>>=
# read the amino acid compositions
aa.annot <- read.csv(system.file("extdata/protein/DS11.csv", package="CHNOSZ"), as.is=TRUE)
aa.phyla <- read.csv(system.file("extdata/protein/DS13.csv", package="CHNOSZ"), as.is=TRUE)
@

Here are the site names for the sampling locations (also referred
to as sites 1\textendash 5).

<<sitename>>=
sites <- c("N", "S", "R", "Q", "P")
sitenames <- paste("bison", sites, sep="")
@

Here are the classifications according to functional annotation:

<<classes>>=
classes <- unique(aa.annot$protein)
classes
@

Here are names of phyla and colors and line types used for plotting
(colors based on Figure 2 of Wu and Eisen, 2008 \citep{WE08}, with
modifications):

<<names>>=
# the names of the phyla in alphabetical order (except Deinococcus-Thermus at end)
phyla.abc <- sort(unique(aa.phyla$organism))[c(1:7,9:11,8)]
# an abbreviation for Dein.-Thermus
phyla.abbrv <- phyla.abc
phyla.abbrv[[11]] <- "Dein.-Thermus"
phyla.cols <- c("#f48ba5", "#f2692f", "#cfdd2a",
  "#962272", "#87c540", "#66c3a2", "#12a64a", "#f58656",
  "#ee3237", "#25b7d5", "#3953a4")
phyla.lty <- c(1:6, 1:5)
phyla.abbrv
@

\section{Average oxidation state of carbon}

The average oxidation state of carbon ($\overline{Z}_{\mathrm{C}}$)
is calculated using
\begin{equation}
\overline{Z}_{\mathrm{C}}=\frac{Z-n_{\mathrm{H}}+2\left(n_{\mathrm{O}}+n_{\mathrm{S}}\right)+3n_{\mathrm{N}}}{n_{\mathrm{C}}}\,,\label{eq:ZC}
\end{equation}
where $n_{\mathrm{C}}$, $n_{\mathrm{H}}$, $n_{\mathrm{N}}$, $n_{\mathrm{O}}$
and $n_{\mathrm{S}}$ are the numbers of the indicated subscripted
elements in the chemical formula of a protein or other chemical species,
and $Z$ is the net charge of the chemical species.

<<ZCplot, fig.width=5, fig.height=5, out.width='.49\\textwidth'>>=
# 2011 plot
ylab <- expression(bar(italic(Z))[C])
plot(0, 0, xlim=c(-0.5, 5), ylim=c(-0.27, -0.11), xlab="location", xaxt="n", ylab=ylab)
axis(1, at=1:5)
col <- c("green", rep("black", 20))
lwd <- c(3, rep(1, 20))
clab <- c("hydrolase", "overall", "protease", "oxidoreductase", "transport", "membrane", "permease")
pf.annot <- protein.formula(aa.annot)
ZC.annot <- ZC(pf.annot)
for(i in 1:length(classes)) {
  lines(1:5, ZC.annot[(1:5)+5*(i-1)], col=col[i], lwd=lwd[i])
  if(classes[i] %in% clab) text(0.8, ZC.annot[1+5*(i-1)], classes[i], adj=1)
}
title(main="annotations")

# 2013 plot
pf.phyla <- protein.formula(aa.phyla)
ZC.phyla <- ZC(pf.phyla)
# set up plot
plot(0, 0, xlim=c(1, 5), ylim=c(-0.27, -0.11), xlab="location", ylab=ylab)
for(i in 1:length(phyla.abc)) {
  # which of the model proteins correspond to this phylum
  iphy <- which(aa.phyla$organism==phyla.abc[i])
  # the locations (of 1, 2, 3, 4, 5) where this phylum is found
  ilocs <- match(aa.phyla$protein[iphy], sitenames)
  # the plotting symbol: determined by alphabetical position of the phylum
  points(ilocs, ZC.phyla[iphy], pch=i-1, cex=1.2)
  # a line to connect same phyla occurring at adjacent sites
  inlocs <- rep(NA, 5)
  inlocs[ilocs] <- ilocs
  lines(inlocs, ZC.phyla[iphy][match(1:5, ilocs)])
}
legend("bottomright", pch=0:10, legend=phyla.abbrv, bg="white", cex=0.9)
title(main="major phyla")
@

