[CHNOSZ-commits] r331 - in pkg/CHNOSZ: . R demo inst vignettes

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Sun Oct 7 12:16:19 CEST 2018 

Author: jedick
Date: 2018-10-07 12:16:05 +0200 (Sun, 07 Oct 2018)
New Revision: 331

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/NAMESPACE
   pkg/CHNOSZ/R/util.plot.R
   pkg/CHNOSZ/demo/yeastgfp.R
   pkg/CHNOSZ/inst/NEWS
   pkg/CHNOSZ/vignettes/anintro.Rmd
Log:
thermo.plot.new(): listen to par("mar") setting for active device


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2018-09-27 13:46:01 UTC (rev 330)
+++ pkg/CHNOSZ/DESCRIPTION	2018-10-07 10:16:05 UTC (rev 331)
@@ -1,6 +1,6 @@
-Date: 2018-09-27
+Date: 2018-10-07
 Package: CHNOSZ
-Version: 1.1.3-38
+Version: 1.1.3-39
 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/NAMESPACE
===================================================================
--- pkg/CHNOSZ/NAMESPACE	2018-09-27 13:46:01 UTC (rev 330)
+++ pkg/CHNOSZ/NAMESPACE	2018-10-07 10:16:05 UTC (rev 331)
@@ -65,7 +65,7 @@
 
 # Imports from default packages
 importFrom("grDevices", "dev.cur", "dev.off", "extendrange",
-  "heat.colors", "png", "rainbow", "topo.colors")
+  "heat.colors", "png", "rainbow", "topo.colors", "dev.list")
 importFrom("graphics", "abline", "axTicks", "axis", "barplot", "box",
   "contour", "image", "legend", "lines", "mtext", "par", "plot",
   "plot.new", "plot.window", "points", "rect", "text", "title")

Modified: pkg/CHNOSZ/R/util.plot.R
===================================================================
--- pkg/CHNOSZ/R/util.plot.R	2018-09-27 13:46:01 UTC (rev 330)
+++ pkg/CHNOSZ/R/util.plot.R	2018-10-07 10:16:05 UTC (rev 331)
@@ -13,7 +13,14 @@
   }
   # 20090324 mar handling: NULL - a default setting; NA - par's setting
   # 20090413 changed mar of top side from 2 to 2.5
-  if(is.null(mar)) mar <- c(3,3.5,2.5,1) else if(is.na(mar[1])) mar <- par('mar')
+  marval <- c(3, 3.5, 2.5, 1)
+  if(identical(mar[1], NA)) marval <- par("mar")
+  # 20181007 get mar from the current device (if it exists) and par("mar") is not the default
+  if(!is.null(dev.list())) {
+    if(!identical(par("mar"), c(5.1, 4.1, 4.1, 2.1))) marval <- par("mar")
+  }
+  # assign marval to mar if the latter is NULL or NA
+  if(!is.numeric(mar)) mar <- marval
   par(mar=mar,mgp=mgp,tcl=0.3,las=las,xaxs=axs,yaxs=axs,cex=cex,lwd=lwd,col=col,fg=col, ...)
   plot.new()
   plot.window(xlim=xlim,ylim=ylim)

Modified: pkg/CHNOSZ/demo/yeastgfp.R
===================================================================
--- pkg/CHNOSZ/demo/yeastgfp.R	2018-09-27 13:46:01 UTC (rev 330)
+++ pkg/CHNOSZ/demo/yeastgfp.R	2018-10-07 10:16:05 UTC (rev 331)
@@ -28,11 +28,11 @@
 a <- affinity(H2O=c(-5, 0, 256), O2=c(-80, -66, 256))
 # setup the plot
 layout(matrix(c(1, 1,2:7), byrow=TRUE, nrow=4), heights=c(0.7, 3, 3, 3))
-par(mar=c(0, 0, 0, 0))
+opar <- 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)
-opar <- par(mar=c(3, 4, 1, 1), xpd=TRUE)
+par(mar=c(3, 4, 1, 1), xpd=TRUE)
 fill <- heat.colors(length(names))
 inames <- 1:length(names)
 for(i in 1:length(nloc)) {
@@ -45,6 +45,7 @@
 }
 # return to plot defaults
 layout(matrix(1))
+par(xpd=FALSE)
 par(opar)
 
 ## Localizations and abundances of proteins from YeastGFP are used here

Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS	2018-09-27 13:46:01 UTC (rev 330)
+++ pkg/CHNOSZ/inst/NEWS	2018-10-07 10:16:05 UTC (rev 331)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.1.3-38 (2018-09-27)
+CHANGES IN CHNOSZ 1.1.3-39 (2018-10-07)
 ---------------------------------------
 
 THERMODYNAMIC DATA
@@ -58,10 +58,15 @@
 
 - diagram(): rename 'what' argument to 'type'.
 
