Author: jedick
Date: 2019-01-22 09:56:26 +0100 (Tue, 22 Jan 2019)
New Revision: 362
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/demo/DEW.R
pkg/CHNOSZ/demo/Shh.R
pkg/CHNOSZ/demo/TCA.R
pkg/CHNOSZ/demo/activity_ratios.R
pkg/CHNOSZ/demo/adenine.R
pkg/CHNOSZ/demo/bison.R
pkg/CHNOSZ/demo/go-IU.R
pkg/CHNOSZ/demo/gold.R
pkg/CHNOSZ/demo/lambda.R
pkg/CHNOSZ/demo/solubility.R
pkg/CHNOSZ/demo/yeastgfp.R
Log:
demos: clean up par() settings
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2019-01-21 15:40:26 UTC (rev 361)
+++ pkg/CHNOSZ/DESCRIPTION 2019-01-22 08:56:26 UTC (rev 362)
@@ -1,6 +1,6 @@
-Date: 2019-01-21
+Date: 2019-01-22
Package: CHNOSZ
-Version: 1.1.3-69
+Version: 1.1.3-70
Title: Thermodynamic Calculations and Diagrams for Geo(bio)chemistry
Authors at R: c(
person("Jeffrey", "Dick", , "j3ffdick at gmail.com", role = c("aut", "cre"),
Modified: pkg/CHNOSZ/demo/DEW.R
===================================================================
--- pkg/CHNOSZ/demo/DEW.R 2019-01-21 15:40:26 UTC (rev 361)
+++ pkg/CHNOSZ/demo/DEW.R 2019-01-22 08:56:26 UTC (rev 362)
@@ -1,7 +1,7 @@
# demo for the Deep Earth Water (DEW) model in CHNOSZ 20170927
# set up subplots
-par(mfrow = c(2, 2), mar=c(3.0, 3.5, 2.5, 1.0), mgp=c(1.7, 0.3, 0), las=1, tcl=0.3, xaxs="i", yaxs="i")
+opar <- par(mfrow = c(2, 2), mar=c(3.0, 3.5, 2.5, 1.0), mgp=c(1.7, 0.3, 0), las=1, tcl=0.3, xaxs="i", yaxs="i")
# activate DEW model
oldwat <- water("DEW")
@@ -213,3 +213,5 @@
data(OBIGT)
water(oldwat)
###########
+
+par(opar)
Modified: pkg/CHNOSZ/demo/Shh.R
===================================================================
--- pkg/CHNOSZ/demo/Shh.R 2019-01-21 15:40:26 UTC (rev 361)
+++ pkg/CHNOSZ/demo/Shh.R 2019-01-22 08:56:26 UTC (rev 362)
@@ -45,6 +45,7 @@
ylab <- expression(bold(A)/2.303*italic(RT)*" vs Shh")
xlab <- expression(log*italic(a)[H[2]][O])
# set up normal plot, or plot with interpretive drawings
+opar <- par(no.readonly = TRUE)
if(interp) {
if(pdf) pdf("tfactor_interp.pdf", width=6, height=6)
plot.new()
@@ -194,4 +195,5 @@
mtext(expression(log*italic(f)[O[2]]), line=2)
}
# all done!
+par(opar)
if(pdf) dev.off()
Modified: pkg/CHNOSZ/demo/TCA.R
===================================================================
--- pkg/CHNOSZ/demo/TCA.R 2019-01-21 15:40:26 UTC (rev 361)
+++ pkg/CHNOSZ/demo/TCA.R 2019-01-22 08:56:26 UTC (rev 362)
@@ -69,7 +69,7 @@
substitute(3*co2 + 4*nred + 2*hplus + atp + h2 * " ", sublist))
)
# set up plot
-par(mfrow=c(3, 3))
+opar <- par(mfrow=c(3, 3))
ylims <- list(
c(-10, 45), c(1, 6), c(-2.5, 7.5),
c(-35, 5), c(-9, 5), c(5, 28),
@@ -92,6 +92,7 @@
else mtitle(as.expression(rtitle[[i]]), line=0.4, cex=0.8)
}
# make an overall title
-opar <- par(xpd=NA)
+par(xpd=NA)
text(-70, 284, "Citric Acid Cycle, after Canovas and Shock, 2016", font=2, cex=1.5)
+par(xpd=FALSE)
par(opar)
Modified: pkg/CHNOSZ/demo/activity_ratios.R
===================================================================
--- pkg/CHNOSZ/demo/activity_ratios.R 2019-01-21 15:40:26 UTC (rev 361)
+++ pkg/CHNOSZ/demo/activity_ratios.R 2019-01-22 08:56:26 UTC (rev 362)
@@ -2,7 +2,7 @@
## These are made with pH = 0 (activity of H+ = 1), so (activity of the ion) is equal to
## (activity of the ion) / [(activity of H+) ^ (charge of the ion)]
-par(mfrow = c(2, 2))
+opar <- par(mfrow = c(2, 2))
res <- 200
fill <- "terrain"
@@ -62,3 +62,5 @@
diagram(a, add = TRUE, col = "blue", col.names = "blue")
title(main = syslab(c("CaO", "Al2O3", "MgO", "SiO2", "H2O")))
legend("topright", describe.property(c("T", "P"), c(300, 500)), bty = "n")
+
+par(opar)
Modified: pkg/CHNOSZ/demo/adenine.R
===================================================================
--- pkg/CHNOSZ/demo/adenine.R 2019-01-21 15:40:26 UTC (rev 361)
+++ pkg/CHNOSZ/demo/adenine.R 2019-01-22 08:56:26 UTC (rev 362)