DOI links for these plots as they appeared in the publications: \href{https://doi.org/10.1371/journal.pone.0022782.g004}{plot 1},
\href{https://doi.org/10.1371/journal.pone.0072395.g001}{plot 2}.
Compared to the papers, a different \emph{y}-axis scale is used here,
in order to have same scale on both plots; permease at lower $\overline{Z}_{\mathrm{C}}$
does not appear in plot 1 here.

\section{Relative stabilities of ``overall'' model proteins}

\subsection{Formation reactions of proteins from basis species}

Function to setup the basis species. The basis species consist of
$\mathrm{HCO_{3}^{-}}$, $\mathrm{H_{2}O}$, $\mathrm{NH_{3}}$, $\mathrm{HS^{-}}$,
$\mathrm{H_{2}}$ and $\mathrm{H^{+}}$ (all aqueous species except
for $\mathrm{H_{2}O}$ liquid).

<<setup.basis>>=
setup.basis <- function() {
  basis(c("HCO3-", "H2O", "NH3", "HS-", "H2", "H+"))
  basis(c("HCO3-", "NH3", "HS-", "H+"), c(-3, -4, -7, -7.933))
}
@

Set up the basis species and the species. Here, we add the proteins
using the previously read amino acid compositions (\texttt{aa.annot}),
and we save their index number (\texttt{ip.annot}) for use later.
For now, we load the species corresponding to the ``overall'' model
proteins (the first 5 in aa.annot).

<<overall>>=
setup.basis()
ip.annot <- add.protein(aa.annot)
species("overall", sitenames)
@

The first 6 columns there represent the stoichiometry of the reactions
to form the proteins from the basis species. The reactions can be
divided by the lengths (number of amino acid residues) of the proteins
to write per-residue formation reactions.

<<residue>>=
pl <- protein.length(ip.annot[1:5])
mysp <- species()
mysp[, 1:6]/pl
@

Note e.g. the higher coefficient on $\mathrm{H_{2}}$ for sites 1
and 2; increasing the activity of $\mathrm{H_{2}}$ (more reducing
conditions) has a relatively more favorable mass-action effect on
the formation of the proteins at the higher temperature sites.

\subsection{Chemical affinities along a chemical gradient}

Function to calculate $\log a_{\mathrm{H_{2}}}$ as a linear equation
in $T$. This was used to fit the spatial distribution of proteins
in the 2011 paper \citep{DS11} (also shown as Equation 2 in 2013
\citep{DS13}).
\begin{equation}
\log a_{\mathrm{H_{2_{\left(aq\right)}}}}=-11+3/40\times T\mathrm{\left(^{\circ}C\right)}\label{eq:logaH2}
\end{equation}

<<logaH2>>=
get.logaH2 <- function(T) -11 + T * 3/40
@

Calculate the residue-normalized chemical affinities of the formation
reactions of the overall model proteins. First set activities of the
proteins equal to unity (logarithm of activity equal to zero). Then
calculate affinities per mole of protein for the temperature, pH and
$\log a_{\mathrm{H_{2}}_{\left(aq\right)}}$ of each site. Use the
lengths of the model proteins to calculate the affinities per residue.

<<affinity>>=
species(1:5, 0)
a <- affinity(T=bison.T, pH=bison.pH, H2=get.logaH2(bison.T))
a.res <- t(as.data.frame(a$values))/pl
a.res
@

\href{https://doi.org/10.1371/journal.pone.0022782.t005}{DOI link}
to published table.

The affinities are expressed as dimensionless values, i.e. $\boldsymbol{A}/2.303RT$
where $\boldsymbol{A}$, $R$ and $T$ stand for chemical affinity,
gas constant, and temperature in Kelvin. The affinities are all negative,
but show a progression from higher for protein (row) 1 at the conditions
of sites (columns) 1 and 2 to higher for protein (row) 4 at the conditions
of sites (columns) 3 to 5.