-- digram(): add new type of diagram, 'saturation', which is used to
+- diagram(): add new type of diagram, 'saturation', which is used to
   plot saturation lines for minerals (where their affinity equals
   zero).
 
+- thermo.plot.new() and, by extension, diagram(), now "listen" to the
+  setting of par("mar"). However, if a new plot is being made, or the
+  device has the default setting of mar from par(), mar is (re)set to
+  the default value in thermo.plot.new().
+
 BUG FIXES
 
 - Fix a bug where subcrt()$reaction$coeffs was incorrect for reactions

Modified: pkg/CHNOSZ/vignettes/anintro.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/anintro.Rmd	2018-09-27 13:46:01 UTC (rev 330)
+++ pkg/CHNOSZ/vignettes/anintro.Rmd	2018-10-07 10:16:05 UTC (rev 331)
@@ -209,7 +209,7 @@
 
 * Use <span style="color:green">`subcrt()`</span> to calculate standard molal thermodynamic properties.
 
-```{r bsad_adenine, fig.margin=TRUE, fig.width=4, fig.height=4, small.mar=TRUE, dpi=dpi, out.width="100%", echo=FALSE, message=FALSE, results="hide", fig.cap="Nucleobase equal-activity diagram at <i>T</i> = 100 °C.", cache=TRUE, pngquant=pngquant, timeit=timeit}
+```{r bsad_adenine, fig.margin=TRUE, fig.width=4, fig.height=4, dpi=dpi, out.width="100%", echo=FALSE, message=FALSE, results="hide", fig.cap="Nucleobase equal-activity diagram at <i>T</i> = 100 °C.", cache=TRUE, pngquant=pngquant, timeit=timeit}
 basis("CHNOSe")
 species(c("adenine", "cytosine", "guanine", "thymine", "uracil"))
 a <- affinity(H2O = c(-12, -0), Eh = c(-0.4, -0.2), T = 100)
@@ -220,7 +220,7 @@
 subcrt("adenine", T = 100)
 ```
 
-```{r equil_adenine, fig.margin=TRUE, fig.width=4, fig.height=4, small.mar=TRUE, dpi=dpi, out.width="100%", echo=FALSE, message=FALSE, results="hide", fig.cap="Activities of nucleobases in metastable equilibrium at <i>T</i> = 100 °C.", cache=TRUE, pngquant=pngquant, timeit=timeit}
+```{r equil_adenine, fig.margin=TRUE, fig.width=4, fig.height=4, dpi=dpi, out.width="100%", echo=FALSE, message=FALSE, results="hide", fig.cap="Activities of nucleobases in metastable equilibrium at <i>T</i> = 100 °C.", cache=TRUE, pngquant=pngquant, timeit=timeit}
 basis("e-", 3.6)
 a <- affinity(H2O = c(-12, 0), T = 100)
 e <- equilibrate(a)
@@ -614,7 +614,7 @@
 That is, running <span style="color:green">`affinity()`</span>`$values` again would give the same result.
 ```
 
-```{r EhpH_plot, fig.margin=TRUE, fig.width=4, fig.height=4, small.mar=TRUE, dpi=dpi, out.width="100%", echo=FALSE, message=FALSE, cache=TRUE, fig.cap="Aqueous sulfur species at 25 °C.", pngquant=pngquant, timeit=timeit}
+```{r EhpH_plot, fig.margin=TRUE, fig.width=4, fig.height=4, dpi=dpi, out.width="100%", echo=FALSE, message=FALSE, cache=TRUE, fig.cap="Aqueous sulfur species at 25 °C.", pngquant=pngquant, timeit=timeit}
 a <- affinity(pH = c(0, 12), Eh = c(-0.5, 1))
 diagram(a, fill = "heat")
 water.lines(a)
@@ -693,7 +693,7 @@
 The first call to <span style="color:green">`diagram()`</span> plots the species of interest; the second adds the predominance fields of the basis species.
 We turn off the gray coloring beyond the water stability limits (`limit.water`) but plot the red dotted lines using <span style="color:green">`water.lines()`</span>:
 
