[CHNOSZ-commits] r318 - in pkg/CHNOSZ: . R demo inst man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sun May 6 08:41:32 CEST 2018
Author: jedick
Date: 2018-05-06 08:41:29 +0200 (Sun, 06 May 2018)
New Revision: 318
Added:
pkg/CHNOSZ/demo/bison.R
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/R/examples.R
pkg/CHNOSZ/demo/00Index
pkg/CHNOSZ/inst/NEWS
pkg/CHNOSZ/man/examples.Rd
Log:
add demo/bison.R
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2018-04-29 08:08:08 UTC (rev 317)
+++ pkg/CHNOSZ/DESCRIPTION 2018-05-06 06:41:29 UTC (rev 318)
@@ -1,6 +1,6 @@
-Date: 2018-04-29
+Date: 2018-05-06
Package: CHNOSZ
-Version: 1.1.3-25
+Version: 1.1.3-26
Title: Thermodynamic Calculations and Diagrams for Geochemistry
Authors at R: c(
person("Jeffrey", "Dick", , "j3ffdick at gmail.com", role = c("aut", "cre"),
@@ -27,7 +27,7 @@
(Sverjensky et al., 2014 <doi:10.1016/j.gca.2013.12.019>) and estimates of parameters in the
extended Debye-Hückel equation (Manning et al., 2013 <doi:10.2138/rmg.2013.75.5>)
to calculate standard-state properties and activity coefficients for given ionic strength at high
- pressure (to 60 kb). Functions are provided to calculate standard-state properties of species and
+ pressure (to 6 GPa). Functions are provided to calculate standard-state properties of species and
reactions, define the basis species of a chemical system, automatically balance reactions, calculate
the chemical affinities of formation reactions for selected species, calculate the equilibrium
activities of those species, and plot the results on chemical activity diagrams.
Modified: pkg/CHNOSZ/R/examples.R
===================================================================
--- pkg/CHNOSZ/R/examples.R 2018-04-29 08:08:08 UTC (rev 317)
+++ pkg/CHNOSZ/R/examples.R 2018-05-06 06:41:29 UTC (rev 318)
@@ -29,7 +29,7 @@
demos <- function(which=c("sources", "protein.equil", "affinity", "NaCl", "density",
"ORP", "revisit", "findit", "ionize", "buffer", "protbuff", "yeastgfp", "mosaic",
"copper", "solubility", "wjd", "bugstab", "Shh", "activity_ratios",
- "adenine", "DEW", "lambda", "TCA", "go-IU"), save.png=FALSE) {
+ "adenine", "DEW", "lambda", "TCA", "go-IU", "bison"), save.png=FALSE) {
# run one or more demos from CHNOSZ with ask=FALSE, and return the value of the last one
for(i in 1:length(which)) {
# say something so the user sees where we are
Modified: pkg/CHNOSZ/demo/00Index
===================================================================
--- pkg/CHNOSZ/demo/00Index 2018-04-29 08:08:08 UTC (rev 317)
+++ pkg/CHNOSZ/demo/00Index 2018-05-06 06:41:29 UTC (rev 318)
@@ -24,3 +24,4 @@
TCA Standard Gibbs energies of steps of the citric acid cycle
go-IU Diagrams using thermodynamic data in the SUPCRTBL compilation
carboxylase Rank abundance distribution for RuBisCO and acetyl-CoA carboxylase
+bison Average oxidation state of carbon in proteins for phyla at Bison Pool
Added: pkg/CHNOSZ/demo/bison.R
===================================================================
--- pkg/CHNOSZ/demo/bison.R (rev 0)
+++ pkg/CHNOSZ/demo/bison.R 2018-05-06 06:41:29 UTC (rev 318)
@@ -0,0 +1,44 @@
+# CHNOSZ/demo/bison.R
+# average oxidation state of carbon (ZC) of metagenome-derived
+# proteins in different microbial phyla at Bison Pool 20171217
+
+par(mar=c(3.5, 4, 2.5, 2), las=1, mgp=c(2.2, 0.8, 0))
+# 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)
+sites <- c("N", "S", "R", "Q", "P")
+sitenames <- paste("bison", sites, sep="")
+# the names of the phyla in alphabetical order (except Deinococcus-Thermus at end)
+phyla.abc <- sort(unique(aa.phyla$organism))[c(1:7,9:11,8)]
+# an abbreviation for Dein.-Thermus
+phyla.abbrv <- phyla.abc
+phyla.abbrv[[11]] <- "Dein.-Thermus"
+phyla.cols <- c("#f48ba5", "#f2692f", "#cfdd2a",