<<affinitymax>>=
apply(a.res, 2, which.max)
@

To go from residue-normalized affinities to the actual progression
of relative stabilities of the proteins (i.e. size-adjusted affinities),
we subtract the logarithm of the protein length from the per-residue
affinities (also see description following Eq. 19 in Ref. \citep{DS11}).

<<affinityadj>>=
a.res <- a.res - log10(pl)
apply(a.res, 2, which.max)
@

This 1-2-4 progression of stabilities is visualized below; for some
groups of proteins, an update to the thermodynamic properties of the
methionine sidechain causes proteins from site 3 also to become stable.

\subsection{Relative stabilities along a chemical gradient}

Set the temperature limits (\texttt{Tlim}) over which to perform the
calculations.

<<Tlim>>=
Tlim <- c(50, 100)
@

Make two plots here. (1) The metastable equilibrium predominance diagram
of the overall model proteins as a function of temperature and logarithm
of activity of hydrogen. The stability fields for the proteins from
the higher temperatures are at higher activities of hydrogen in the
diagram. The dotted line passes through the stability fields of the
model proteins at approximately the actual environmental temperatures.
(2) Combine the gradients of temperature, pH and hydrogen activity
to calculate the metastable equilibrium activities of the proteins.
The total activity of residues is set by reference activities of the
proteins equal to $10^{-3}$. In order to label the $x$-axis ``distance'',
modify a couple of entries in the list returned by \texttt{affinity()}
(\texttt{vars}, \texttt{vals}); otherwise the $x$-axis would represent
temperature (the first variable in the argument list to \texttt{affinity()}).

<<TlogaH2plot, fig.width=6, fig.height=3, message=FALSE, results='hide'>>=
par(mfrow=c(1, 2))
# first plot
a <- affinity(T=Tlim, H2=c(-7, -4))
diagram(a, fill=NULL, names=1:5, normalize=TRUE)
lines(Tlim, get.logaH2(Tlim), lty=3)
# second plot
species(1:5, -3)
xT <- Tfun(xpoints)
xpH <- pHfun(xpoints)
xH2 <- get.logaH2(xT)
a <- affinity(T=xT, pH=xpH, H2=xH2)
a$vars[1] <- "distance, m"
a$vals[[1]] <- xpoints
e <- equilibrate(a, normalize=TRUE)
diagram(e, legend.x=NULL)
legend("bottom", lty=1:5, legend=1:5, bty="n", cex=0.6)
@

\href{https://doi.org/10.1371/journal.pone.0022782.g005}{DOI link}
to published figure (panels B and F).

\clearpage

Plot the equilibrium degrees of formation as a function of distance
for different classes of proteins. Calculate the affinities for all
of the proteins. For each group of three, make strip charts using
the \texttt{strip()} function in CHNOSZ. The heights of the bars represent
the relative abundances of the model proteins. The five steps of the
color code go from site 1 (red) to site 5 (blue).

<<stripplot, fig.width=6, fig.height=3.5, message=FALSE, results='hide'>>=
loadclass <- function(class) {
  species(delete=TRUE)
  species(rep(class, each=5), rep(sitenames, length(class)))
}
xclasses <- c("overall", "transferase", "transport", "synthetase", "membrane", "permease")
loadclass(xclasses)
a <- affinity(T=xT, pH=xpH, H2=xH2)
a$vars[1] <- "distance, m"
a$vals[[1]] <- xpoints
col <- c("red", "orange", "yellow", "green", "blue")
par(mfrow=c(1, 2), mar=c(4, 4, 1, 1))
for(i in 1:2) {
  ispecies <- lapply((1:3)+(i-1)*3, function(x) {1:5+(x-1)*5} )
  names(ispecies) <- xclasses[(1:3)+(i-1)*3]
  strip(a = a, ispecies = ispecies, col = col, xticks = distance, cex.names = 1)
}
@

\href{https://doi.org/10.1371/journal.pone.0022782.g007}{DOI link}
to published figure.