-```{r copper_mosaic, fig.margin=TRUE, fig.width=4, fig.height=4, small.mar=TRUE, dpi=dpi, out.width="100%", message=FALSE, cache=TRUE, fig.cap="Copper minerals and aqueous complexes with chloride, 200 °C.", pngquant=pngquant, timeit=timeit}
+```{r copper_mosaic, fig.margin=TRUE, fig.width=4, fig.height=4, dpi=dpi, out.width="100%", message=FALSE, cache=TRUE, fig.cap="Copper minerals and aqueous complexes with chloride, 200 °C.", pngquant=pngquant, timeit=timeit}
 T <- 200
 res <- 200
 bases <- c("H2S", "HS-", "HSO4-", "SO4-2")
@@ -714,7 +714,7 @@
 For instance, we can use H<sub>2</sub> or `r o2` in place of *e*<sup>-</sup>.
 To do that, let's write a function to swap those basis species and make a diagram.
 We use R's `do.call()` to construct the argument list for <span style="color:green">`mosaic()`</span>; this way, the name of the `newvar` argument to our function indicates the chosen variable.
-```{r mosaicfun, fig.fullwidth=TRUE, fig.width=9, fig.height=3, small.mar=TRUE, dpi=dpi, out.width="85%", message=FALSE, results="hide", cache=TRUE, fig.cap="The same chemical system projected into different sets of basis species.", pngquant=pngquant, timeit=timeit}
+```{r mosaicfun, fig.fullwidth=TRUE, fig.width=9, fig.height=3, dpi=dpi, out.width="85%", message=FALSE, results="hide", cache=TRUE, fig.cap="The same chemical system projected into different sets of basis species.", pngquant=pngquant, timeit=timeit}
 mosaicfun <- function(newvar, T = 200) {
   swap.basis("e-", names(newvar))
   if (names(newvar) == "O2") basis("O2", "gas")
@@ -779,7 +779,7 @@
 a$values <- lapply(a$values, `*`, -0.001)
 ```
 
-```{r rainbow_diagram, fig.margin=TRUE, fig.width=4, fig.height=4, small.mar=TRUE, dpi=dpi, out.width="100%", echo=FALSE, message=FALSE, cache=TRUE, fig.cap="Affinities of organic synthesis in a hydrothermal system, after Shock and Canovas (2010).", pngquant=pngquant, timeit=timeit}
+```{r rainbow_diagram, fig.margin=TRUE, fig.width=4, fig.height=4, dpi=dpi, out.width="100%", echo=FALSE, message=FALSE, cache=TRUE, fig.cap="Affinities of organic synthesis in a hydrothermal system, after Shock and Canovas (2010).", pngquant=pngquant, timeit=timeit}
 diagram(a, balance = 1, ylim = c(-100, 100), ylab = axis.label("A", prefix="k"),
         col = rainbow(8), lwd = 2, bg = "slategray3")
 abline(h = 0, lty = 2, lwd = 2)
@@ -842,7 +842,7 @@
 ```
 