+ "#962272", "#87c540", "#66c3a2", "#12a64a", "#f58656",
+ "#ee3237", "#25b7d5", "#3953a4")
+# set Chlorobi color to NA because no line is needed (it's identifed only at one location)
+phyla.cols[4] <- NA
+# chemical formula and ZC of proteins
+pf.phyla <- protein.formula(aa.phyla)
+ZC.phyla <- ZC(pf.phyla)
+# set up plot
+plot(0, 0, xlim=c(1, 5), ylim=c(-0.23, -0.14), xlab="distance from source, m", ylab=NA, xaxt="n")
+distance <- c(0, 6, 11, 14, 22)
+axis(1, at=1:5, labels=distance)
+mtext(axis.label("ZC"), side=2, line=3, las=0)
+for(i in 1:length(phyla.abc)) {
+ # skip Euryarchaeota because it occurs at one location, on top of Dein.-Thermus and Firmicutes
+ if(phyla.abc[i]=="Euryarchaeota") next
+ # which of the model proteins correspond to this phylum
+ iphy <- which(aa.phyla$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)
+ # lines to connect the phyla
+ lines(ilocs, ZC.phyla[iphy], type="c", col=phyla.cols[i], lwd=2)
+}
+text(c(4.75, 2.0, 4.0, 4.0, 4.0, 2.0, 3.0, NA, 2.9, 1.3, 3.0),
+ c(-0.146, -0.224, -0.161, -0.184, -0.145, -0.201, -0.144, NA, -0.176, -0.158, -0.192),
+ phyla.abbrv, cex=0.9)
+title(main="Bison Pool hot spring, Yellowstone National Park")
Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS 2018-04-29 08:08:08 UTC (rev 317)
+++ pkg/CHNOSZ/inst/NEWS 2018-05-06 06:41:29 UTC (rev 318)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.1.3-25 (2018-04-29)
+CHANGES IN CHNOSZ 1.1.3-26 (2018-05-06)
---------------------------------------
THERMODYNAMIC DATA
@@ -81,6 +81,8 @@
plot saturation lines for minerals (where their affinity equals
zero).
+- Add demo/bison.R (average oxidation state of carbon of metagenome-
+ derived proteins in different microbial phyla at Bison Pool)
CHANGES IN CHNOSZ 1.1.3 (2017-11-13)
------------------------------------
Modified: pkg/CHNOSZ/man/examples.Rd
===================================================================
--- pkg/CHNOSZ/man/examples.Rd 2018-04-29 08:08:08 UTC (rev 317)
+++ pkg/CHNOSZ/man/examples.Rd 2018-05-06 06:41:29 UTC (rev 318)
@@ -17,7 +17,7 @@
"density", "ORP", "revisit", "findit", "ionize", "buffer",
"protbuff", "yeastgfp", "mosaic", "copper", "solubility",
"wjd", "bugstab", "Shh", "activity_ratios", "adenine",
- "DEW", "lambda", "TCA", "go-IU"),
+ "DEW", "lambda", "TCA", "go-IU", "bison"),
save.png=FALSE)
}
@@ -57,6 +57,7 @@
\code{TCA} \tab * Standard Gibbs energies of the tricarboxylic (citric) acid cycle (Canovas and Shock, 2016) \cr
\code{go-IU} \tab * Diagrams using thermodynamic data in the SUPCRTBL compilation (Zimmer et al., 2016) \cr
\code{carboxylase} \tab * Rank abundance distribution for RuBisCO and acetyl-CoA carboxylase \cr
+ \code{bison} \tab Average oxidation state of carbon in proteins for phyla at Bison Pool (Dick and Shock, 2013) \cr
}
For either function, if \code{save.png} is TRUE, the plots are saved in \code{\link{png}} files whose names begin with the names of the help topics or demos.
@@ -94,6 +95,8 @@
Dick, J. M. and Shock, E. L. (2011) Calculation of the relative chemical stabilities of proteins as a function of temperature and redox chemistry in a hot spring. \emph{PLoS ONE} \bold{6}, e22782. \url{https://doi.org/10.1371/journal.pone.0022782}
+Dick, J. M. and Shock, E. L. (2013) A metastable equilibrium model for the relative abundance of microbial phyla in a hot spring. \emph{PLoS ONE} \bold{8}, e72395. \url{https://doi.org/10.1371/journal.pone.0072395}
+
Dick, J. M. (2015) Chemical integration of proteins in signaling and development. \emph{bioRxiv}. \url{https://doi.org/10.1101/015826}
Dick, J. M. (2016) Proteomic indicators of oxidation and hydration state in colorectal cancer. \emph{PeerJ} \bold{4}:e2238. \url{https://doi.org/10.7717/peerj.2238}
More information about the CHNOSZ-commits
mailing list