\clearpage

\section{Comparing old and new methionine sidechain parameters}

Make some $T-\log a_{\mathrm{H_{2}}}$ metastable equilibrium predominance
diagrams using different values for the thermodynamic properties of
the methionine sidechain group {[}Met{]}. The first row shows the
results using the old values (defined on page 1); for the second row
(j=2), we reset the database to use the current (revised) parameters.

<<methionine, fig.width=6, fig.height=4, message=FALSE, results='hide', cache=TRUE>>=
par(mfrow=c(2, 3))
for(j in 1:2) {
  # use old [Met] for first row and new [Met] for second row
  if(j==2) {
    data(thermo)
    ip.annot <- add.protein(aa.annot)
  }
  # setup basis species and proteins
  setup.basis()
  # make the plots
  for(annot in c("overall", "transferase", "synthase")) {
    ip <- ip.annot[aa.annot$protein==annot]
    a <- affinity(T=c(50, 100), H2=c(-7, -4), iprotein=ip)
    diagram(a, fill=NULL, names=1:5, normalize=TRUE)
    # add logaH2-T line
    lines(par("usr")[1:2], get.logaH2(par("usr")[1:2]), lty=3)
    # add a title
    title(main=annot)
  }
}
@

\href{https://doi.org/10.1371/journal.pone.0072395.g002}{DOI link}
to published figure, which was made with higher resolution (256) and
manual placement of some labels.

\section{Relative abundance calculations}

Function to return the fractional abundances based on BLAST counts,
stored in the \texttt{ref} column of \texttt{aa.phyla}.

<<alpha.blast>>=
alpha.blast <- function() {
  out <- xtabs(ref ~ protein + organism, aa.phyla)
  # put it in correct order, then turn counts into fractions
  out <- out[c(1,5:2), c(1:7,9:11,8)]
  out <- out/rowSums(out)
  return(out)
}
@

Function to calculate metastable equilibrium degrees of formation
of proteins (normalized to residues) as a function of $\log a_{\mathrm{H_{2}}}$
for a specified location. Note: in the call to \texttt{affinity()},
increase the resolution from 101 to 1001 to reproduce the calculations
in paper.

<<alpha.equil>>=
alpha.equil <- function(i=1) {
  # order the names and counts to go with the alphabetical phylum list
  iloc <- which(aa.phyla$protein==sitenames[i])
  iloc <- iloc[order(match(aa.phyla$organism[iloc], phyla.abc))]
  # set up basis species, with pH specific for this location
  setup.basis()
  basis("pH", bison.pH[i])
  # calculate metastable equilibrium activities of the residues
  a <- affinity(H2=c(-11, -1, 101), T=bison.T[i], iprotein=ip.phyla[iloc])
  e <- equilibrate(a, loga.balance=0, as.residue=TRUE)
  # remove the logarithms to get relative abundances
  a.residue <- 10^sapply(e$loga.equil, c)
  colnames(a.residue) <- aa.phyla$organism[iloc]
  # the BLAST profile
  a.blast <- alpha.blast()
  # calculate Gibbs energy of transformation (DGtr) and find optimal logaH2
  iblast <- match(colnames(a.residue), colnames(a.blast))
  r <- revisit(e, "DGtr", log10(a.blast[i, iblast]), plot.it=FALSE)
  # return the calculated activities, logaH2 range, DGtr values, and optimal logaH2
  return(list(alpha=a.residue, H2vals=a$vals[[1]], DGtr=r$H, logaH2.opt=r$xopt))
}
@

Now we're ready to make a plot! We start by adding the proteins with
amino acid composition that were read from the file. Then plot the
degrees of formation as a function of $\log a_{\mathrm{H_{2}}}$ at
sites 1, 3 and 5, but record the results (including calculated relative
abundances and optimal values of $\log a_{\mathrm{H_{2}}}$) at all
5 sites.