 <!-- put demo(buffer) here for appealing placement on page -->
-```{r demo_buffer_noecho, fig.margin=TRUE, fig.width=4, fig.height=4, small.mar=TRUE, dpi=dpi, out.width="100%", message=FALSE, echo=FALSE, cache=TRUE, fig.cap="Values of log<i>f</i><sub>H<sub>2</sub></sub> corresponding to mineral buffers or to given activities of aqueous species.", pngquant=pngquant, timeit=timeit}
+```{r demo_buffer_noecho, fig.margin=TRUE, fig.width=4, fig.height=4, dpi=dpi, out.width="100%", message=FALSE, echo=FALSE, cache=TRUE, fig.cap="Values of log<i>f</i><sub>H<sub>2</sub></sub> corresponding to mineral buffers or to given activities of aqueous species.", pngquant=pngquant, timeit=timeit}
 demo(buffer, echo = FALSE)
 ```
 Et voilà! We have found log*a*<sub>H<sub>2</sub>S</sub> and `r logfO2` that are compatible with the coexistence of the three minerals.
@@ -888,7 +888,7 @@
 The method based on the Boltzmann equation is fast, but is applicable only to systems where the coefficient on the balanced basis species in each of the formation reactions is one.
 The reaction-matrix method is slower, but can be applied to systems were the balanced basis species has reaction coefficients other than one.
 
-```{r bjerrum_diagram, fig.margin=TRUE, fig.width=3, fig.height=6, small.mar=TRUE, dpi=dpi, out.width="100%", echo=FALSE, results="hide", message=FALSE, cache=TRUE, fig.cap="Three views of carbonate speciation: affinity, activity, degree of formation.", pngquant=pngquant, timeit=timeit}
+```{r bjerrum_diagram, fig.margin=TRUE, fig.width=3, fig.height=6, dpi=dpi, out.width="100%", echo=FALSE, results="hide", message=FALSE, cache=TRUE, fig.cap="Three views of carbonate speciation: affinity, activity, degree of formation.", pngquant=pngquant, timeit=timeit}
 par(mfrow = c(3, 1))
 basis("CHNOS+")
 species(c("CO2", "HCO3-", "CO3-2"))
@@ -1007,7 +1007,7 @@
 We do this by setting the names and line types for the *other* species to values that prevent them from being plotted:
 ```{r groups_diagram, echo=-(1:4), eval=FALSE}
 ```
-```{r groups_diagram, fig.fullwidth=TRUE, fig.width=9, fig.height=3, small.mar=TRUE, dpi=dpi, out.width="85%", echo=FALSE, message=FALSE, results="hide", cache=TRUE, fig.cap="Distribution of inorganic and groups of organic species (left plot) and of alcohols and ketones (middle and right plots) as a function of <i>T</i>, pH, and log<i>f</i><sub>O<sub>2</sub></sub>.", pngquant=pngquant, timeit=timeit}
+```{r groups_diagram, fig.fullwidth=TRUE, fig.width=9, fig.height=3, dpi=dpi, out.width="85%", echo=FALSE, message=FALSE, results="hide", cache=TRUE, fig.cap="Distribution of inorganic and groups of organic species (left plot) and of alcohols and ketones (middle and right plots) as a function of <i>T</i>, pH, and log<i>f</i><sub>O<sub>2</sub></sub>.", pngquant=pngquant, timeit=timeit}
 ```
 