@@ -39,6 +39,7 @@
TK <- seq(275, 425)
P <- water("Psat", TK)$Psat
# set up plots
+opar <- par(no.readonly = TRUE)
layout(matrix(1:3), heights=c(1, 8, 8))
# title at top
par(mar=c(0, 0, 0, 0), cex=1)
@@ -116,3 +117,5 @@
)
# reset database and computational settings
data(thermo)
+
+par(opar)
Modified: pkg/CHNOSZ/demo/bison.R
===================================================================
--- pkg/CHNOSZ/demo/bison.R 2019-01-21 15:40:26 UTC (rev 361)
+++ pkg/CHNOSZ/demo/bison.R 2019-01-22 08:56:26 UTC (rev 362)
@@ -2,7 +2,8 @@
# 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))
+# set default xaxs, yaxs, and tcl here becuase they are affected by previous demos
+par(mar=c(3.5, 4, 2.5, 2), las=1, mgp=c(2.2, 0.8, 0), xaxs="r", yaxs="r", tcl=-0.5)
# 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)
Modified: pkg/CHNOSZ/demo/go-IU.R
===================================================================
--- pkg/CHNOSZ/demo/go-IU.R 2019-01-21 15:40:26 UTC (rev 361)
+++ pkg/CHNOSZ/demo/go-IU.R 2019-01-22 08:56:26 UTC (rev 362)
@@ -3,7 +3,7 @@
# (BL = Bloomington campus of Indiana University)
## set up plotting area
-par(mfrow=c(2, 2))
+opar <- par(mfrow=c(2, 2))
## start with default database
data(thermo)
@@ -153,3 +153,5 @@
### clean up: restore thermodynamic database to default
###########
data(thermo)
+
+par(opar)
Modified: pkg/CHNOSZ/demo/gold.R
===================================================================
--- pkg/CHNOSZ/demo/gold.R 2019-01-21 15:40:26 UTC (rev 361)
+++ pkg/CHNOSZ/demo/gold.R 2019-01-22 08:56:26 UTC (rev 362)
@@ -201,8 +201,9 @@
}
# make plots
-par(mfrow=c(2, 2))
+opar <- par(mfrow=c(2, 2))
Au_pH1()
Au_pH2()
Au_T1()
Au_T2()
+par(opar)
Modified: pkg/CHNOSZ/demo/lambda.R
===================================================================
--- pkg/CHNOSZ/demo/lambda.R 2019-01-21 15:40:26 UTC (rev 361)
+++ pkg/CHNOSZ/demo/lambda.R 2019-01-22 08:56:26 UTC (rev 362)
@@ -1,11 +1,12 @@
# plot effects of lambda transition in quartz
# after Berman 1988 Figs. 1 and 2
+opar <- par(no.readonly = TRUE)
layout(matrix(c(1, 4:2, 1, 7:5), nrow=4), heights=c(0.7, 3, 3, 3))
# plot title first
par(mar=c(0, 0, 0, 0))
plot.new()
text(0.5, 0.5, "Effects of lambda transition in quartz, after Berman (1988) Figs. 1 and 2", cex=1.8)
-opar <- par(mar=c(4, 4.5, 1, 0.5), cex=0.8)
+par(mar=c(4, 4.5, 1, 0.5), cex=0.8)
TC <- 0:1200
T <- convert(TC, "K")
Modified: pkg/CHNOSZ/demo/solubility.R
===================================================================
--- pkg/CHNOSZ/demo/solubility.R 2019-01-21 15:40:26 UTC (rev 361)
+++ pkg/CHNOSZ/demo/solubility.R 2019-01-22 08:56:26 UTC (rev 362)
@@ -10,6 +10,7 @@
# Manning et al., 2013, Reviews in Mineralogy & Geochemistry, v. 75, pp. 109-148
# (doi: 10.2138/rmg.2013.75.5)
+opar <- par(no.readonly = TRUE)
layout(matrix(1:4, nrow = 2))
# set pH and T range and resolution, constant temperature and ionic strength
@@ -67,3 +68,5 @@
s <- solubility(a)
diagram(s, type = "loga.balance")
title(main = "Solubility of calcite", font.main = 1)
+
+par(opar)
Modified: pkg/CHNOSZ/demo/yeastgfp.R
===================================================================
--- pkg/CHNOSZ/demo/yeastgfp.R 2019-01-21 15:40:26 UTC (rev 361)
+++ pkg/CHNOSZ/demo/yeastgfp.R 2019-01-22 08:56:26 UTC (rev 362)
@@ -27,8 +27,9 @@
species(names, "Sce")
a <- affinity(H2O=c(-5, 0, 256), O2=c(-80, -66, 256))
# setup the plot
+opar <- par(no.readonly = TRUE)
layout(matrix(c(1, 1,2:7), byrow=TRUE, nrow=4), heights=c(0.7, 3, 3, 3))
-opar <- par(mar=c(0, 0, 0, 0))
+par(mar=c(0, 0, 0, 0))
plot.new()
text(0.5, 0.7, expression("Proteins in subcellular locations of"~italic("S. cerevisiae")~"(Dick, 2009)"), cex=1.5)
text(0.5, 0.2, describe.basis(ibasis=c(1, 3, 4, 6), oneline=TRUE), cex=1.5)