<<alphaplot, fig.width=8, fig.height=6, tidy=FALSE, message=FALSE, results='hide', cache=TRUE>>=
ip.phyla <- add.protein(aa.phyla)
layout(matrix(1:6, ncol=3), heights=c(2, 1))
equil.results <- list()
for(i in 1:5) {
  # get the equilibrium degrees of formation and the optimal logaH2
  ae <- alpha.equil(i)
  equil.results[[i]] <- ae
  if(i %in% c(1, 3, 5)) {
    iphy <- match(colnames(ae$alpha), phyla.abc)
    # top row: equilibrium degrees of formation
    thermo.plot.new(xlim=range(ae$H2vals), ylim=c(0, 0.5), xlab=axis.label("H2"),
      ylab=expression(alpha[equil]), yline=2, cex.axis=1, mgp=c(1.8, 0.3, 0))
    for(j in 1:ncol(ae$alpha)) {
      lines(ae$H2vals, ae$alpha[, j], lty=phyla.lty[iphy[j]])
      ix <- seq(1, length(ae$H2vals), length.out=11)
      ix <- head(tail(ix, -1), -1)
      points(ae$H2vals[ix], ae$alpha[, j][ix], pch=iphy[j]-1)
    } 
    title(main=paste("site", i))
    legend("topleft", pch=iphy-1, lty=phyla.lty[iphy], legend=phyla.abbrv[iphy], bg="white")
    # bottom row: Gibbs energy of transformation and position of minimum
    thermo.plot.new(xlim=range(ae$H2vals), ylim=c(0, 1/log(10)), xlab=axis.label("H2"),
      ylab=expr.property("DGtr/2.303RT"), yline=2, cex.axis=1, mgp=c(1.8, 0.3, 0))
    lines(ae$H2vals, ae$DGtr)
    abline(v=ae$logaH2.opt, lty=2)
    abline(v=get.logaH2(bison.T[i]), lty=3, lwd=1.5)
    if(i==1) legend("bottomleft", lty=c(3, 2), lwd=c(1.5, 1), bg="white",
      legend=c("Equation 2", "optimal"))
  }
}
@

\href{https://doi.org/10.1371/journal.pone.0072395.g003}{DOI link}
to published version of the figure.

\clearpage

\section{Activity of hydrogen comparison}

Let's compare the computed activities of hydrogen with various redox
indicators measured in the field.

\subsection{Conversion of field measurements}

\paragraph{ORP}

Oxidation-reduction potential (ORP), measured in the field using a
portable probe and pH/voltmeter, can be converted to Eh by adding
the potential of the reference electrode, in this case silver-silver
chloride (Ag/AgCl) in saturated KCl. As an approximation, the following
equation from Ref. \citep{BPJ85} for Ag/AgCl (1M KCl) is used, with
temperature in $^{\circ}$C and potential in volts.

<<E.AgAgCl>>=
E.AgAgCl <- function(T) {
  0.23737 - 5.3783e-4 * T - 2.3728e-6 * T^2 - 2.2671e-9 * (T+273)
}
@

Data from Bison Pool and another hot spring shown in Fig. 9 of Ref.
\citep{DS11} are both included, but for simplicity here they are
lumped together. The ORP values have units of mV.

<<meters>>=
T.ORP <- c(93.9, 87.7, 75.7, 70.1, 66.4, 66.2)
pH.ORP <- c(8.28, 8.31, 7.82, 7.96, 8.76, 8.06)
ORP <- c(-258, -227, -55, -58, -98, -41)
@

Convert ORP to effective values of $\log a_{\mathrm{H_{2}}_{\left(aq\right)}}$.
First convert to Eh (in volts). Then convert Eh to pe. Then combine
Eh and pH with the law of mass action for
\[
2e^{-}+2\mathrm{H^{+}}\rightleftharpoons\mathrm{H_{2}}_{\left(aq\right)}
\]
to calculate $\log a_{\mathrm{H_{2}}_{\left(aq\right)}}$. The ``law
of mass action'' is the equality between the equilibrium constant
($K$) and the activity product ($Q$) of the species in the reaction.