 ## Balancing differently
@@ -1033,7 +1033,7 @@
 There, we set `balance = 1`, which indicates that moles of species are conserved; this is equivalent to balancing on the amino acid backbone.
 In the remaining plots, the balance is set to each of the basis species in turn (except for O<sub>2</sub>), then on volume.
 <span style="color:green">`expr.species()`</span> together with R's `substitute()` is used to make titles that include formatted chemical formulas:
-```{r aafun, fig.fullwidth=TRUE, fig.width=12.5, fig.height=2.5, small.mar=TRUE, dpi=dpi, out.width="100%", message=FALSE, results="hide", fig.cap="Plots of maximum affinity at 250 °C and 265 bar using different reaction balances for 20 amino acids.", cache=TRUE, pngquant=pngquant, timeit=timeit}
+```{r aafun, fig.fullwidth=TRUE, fig.width=12.5, fig.height=2.5, dpi=dpi, out.width="100%", message=FALSE, results="hide", fig.cap="Plots of maximum affinity at 250 °C and 265 bar using different reaction balances for 20 amino acids.", cache=TRUE, pngquant=pngquant, timeit=timeit}
 aafun <- function(balance) {
   diagram(a, balance = balance, fill = col)
   blab <- expr.species(balance)
@@ -1519,7 +1519,7 @@
 Here, we plot the information-theoretic free energy Δ*G<sub>inf</sub>* (calculated from the relative entropy or Kullback--Leibler divergence):
 ```{r yeastplot, eval=FALSE, echo=10}
 ```
-```{r yeastplot, fig.fullwidth=TRUE, fig.width=7.5, fig.height=2.5, small.mar=TRUE, dpi=ifelse(dpi==50, 50, 100), out.width="85%", echo=FALSE, message=FALSE, results="hide", cache=TRUE, fig.cap="ER-to-Golgi proteins: calculations without and with length normalization, and free energy difference between experimental and calculated abundances in metastable equilibrium with normalization.", pngquant=pngquant, timeit=timeit}
+```{r yeastplot, fig.fullwidth=TRUE, fig.width=7.5, fig.height=2.5, dpi=ifelse(dpi==50, 50, 100), out.width="85%", echo=FALSE, message=FALSE, results="hide", cache=TRUE, fig.cap="ER-to-Golgi proteins: calculations without and with length normalization, and free energy difference between experimental and calculated abundances in metastable equilibrium with normalization.", pngquant=pngquant, timeit=timeit}
 ```
 
 The minimum free energy difference occurs near `r logfO2` = -78.
@@ -1573,7 +1573,7 @@
 Here, `adj = 0` makes the labels left-aligned, `dy = 0.1` adds a *y* offset to the labels, and `format.names = FALSE` prevents formatting of the names as if they were chemical formulas (that causes subscripted numbers to appear).
 The last few lines are used to make a second *x* axis, using a label generated with <span style="color:green">`axis.label()`</span>:
 
-```{r Shh_diagram, fig.margin=TRUE, fig.width=4, fig.height=4, small.mar=TRUE, dpi=dpi, out.width="100%", echo=FALSE, results="hide", message=FALSE, fig.cap="Per-residue affinities for formation of transcription factors relative to Shh.", cache=TRUE, pngquant=pngquant, timeit=timeit}
+```{r Shh_diagram, fig.margin=TRUE, fig.width=4, fig.height=4, dpi=dpi, out.width="100%", echo=FALSE, results="hide", message=FALSE, fig.cap="Per-residue affinities for formation of transcription factors relative to Shh.", cache=TRUE, pngquant=pngquant, timeit=timeit}
 # line type, width, and color
 twc <- lapply(c(3, 1, 1), rep, length(pname))
 ihigh <- c(2, 5, 7, 8, 1)
@@ -1727,7 +1727,7 @@
 We read a data file of amino acid compositions produced in that study, taking those labeled "transferase".
 Then we add the proteins and get their indices using <span style="color:red">`add.protein()`</span>, set the basis, calculate the affinities, and make a potential diagram with temperature and activity of dissolved hydrogen as variables:
 
-```{r bison_transferase, fig.margin=TRUE, fig.width=4, fig.height=4, small.mar=TRUE, dpi=dpi, out.width="100%", echo=FALSE, results="hide", message=FALSE, fig.cap='Potential diagram for metagenomically identified sequences of transferases in Bison Pool hot spring. See also the vignette [<span style="color:blue">*Hot-spring proteins in CHNOSZ*</span>](hotspring.pdf).', cache=TRUE, pngquant=pngquant, timeit=timeit}
+```{r bison_transferase, fig.margin=TRUE, fig.width=4, fig.height=4, dpi=dpi, out.width="100%", echo=FALSE, results="hide", message=FALSE, fig.cap='Potential diagram for metagenomically identified sequences of transferases in Bison Pool hot spring. See also the vignette [<span style="color:blue">*Hot-spring proteins in CHNOSZ*</span>](hotspring.pdf).', cache=TRUE, pngquant=pngquant, timeit=timeit}
 file <- system.file("extdata/protein/DS11.csv", package = "CHNOSZ")
 aa <- read.csv(file, as.is = TRUE)
 aa <- aa[grep("transferase", aa$protein), ]
@@ -1868,7 +1868,7 @@
 ```{r smoker_plot, eval=FALSE, echo=23:25}
 ```
 
-```{r smoker_plot, fig.fullwidth=TRUE, fig.width=9, fig.height=5, small.mar=TRUE, dpi=dpi, out.width="85%", echo=FALSE, message=FALSE, results="hide", cache=TRUE, fig.cap="Optimization of a thermodynamic model for relative abundances of amino acids in a 270 °C black smoker fluid using 1, 2, or 3 variables (left to right).", pngquant=pngquant, timeit=timeit}
+```{r smoker_plot, fig.fullwidth=TRUE, fig.width=9, fig.height=5, dpi=dpi, out.width="85%", echo=FALSE, message=FALSE, results="hide", cache=TRUE, fig.cap="Optimization of a thermodynamic model for relative abundances of amino acids in a 270 °C black smoker fluid using 1, 2, or 3 variables (left to right).", pngquant=pngquant, timeit=timeit}
 ```
 
 The calculation using <span style="color:red">`findit()`</span>, in which the added variable log*a*<sub>`r h2o`</sub> optimizes to ca. -2.4, shows that measured concentrations of 6 amino acids fall within 1--2 log units of the relative abundances in metastable equilibrium.

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