<<ORP2Eh, message=FALSE, results='hide'>>=
Eh <- ORP/1000 + E.AgAgCl(T.ORP)
pe <- convert(Eh, "pe", T=convert(T.ORP, "K"))
logK.ORP <- subcrt(c("e-", "H+", "H2"), c(-2, -2, 1), T=T.ORP)$out$logK
logaH2.ORP <- logK.ORP - 2*pe - 2*pH.ORP
@

\paragraph{Sulfide/Sulfate}

For sulfide/sulfate, assign activities that are equal to concentrations
(in molal units) measured in the field season of 2005, and use the
law of mass action for
\[
\mathrm{HS^{-}}+4\mathrm{H_{2}O}\rightleftharpoons\mathrm{SO_{4}}^{-2}+\mathrm{H^{+}}+4\mathrm{H_{2}}_{\left(aq\right)}
\]
to calculate an effective activity of hydrogen. Sulfide was determined
spectrophotometrically at the hot spring, and sulfate was determined
using ion chromatography on water samples returned from the field.

<<sulfur, message=FALSE, results='hide'>>=
loga.HS <- log10(c(4.77e-6, 2.03e-6, 3.12e-7, 4.68e-7, 2.18e-7))
loga.SO4 <- log10(c(2.10e-4, 2.03e-4, 1.98e-4, 2.01e-4, 1.89e-4))
logK.S <- subcrt(c("HS-", "H2O", "SO4-2", "H+", "H2"), c(-1, -4, 1, 1, 4), T=bison.T)$out$logK
logaH2.S <- (logK.S + bison.pH - loga.SO4 + loga.HS) / 4
@

\paragraph{Dissolved Oxygen}

Calculate the effective activity of hydrogen corresponding to the
dissolved oxygen concentration using the law of mass action for
\[
0.5\mathrm{O_{2}}_{\left(aq\right)}+\mathrm{H_{2}}_{\left(aq\right)}\rightleftharpoons\mathrm{H_{2}O}\,.
\]
Convert the dissolved oxygen concentrations (mg/L) to molarities (mol/L)
to set the activity of $\mathrm{O_{2}}_{\left(aq\right)}$.

<<oxygen, message=FALSE, results='hide'>>=
DO <- c(0.173, 0.776, 0.9, 1.6, 2.8)
logaO2 <- log10(DO/1000/32)
logK <- subcrt(c("O2", "H2", "H2O"), c(-0.5, -1, 1), T=bison.T)$out$logK
logaH2.O <- 0 - 0.5*logaO2 - logK
@

\paragraph{Plot it!}

The points in the left plot represent field-based indicators for redox
potential, while the points in the right plot are the optimal values
of $\log a_{\mathrm{H_{2}}}$ for the microbial phylum abundance model.
The various redox indicators are not in equilibrium with each other
(the $\log a_{\mathrm{H_{2}}}$ values are different), but they all
show an increase in apparent $\log a_{\mathrm{H_{2}}}$ with temperature.
The dotted line in both plots portrays Equation (\ref{eq:logaH2}).

<<logaH2plot, fig.width=4, fig.height=4, out.width='.45\\textwidth', cache=TRUE>>=
# 2011 plot
xlab <- axis.label("T")
ylab <- axis.label("H2")
plot(Tlim, get.logaH2(Tlim), xlim=Tlim, ylim=c(-45,0),
  xlab=xlab, ylab=ylab, type="l", lty=3)
points(T.ORP, logaH2.ORP, pch=15)
lines(T.ORP, logaH2.ORP, lty=2)
points(bison.T, logaH2.O, pch=16)
lines(bison.T, logaH2.O, lty=2)
points(bison.T, logaH2.S, pch=17)
lines(bison.T, logaH2.S, lty=2)
llab <- c("Equation 2", "ORP", "dissolved oxygen", "sulfate/sulfide")
text(c(65, 80, 80, 74), c(-4, -25, -40, -11), llab)

# 2013 plot
plot(Tlim, get.logaH2(Tlim), xlim=Tlim, ylim=c(-11,-2),
  xlab=xlab, ylab=ylab, type="l", lty=3)
lines(bison.T, sapply(equil.results, "[", "logaH2.opt"), lty=2)
points(bison.T, sapply(equil.results, "[", "logaH2.opt"), pch=21, bg="white")
text(90, -5.3, "Equation 2")
text(66, -9, "optimal parameterization\nfor observed\nphylum abundances", adj=0)
@

DOI links to published versions: \href{https://doi.org/10.1371/journal.pone.0022782.g009}{plot 1},
\href{https://doi.org/10.1371/journal.pone.0072395.g004}{plot 2}.

\section{Relative abundance comparison}

Let's make some plots comparing the relative abundances calculated
above (stored in \texttt{equil.results}) with the abundances from
BLAST counts. We'll also store the results of the optimized models
in \texttt{equil.opt}.

<<alphaplot5, fig.width=9, fig.height=6, out.width='.88\\textwidth', cache=TRUE>>=
layout(matrix(c(1, 2, 3, 4, 5, 6), nrow=2, byrow=TRUE), widths=c(2, 2, 2))
par(mar=c(2.5, 0, 2.5, 0))
plot.new()
legend("topright", pch=0:11, legend=phyla.abbrv, bty="n", cex=1.5)
lim <- c(-6, -0.5)
equil.opt <- a.blast <- alpha.blast()
for(iloc in 1:5) {
  a.equil <- equil.results[[iloc]]
  iopt <- match(a.equil$logaH2.opt, a.equil$H2vals)
  ae.opt <- a.equil$alpha[iopt, ]
  # which are these phyla in the alphabetical list of phyla
  iphy <- match(names(ae.opt), phyla.abc)
  equil.opt[iloc, iphy] <- ae.opt
  mar <- c(2.5, 4.0, 2.5, 1)
  thermo.plot.new(xlab=expression(log[2]*alpha[obs]), ylab=expression(log[2]*alpha[equil]),
    xlim=lim, ylim=lim, mar=mar, cex=1, yline=1.5)
  # add points and 1:1 line
  points(log2(a.blast[iloc, iphy]), log2(ae.opt), pch=iphy-1)
  lines(lim, lim, lty=2)
  title(main=paste("site", iloc))
  # within-plot legend: DGtr
  DGexpr <- as.expression(quote(Delta*italic(G[tr])/italic(RT) == phantom()))
  DGval <- format(round(2.303*a.equil$DGtr[iopt], 3), nsmall=3)
  legend("bottomright", bty="n", legend=c(DGexpr, DGval))
}
@

\href{https://doi.org/10.1371/journal.pone.0072395.g005}{DOI link}
to published figure.

\clearpage

Finally, a comparison in the form of two barplots.

<<barchart, fig.width=6, fig.height=3>>=
par(mar=c(4, 4, 3, 0), mgp=c(1.8, 0.7, 0))
par(mfrow=c(1, 3), cex=1)
# make the blast plot
ab <- alpha.blast()
rownames(ab) <- 1:5
barplot(t(ab), col=phyla.cols, ylab=NULL, xlab="site", axes=TRUE, cex.axis=0.8, cex.names=0.8, las=1)
mtext(expression(alpha[obs]), 2, 2, cex=1.1*par("cex"))
title(main="BLAST profile", cex.main=0.8)
# make the equilibrium plot
rownames(equil.opt) <- 1:5
barplot(t(equil.opt), col=phyla.cols, ylab=NULL, xlab="site", axes=TRUE, cex.axis=0.8,
  cex.names=0.8, las=1)
mtext(expression(alpha[equil]), 2, 2, cex=1.1*par("cex"))
title(main="metastable\nequilibrium", cex.main=0.8)
# add legend
par(mar=c(4, 1, 3, 0))
plot.new()
legend("bottomleft", legend=rev(phyla.abbrv), fill=rev(phyla.cols), bty="n", cex=0.7)
@

\href{https://doi.org/10.1371/journal.pone.0072395.g006}{DOI link}
to published figure.

\section{Document history}
\begin{itemize}
\item 2011-08-23 Initial version (CHNOSZ\_0.9-7)
\item 2012-01-07 Use \texttt{add.obigt()} for superseded properties of methionine
sidechain group (changed to \texttt{mod.obigt()} on 2016-12-21).
\item 2014-02-01 Include results from 2013 paper and change VignetteEngine
to knitr.
\end{itemize}
\bibliographystyle{unsrtnat}
\bibliography{vig}

\end{document}
